*>>>>>> Combined CHARMM All-Hydrogen Parameter File for <<<<<<<<< *>>>>>>> CHARMM22 Proteins and CHARMM27 Nucleic Acids <<<<<<<<<< *from *>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<< *>>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< *and * \\\\ CHARMM27 All-Hydrogen Nucleic Acid Parameter File //// * \\\\\\\\\\\\\\\\\\ Developmental //////////////////////// * Alexander D. MacKerell Jr. and Nicolas Foloppe * August 1999 * All comments to ADM jr. email: alex,mmiris.ab.umd.edu * telephone: 410-706-7442 * ! references ! !PROTEINS ! !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. ! !PHOSPHOTYROSINE ! !Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. !Structural Characterization of the Phosphotyrosine Binding Region of a !High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics !Simulation and Chemical Shift Calculations. Journal of the American !Chemical Society, 1996, 118: 11265-11277. ! !IONS (see lipid and nucleic acid topology and parameter files for !additional ions ! !ZINC ! !Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: !Structure, Function, and Genetics 23:12-31 (1995) ! !NUCLEIC ACIDS ! !Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for !Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and !Condensed Phase Macromolecular Target Data. Journal of Computational !Chemistry, 2000, 21:86-104. ! !and ! !MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for !Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA !and RNA in Solution. Journal of Computational !Chemistry, 2000, 21:105-120. ! !NAD(P)+, NAD(P)H and PPI ! !Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A !Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate !Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18: !221-239. ! !IONS ! !all ions from Roux and coworkers ! !Sodium ! !Beglov, D. and Roux, B., Finite Representation of an Infinite !Bulk System: Solvent Boundary Potential for Computer Simulations, !Journal of Chemical Physics, 1994, 100: 9050-9063 ! BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! C C 600.000 1.3350 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) CA CA 305.000 1.3750 ! ALLOW ARO ! benzene, JES 8/25/89 CE1 CE1 440.000 1.3400 ! ! for butene; from propene, yin/adm jr., 12/95 CE1 CE2 500.000 1.3420 ! ! for propene, yin/adm jr., 12/95 CE1 CT2 365.000 1.5020 ! ! for butene; from propene, yin/adm jr., 12/95 CE1 CT3 383.000 1.5040 ! ! for butene, yin/adm jr., 12/95 CE2 CE2 510.000 1.3300 ! ! for ethene, yin/adm jr., 12/95 CP1 C 250.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 CC 250.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 CD 200.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 222.500 1.5270 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP2 222.500 1.5370 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 CP2 222.500 1.5370 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPB C 450.000 1.3800 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPA 299.800 1.4432 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB CPB 340.700 1.3464 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH1 CPH1 410.000 1.3600 ! ALLOW ARO ! histidine, adm jr., 6/27/90 CPM CPA 360.000 1.3716 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT CA 305.000 1.3680 ! ALLOW ARO ! adm jr., 12/30/91, for jwk CPT CPT 360.000 1.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT1 CT1 222.500 1.5000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT2 CA 230.000 1.4900 ! ALLOW ALI ARO ! phe,tyr, JES 8/25/89 CT2 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT2 CPB 230.000 1.4900 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPH1 229.630 1.5000 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals CT2 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT2 222.500 1.5300 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT3 CA 230.000 1.4900 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 CT3 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT3 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT3 CPB 230.000 1.4900 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPH1 229.630 1.5000 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals CT3 CS 190.000 1.5310 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 222.500 1.5280 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT3 222.500 1.5300 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CY CA 350.000 1.3650 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CY CPT 350.000 1.4400 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CT2 230.000 1.5100 ! ALLOW ARO !JWK Kb from alkane freq.. b0 from TRP crystal FE CM 258.000 1.9000 ! ALLOW HEM ! Heme (6-liganded): CO ligand (KK 05/13/91) FE CPM 0.000 3.3814 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) H CD 330.000 1.1100 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA C 330.000 1.1000 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) HA CA 340.000 1.0830 ! ALLOW ARO ! trp, adm jr., 10/02/89 HA CC 317.130 1.1000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations HA CP2 309.000 1.1110 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 309.000 1.1110 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CPM 367.600 1.0900 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CS 300.000 1.1110 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT1 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CY 330.000 1.0800 ! ALLOW ARO ! JWK 05/14/91 new r0 from indole HE1 CE1 360.500 1.1000 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 365.000 1.1000 ! ! for ethene, yin/adm jr., 12/95 HB CP1 330.000 1.0800 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HP CA 340.000 1.0800 ! ALLOW ARO ! phe,tyr JES 8/25/89 HP CY 350.000 1.0800 ! ALLOW ARO !adm jr., 12/30/91, for jwk HR1 CPH1 375.000 1.0830 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 340.000 1.0900 ! ALLOW ARO ! his, adm jr., 6/28/29 HR2 CPH2 333.000 1.0700 ! ALLOW ARO ! his, adm jr., 6/27/90 HR3 CPH1 365.000 1.0830 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HT HT 0.000 1.5139 ! ALLOW WAT ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 320.000 1.4340 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 320.000 1.4550 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO ! 403.0->463.0, 1.305->1.365 guanidinium (KK) NC2 CT2 261.000 1.4900 ! ALLOW ALI POL ! arg, (DS) NC2 CT3 261.000 1.4900 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 NC2 HC 455.000 1.0000 ! ALLOW POL ! 405.0->455.0 GUANIDINIUM (KK) NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO ! (DS) NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide NH2 CT2 240.000 1.4550 ! from NH2 CT3, neutral glycine, adm jr. NH2 CT3 240.000 1.4550 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH2 H 480.000 1.0000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 HC 460.000 1.0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT2 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT3 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) NP CP1 320.000 1.4850 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 320.000 1.5020 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP HC 460.000 1.0060 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NPH CPA 377.200 1.3757 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH FE 270.200 1.9580 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 400.000 1.3800 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 CPH2 400.000 1.3600 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 H 466.000 1.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 400.000 1.3800 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH2 400.000 1.3200 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 FE 65.000 2.2000 ! ALLOW HEM ! Heme (6-liganded): His ligand (KK 05/13/91) NR3 CPH1 380.000 1.3700 ! ALLOW ARO ! his, adm jr., 6/28/90 NR3 CPH2 380.000 1.3200 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 H 453.000 1.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 NY CA 270.000 1.3700 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CPT 270.000 1.3750 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY H 465.000 0.9760 ! ALLOW ARO ! indole JWK 08/28/89 O C 620.000 1.2300 ! ALLOW PEP POL ARO ! Peptide geometry, condensed phase (LK) O CC 650.000 1.2300 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide OB CC 750.000 1.2200 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid vibrations and geom. OB CD 750.000 1.2200 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 8/27/91, phenoxide OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid OC CT2 450.000 1.3300 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT3 450.000 1.3300 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 OH1 CA 334.300 1.4110 ! ALLOW ARO ALC ! MeOH, EMB 10/10/89, OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC ! adm jr. 5/02/91, acetic acid pure solvent OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 H 545.000 0.9600 ! ALLOW ALC ARO ! EMB 11/21/89 methanol vib fit OM CM 1115.000 1.1280 ! ALLOW HEM ! Heme (6-liganded): CO ligand (KK 05/13/91) OM FE 250.000 1.8000 ! ALLOW HEM ! Heme (6-liganded): O2 ligand (KK 05/13/91) OM OM 600.000 1.2300 ! ALLOW HEM ! Heme (6-liganded): O2 ligand (KK 05/13/91) OS CD 150.000 1.3340 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent OS CT3 340.000 1.4300 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OT HT 450.000 0.9572 ! ALLOW WAT ! FROM TIPS3P GEOM S CT2 198.000 1.8180 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) S CT3 240.000 1.8160 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) S HS 275.000 1.3250 ! ALLOW SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 SM CT2 214.000 1.8160 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SM CT3 214.000 1.8160 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SM SM 173.000 2.0290 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SS CS 205.000 1.8360 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr. ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr. !nucleic acid section ! !NICH parameters to maintain back compatibility following !atom type switch from HN3 to HN6 CN3C HN6 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95 CN3 HN6 350.0 1.09 !nadh, adm jr., 8/98 ! CN1 CN3 302.0 1.409 !U, adm jr. 11/97 CN1 CN3T 302.0 1.403 !T, adm jr. 11/97 CN1A CN3 302.0 1.480 !nad/ppi, jjp1/adm jr. 7/95 CN1 CN5G 302.0 1.360 !G, adm jr. 11/97 CN1A NN1 560.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 CN1 NN2 380.0 1.367 !C, adm jr. 11/97 CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97 CN1 NN2G 340.0 1.396 !G, adm jr. 11/97 CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97 CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97 CN1 NN3 350.0 1.335 !C, adm jr. 11/97 CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91 CN1A ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91 CN2 CN3 320.0 1.406 !C, adm jr. 11/97 CN2 CN3D 260.0 1.405 !5mc, adm jr. 9/9/93, from cn2 cn3 CN2 CN5 360.0 1.358 !A, adm jr. 11/97 CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91 CN2 NN2G 400.0 1.392 !G CN2 NN3 450.0 1.343 !C CN2 NN3A 400.0 1.342 !A, adm jr. 11/97 CN2 NN3G 320.0 1.326 !G, adm jr. 11/97 CN3 CN3 500.0 1.326 !C,U adm jr. 11/97 CN3 CN3T 560.0 1.320 !T, adm jr. 11/97 CN3A CN3 450.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 420.0 1.350 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 420.0 1.320 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN3 560.0 1.335 !5mc, adm jr. 9/9/93, from cn3 cn3 CN3 CN8 222.5 1.490 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN9 230.0 1.480 !5mc, adm jr. 9/9/93, from cn3 cn9 CN3T CN9 230.0 1.478 !T, adm jr. 11/97 CN3 HN3 350.0 1.09 !C,U, JWK CN3T HN3 350.0 1.09 !T, JWK CN3 HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3A HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3B HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3C HN3 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95 CN3 NN2 302.0 1.343 !C, adm jr. 11/97 CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97 CN3B NN2 420.0 1.315 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 420.0 1.355 !nadh/ppi, jjp1/adm jr. 7/95 CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91 CN4 NN2 320.0 1.374 !A, adm jr. 11/97 CN4 NN2B 300.0 1.378 !G, adm jr. 11/97 CN4 NN2G 350.0 1.365 !Inosine, adm jr. 2/94 CN4 NN3A 420.0 1.322 !A, adm jr. 11/97 CN4 NN3I 450.0 1.295 !Inosine, adm jr. 2/94 CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97 CN5 CN5 310.0 1.361 !A, adm jr. 11/97 CN5 CN5G 320.0 1.350 !G, adm jr. 11/97 CN5 NN2 300.0 1.375 !A, adm jr. 11/97 CN5 NN2B 302.0 1.375 !G, adm jr. 11/97 CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91 CN5 NN3G 350.0 1.315 !G, adm jr. 11/97 CN5 NN3I 350.0 1.332 !Inosine, adm jr. 9/98 CN5 NN4 310.0 1.355 !A, adm jr. 11/97 CN5G NN4 310.0 1.365 !G, adm jr. 11/97 CN8 CN8 222.50 1.528 !Alkanes, sacred CN8 CN9 222.50 1.528 !Alkanes, sacred CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR. CN8 ON5 428.0 1.42 !RIBOSE, MeOH CN9 HN9 322.0 1.111 !alkanes CN9 ON2 340.0 1.43 !DMP, ADM Jr. HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91 HN2 NN2 474.0 1.01 !C,U, JWK HN2 NN2B 474.0 1.01 !G, adm jr. 11/97 HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91 HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91 HN4 ON4 545.0 0.960 !MP_1, ADM Jr. !HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) !HT OT 450.0 0.9572 ! from TIPS3P geometry ON2 P 270.0 1.60 !DMP, ADM Jr. ON3 P 580.0 1.48 !DMP, ADM Jr. ON4 P 237.0 1.58 !MP_1, ADM Jr. ON2 P2 300.0 1.68 !nad/ppi, jjp1/adm jr. 7/95 ON3 P2 480.0 1.53 !nad/ppi, jjp1/adm jr. 7/95 NN5 HN1 460.0 1.01 !sugar model, adm jr. !@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@ CN7B ON6 260.0 1.420 ! From exp CN7B CN8 200.0 1.518 ! From exp CN7 ON6 240.0 1.446 ! Fom exp. CN7 CN8 222.5 1.516 ! From exp. CN7 CN7 222.5 1.529 ! From exp CN7 HN7 309.0 1.111 !Alkanes, sacred CN8 HN8 309.0 1.111 !Alkanes, sacred CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF) !@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@ !@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@ CN7B ON6B 260.0 1.420 ! From CN7B ON6 CN7 ON6B 240.0 1.480 ! From CN7 ON6 CN7B CN7B 200.0 1.450 ! CN7 CN7B 222.5 1.460 ! Specific to RNA !@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@ !@@@@@@@@@ Begining of endocyclic bonds for arabinose @@@@@@@@@ ! Transfered from DNA CN7B CN7C 200.0 1.518 ! For arabinose, from CN7B CN8 CN7 CN7C 222.5 1.516 ! For arabinose, from CN7 CN8 CN7C HN7 309.0 1.111 ! From CN8 HN7 !@@@@@@@@@ End of endocyclic bonds for arabinose @@@@@@@@@ !@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@ CN7 CN8B 222.5 1.512 ! From exp. CN8B ON2 320.0 1.44 ! From exp !CN8B ON5 250.0 1.44 ! From CN8B ON2 CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98 CN7 ON2 310.0 1.433 ! From exp CN7B ON2 310.0 1.433 ! From exp, for NADPH etc. !CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98 ! C1'-N9 (purines)/C1'-N1 (pyrimidines) CN9 NN2 400.0 1.456 !9-M-A/C, adm jr. CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr. CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr. CN7B NN2 220.0 1.456 !A/C CN7B NN2B 220.0 1.458 !G/T/U ! C5'-H in model compounds and DNA CN8B HN8 309.0 1.111 !Alkanes, sacred ON5 HN5 545.0 0.960 !RIBOSE, MeOH !@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@ !@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@ !CN7B ON5 250.0 1.400 ! From CN7 ON5 CN7B ON5 428.0 1.400 ! check adm jr., !FC should be 428.000 based on Meoh !@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@ !@@@@@@@@@ Begining of exocyclic bonds for arabinose @@@@@@@@@ !CN7C ON5 250.0 1.400 ! From CN7 ON5 CN7C ON5 428.0 1.400 ! check adm jr., !FC should be 428.000 based on Meoh !@@@@@@@@@ End of exocyclic bonds for arabinose @@@@@@@@@ !@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@ CN8 ON2 340.0 1.44 ! !@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@ ! C1'-ND1 in imidazole model compound CN7B NR1 220.000 1.4620 ! From crystal nucleosides A/G (NF) !NR1 CPH1 400.000 1.3800 ! From imidazole (NF) !NR1 CPH2 400.000 1.3600 ! From imidazole (NF) !NR2 CPH1 400.000 1.3800 ! From imidazole (NF) !NR2 CPH2 400.000 1.3200 ! From imidazole (NF) !CPH1 CPH1 410.000 1.3600 ! From imidazole (NF) !HR1 CPH2 340.000 1.0900 ! From imidazole (NF) !HR3 CPH1 365.000 1.0830 ! From imidazole (NF) ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types Ktheta Theta0 Kub S0 ! CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO ! JES 8/25/89 CE1 CE1 CT3 48.00 123.50 ! ! for 2-butene, yin/adm jr., 12/95 CE1 CT2 CT3 32.00 112.20 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CE2 CE1 CT2 48.00 126.00 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CE2 CE1 CT3 47.00 125.20 ! ! for propene, yin/adm jr., 12/95 CP1 N C 60.000 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 C 52.000 112.3000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C 60.000 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 100.000 114.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 100.000 111.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPA CPB C 70.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPA CPM CPA 94.200 125.1200 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPA NPH CPA 139.300 103.9000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB C C 70.000 121.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPB C 70.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPB CPA 30.800 106.5100 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPM CPA CPB 61.600 124.0700 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT CA CA 60.000 118.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT CPT CA 60.000 122.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT NY CA 110.000 108.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO ! PARALLH19 (JES) CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! from CT2 CT1 C, for lactams, adm jr. CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT2 CY CA 45.800 129.4000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CT2 CY CPT 45.800 124.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO ! 107.5->120.0 to make planar Arg (KK) CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO ! ethylbenzene, adm jr., 3/7/92 CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO ! methylguanidinium, adm jr., 3/26/92 CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CY CPT CA 160.000 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CPT CPT 110.000 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CT2 CT1 58.350 114.0000 ! ALLOW ARO ! from TRP crystal, JWK CY CT2 CT3 58.350 114.0000 ! ALLOW ARO ! from TRP crystal, JWK FE NPH CPA 96.150 128.0500 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO ! his, adm jr. 8/13/90 acetamide geometry and vibrations H NH2 H 23.000 120.0000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NY CA 28.000 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT 28.000 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO ! JES 8/25/89 phenol H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 HA C C 50.000 120.5000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) HA C CPB 50.000 120.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO ! trp, adm jr., 10/02/89 HA CA CPT 41.000 122.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CPM CPA 12.700 117.4400 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CPM FE 0.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd ! based on HA CT2 HA HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT2 CE1 45.00 111.50 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HA CT2 CPB 50.000 109.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CY 33.430 109.5000 ! ALLOW ARO ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT3 CE1 42.00 111.50 ! ! for 2-butene, yin/adm jr., 12/95 HA CT3 CPB 50.000 109.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HE1 CE1 CE1 52.00 119.50 ! ! for 2-butene, yin/adm jr., 12/95 HE1 CE1 CE2 42.00 118.00 ! ! for propene, yin/adm jr., 12/95 HE1 CE1 CT2 40.00 116.00 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HE1 CE1 CT3 22.00 117.00 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 CE1 45.00 120.50 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 CE2 55.50 120.50 ! ! for ethene, yin/adm jr., 12/95 HE2 CE2 HE2 19.00 119.00 ! ! for propene, yin/adm jr., 12/95 HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent HB CT1 CT1 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CT2 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent HB CT2 HB 36.000 115.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO ! 35.3->49.0 GUANIDINIUM (KK) HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI ! 107.5->120.0 to make planar Arg (KK) HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI ! methylguanidinium, adm jr., 3/26/92 HC NC2 HC 25.000 120.0000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) HC NH2 CT2 50.000 111.0000 ! ALLOW POL ! from HC NH2 CT3, neutral glycine, adm jr. HC NH2 CT3 50.000 111.0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 HC NH2 HC 39.000 106.5000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP HC 51.000 107.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO ! adm jr., 6/27/90, his HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 HT OT HT 55.000 104.5200 ! ALLOW WAT ! TIP3P GEOMETRY, ADM JR. N C CP1 20.000 112.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 C 50.000 108.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CC 50.000 108.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CP2 70.000 110.8000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 CP2 70.000 110.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO ! changed from 60.0/120.3 for guanidinium (KK) NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL ! arg, (DS) NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL ! arg, (DS) NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! Alanine Dipeptide ab initio calc's (LK) NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/20/92, for asn,asp,gln,glu and cters NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! from NH1 CT1 CT2, for lactams, adm jr. NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO ! from NH1 CT3 HA, for lactams, adm jr. NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO ! NMA crystal (JCS) NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations NH2 CT2 HB 38.000 109.50 50.00 2.14000 !from NH2 CT3 HA, neutral glycine, adm jr. NH2 CT2 CD 52.000 108.0000 !from CT2 CT2 CD, neutral glycine, adm jr. NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! alanine (JCS) NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL ! alanine (JCS) NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NP CP1 C 50.000 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CC 50.000 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NPH CPA CPB 122.000 111.5400 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPA CPM 88.000 124.3900 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH FE CM 50.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NPH FE CPM 0.000 45.0000 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) NPH FE NPH 14.390 90.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 FE CM 50.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NR2 FE NPH 50.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole NY CPT CA 160.000 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CPT CPT 110.000 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk O C CP1 80.000 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C H 50.000 121.7000 ! ALLOW PEP POL ARO ! acetaldehyde (JCS) O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC HA 44.000 122.0000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO ! adm jr. 4/10/91, acetamide update OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OC CA CA 40.000 120.0000 ! ALLOW POL ARO ! adm jr. 8/27/91, phenoxide OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) OC CT2 CT3 65.000 122.0000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT2 HA 65.000 118.3000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT3 HA 65.000 118.3000 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC ! PARALLH19 WITH [122.3] (JES) OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OM CM FE 35.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OM FE NPH 5.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OM OM FE 0.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SS CS CT3 55.000 118.0000 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 SS CS HA 40.000 112.3000 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CA CA ON2b 75.0 120.0 !phenol phosphate, 6/94, adm jr. CA ON2b P 90.0 120.0 20. 2.30 !phenol phosphate, 6/94, adm jr. ON4 P ON2b 48.1 108.0 !phenol phosphate, 6/94, adm jr. ON3 P ON2b 98.9 103.0 !phenol phosphate, 6/94, adm jr. !nucleic acid section !NICH parameters to maintain back compatibility following !atom type switch from HN3 to HN6 NN2 CN3C HN6 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 HN6 CN3C CN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 HN6 CN3 CN8 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3C CN3 HN6 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 ! pyrmidines !@@@@@@@@ Adenine ! ade 6-mem ring CN2 NN3A CN4 90.0 117.8 !6R) adm jr. 11/97 NN3A CN4 NN3A 60.0 133.0 !6R) CN4 NN3A CN5 90.0 110.1 !6R) CN5 CN5 NN3A 60.0 127.4 !6R) bridgeC4 CN2 CN5 CN5 60.0 121.0 !6R) bridgeC5 CN5 CN2 NN3A 60.0 110.7 !6R) CN5 CN5 NN2 100.0 105.7 !5R) bridgeC4 CN5 CN5 NN4 100.0 110.0 !5R) bridgeC5 CN4 NN4 CN5 120.0 104.6 !5R) NN2 CN4 NN4 100.0 113.4 !5R) CN4 NN2 CN5 100.0 106.3 !5R) NN2 CN5 NN3A 100.0 126.9 !bridgeC4 CN2 CN5 NN4 100.0 129.0 !bridgeC5 HN3 CN4 NN3A 38.0 113.5 !h2 NN3A CN2 NN1 50.0 130.7 !n6 CN5 CN2 NN1 50.0 118.6 ! CN2 NN1 HN1 40.0 121.5 !h61,h62, C,A,G HN1 NN1 HN1 31.0 117.0 !C,A,G NN4 CN4 HN3 39.0 124.8 !h8, G,A NN2 CN4 HN3 39.0 121.8 ! CN5 NN2 HN2 30.0 129.4 !h9 CN4 NN2 HN2 30.0 125.0 ! !@@@@@@@@ Guanine ! gua 6-mem ring CN1 NN2G CN2 70.0 131.1 !6R)G, adm jr. 11/97 NN2G CN2 NN3G 70.0 122.2 !6R) CN2 NN3G CN5 90.0 109.4 !6R) CN5G CN5 NN3G 70.0 129.9 !6R) bridgeC4 CN1 CN5G CN5 70.0 119.6 !6R) bridgeC5 CN5G CN1 NN2G 70.0 107.8 !6R) CN5G CN5 NN2B 100.0 104.6 !5R) bridgeC4 CN5 CN5G NN4 100.0 111.4 !5R) bridgeC5 CN4 NN4 CN5G 120.0 103.8 !5R) NN2B CN4 NN4 100.0 113.0 !5R) CN4 NN2B CN5 100.0 107.2 !5R) NN2B CN5 NN3G 140.0 125.5 ! bridgeC4 CN1 CN5G NN4 125.0 129.0 ! bridgeC5 CN1 NN2G HN2 45.0 113.3 ! h1 CN2 NN2G HN2 45.0 115.6 ! NN1 CN2 NN2G 95.0 115.4 ! n2 NN1 CN2 NN3G 95.0 122.4 ! NN2G CN1 ON1 50.0 127.5 ! o6 CN5G CN1 ON1 50.0 124.7 ! HN3 CN4 NN2B 40.0 122.2 ! h8 (NN4 CN4 HN3 124.8) CN4 NN2B HN2 30.0 124.6 ! h9 CN5 NN2B HN2 30.0 129.3 ! !@@@@@@@@ Cytosine ! cyt 6-mem ring CN1 NN2 CN3 50.0 124.1 !C, adm jr. 11/97 NN2 CN1 NN3 50.0 116.8 !C CN1 NN3 CN2 85.0 119.1 !C CN3 CN2 NN3 85.0 119.3 !C CN2 CN3 CN3 85.0 117.8 !C CN3 CN3 NN2 85.0 122.9 !C CN1 NN2 HN2 37.0 121.2 !C, h1 CN3 NN2 HN2 37.0 114.7 !C NN2 CN1 ON1C 130.0 119.4 !C, o2 NN3 CN1 ON1C 130.0 123.8 !C NN3 CN2 NN1 81.0 122.3 !C, n4 CN3 CN2 NN1 81.0 118.4 !C CN2 CN3 HN3 38.0 120.1 !C h5 CN3 CN3 HN3 38.0 122.1 !C,U HN3 CN3 NN2 44.0 115.0 !C, h6 !@@@@@@@@ Uracil ! ura 6-mem ring CN1T NN2B CN3 70.0 122.0 !U, adm jr. 11/97 NN2B CN1T NN2U 50.0 114.0 !U CN1T NN2U CN1 50.0 130.2 !U NN2U CN1 CN3 70.0 112.6 !U CN1 CN3 CN3 100.0 117.6 !U CN3 CN3 NN2B 100.0 123.6 !U CN1T NN2B HN2 40.5 122.0 !U, h1 CN3 NN2B HN2 32.0 116.0 !U NN2B CN1T ON1 100.0 121.6 !U, o2 NN2U CN1T ON1 100.0 124.4 !U CN1T NN2U HN2 40.5 114.4 !U, h3 CN1 NN2U HN2 40.5 115.4 !U NN2U CN1 ON1 100.0 121.9 !U, o4 CN3 CN1 ON1 100.0 125.5 !U, CN1 CN3 HN3 30.0 120.3 !U, h5 HN3 CN3 NN2B 30.0 114.3 !U, h6 ! thymine 6-mem ring (unique from ura) CN3T CN1 NN2U 70.0 113.5 !T, adm jr. 11/97 CN1 CN3T CN3 120.0 116.7 !T CN3T CN3 NN2B 120.0 123.6 !125.3 !T CN3T CN1 ON1 100.0 124.6 !T, o4 CN1 CN3T CN9 38.0 118.7 !T, c5 methyl CN3 CN3T CN9 38.0 124.6 !T CN3T CN3 HN3 30.0 122.1 !T, h6 ! Inosine, adm jr., 9/98 update HN3 CN4 NN3I 35.0 116.75 !c2 HN3 CN4 NN2G 35.0 115.75 !c2 NN3I CN4 NN2G 80.0 127.5 !c2 CN5G CN5 NN3I 100.0 127.0 !c4, r6 NN2B CN5 NN3I 140.0 128.4 !c4, r5 CN1 NN2G CN4 125.0 129.7 !n1 CN4 NN2G HN2 40.5 117.0 !n1 CN4 NN3I CN5 90.0 108.4 !n3 ! base to methyl connection CN1T NN2B CN9 70.0 116.0 !1-M-T/U, adm jr. CN3 NN2B CN9 70.0 122.0 !1-M-T/U, adm jr. 7/24/91 CN1 NN2 CN9 70.0 115.4 !1-M-C, adm jr. CN3 NN2 CN9 70.0 120.5 !1-M-C, adm jr. 7/24/91 CN5 NN2 CN9 70.0 125.9 !9-M-A, adm jr. CN4 NN2 CN9 70.0 127.8 !9-M-A, adm jr. CN5 NN2B CN9 70.0 125.9 !9-M-G, adm jr. CN4 NN2B CN9 70.0 126.9 !9-M-G, adm jr. CN5 NN2B CN8 70.0 125.9 !9-E-G, adm jr. CN4 NN2B CN8 70.0 126.9 !9-E-G, adm jr. NN2B CN8 CN9 70.0 113.7 !9-E-G, adm jr. !===== For glycosydic linkage, base to c1' CN1T NN2B CN7B 45.0 118.4 !U/T, FC from A CN3 NN2B CN7B 45.0 119.6 !U/T CN1 NN2 CN7B 45.0 120.0 !C, FC from A CN3 NN2 CN7B 45.0 115.9 !C CN5 NN2 CN7B 45.0 126.1 !A CN4 NN2 CN7B 45.0 127.6 !A CN5 NN2B CN7B 45.0 126.5 !G CN4 NN2B CN7B 45.0 126.3 !G ON6 CN7B NN2 110.0 108.0 !C/A DNA ON6B CN7B NN2 110.0 112.0 !C/A RNA CN8 CN7B NN2 110.0 113.7 !C/A CN7B CN7B NN2 110.0 111.0 !C/A, RNA CN7C CN7B NN2 110.0 111.0 !C/A, Arabinose (NF) ON6 CN7B NN2B 110.0 108.0 !T/U/G (DNA) FC from A ON6B CN7B NN2B 110.0 112.0 !T/U/G (RNA) FC from A CN8 CN7B NN2B 110.0 113.7 !T/U/G CN7B CN7B NN2B 110.0 111.0 !T/U/G, RNA CN7C CN7B NN2B 110.0 111.0 !T/U/G, Arabinose (NF) HN7 CN7B NN2 43.0 111.0 ! HN7 CN7B NN2B 43.0 111.0 !From HN7 CN7B NN2 !===== End of glycosydic linkage ! remaining terms ordered based on central atom CN3 CN1A NN1 85.0 113.0 80.0 2.46 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN1A ON1 85.0 118.5 20.0 2.43 !nad/ppi, jjp1/adm jr. 7/95 NN1 CN1A ON1 85.0 128.5 20.0 2.17 !nad/ppi, jjp1/adm jr. 7/95 CN3D CN2 NN1 110.0 116.4 !5mc, adm jr. 9/9/93 CN3D CN2 NN3 30.0 121.3 !5mc, adm jr. 9/9/93 CN1A CN3 CN3C 5.0 107.8 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN8 125.0 124.2 !nadh/ppi, jjp1/adm jr. 7/95 CN2 CN3D CN3 100.0 117.8 !5mc, adm jr. 9/9/93 CN2 CN3D CN9 40.0 118.0 !5mc, adm jr. 9/9/93 CN3A CN3 CN1A 40.0 110.2 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A 10.0 131.8 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A CN3 50.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN3B 40.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3 CN8 53.5 108.5 !nadh/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN8 53.5 108.5 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 CN8 43.5 128.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3D CN9 40.0 124.2 !5mc, adm jr. 9/9/93 CN3D CN3 HN3 30.0 122.0 !5mc, adm jr. 9/9/93 CN3B CN3 HN3B 30.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 HN3B 30.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3C HN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3C CN3 HN3 42.0 116.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A HN3B 80.0 121.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3B HN3B 80.0 120.5 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3B NN2 120.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3C NN2 60.0 122.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN3 NN2 100.0 124.2 !5mc, adm jr. 9/9/93 CN8 CN3 HN3 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95 HN3B CN3B NN2 80.0 117.5 !nad/ppi, jjp1/adm jr. 7/95 HN3 CN3C NN2 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN8 CN3 125.0 108.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3 CN8 HN8 55.0 110.10 !nadh/ppi, jjp1/adm jr. 7/95 CN9 CN8 HN8 34.6 110.10 22.53 2.179 ! Alkanes, sacred HN8 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM HN8 CN8 ON5 45.9 108.89 !RIBOSE, Adm Jr. MeOH CN3 CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN3T CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN3D CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN8 CN9 HN9 34.60 110.10 22.53 2.179 ! Alkanes, sacred HN9 CN9 NN2 33.43 110.1 !FOR 9-M-A(T), adm jr. HN9 CN9 NN2B 33.43 110.1 !FOR 9-M-G(C), adm jr. HN8 CN8 NN2B 33.43 110.1 !FOR 9-E-G, adm jr. HN9 CN9 ON2 60.0 109.5 !DMP, ADM Jr. CN1A NN1 HN1 35.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B NN2 CN3B 30.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN3C 20.0 114.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3B NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 CN3B NN2 HN2 32.0 117.4 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 HN2 39.0 123.0 !nad/ppi, jjp1/adm jr. 7/95 HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr. CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr. CN9 ON2 P2 20.0 120.0 35. 2.33 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. HN5 ON5 CN8 57.5 106.0 !RIBOSE, Adm Jr. MeOH HN5 ON5 CN9 57.5 106.0 !RIBOSE, Adm Jr. MeOH ON2 P ON2 80.0 104.3 !DMP, ADM Jr. ON2 P ON4 48.1 108.0 !MP_1, ADM Jr. ON3 P ON4 98.9 108.23 !MP_1, ADM Jr. ON4 P ON4 98.9 104.0 !MP_0, ADM Jr. ON2 P2 ON2 80.0 104.3 !nad/ppi, jjp1/adm jr. 7/95 ON2 P2 ON3 88.9 111.6 !nad/ppi, jjp1/adm jr. 7/95 ON3 P2 ON3 104.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN7 CN8 ON5 75.7 110.10 !RIBOSE, adm jr. MeOH HN9 CN9 HN9 35.500 108.40 5.40 1.802 !alkane update, adm jr. 3/2/92 !@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@ CN7 ON6 CN7B 110.0 108.0 ! NF, 11/97, C4'O4'C1' ON6 CN7B CN8 90.0 102.0 ! NF, 11/97, C4'O4'C1' CN7B CN8 CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3' CN8 CN7 CN7 60.00 102.0 8.0 2.561 !NF, 11/97, C2'C3'C4' CN7 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4' HN7 CN7 ON6 45.2 107.24 ! HN7 CN7B ON6 45.2 107.24 ! HN7 CN7 CN7 40.0 108.00 ! CN7B CN8 HN8 33.4 110.10 22.53 2.179 ! following terms directly CN8 CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes HN7 CN7 CN8 34.5 110.1 22.53 2.179 ! HN8 CN8 CN7 34.53 110.10 22.53 2.179 ! HN8 CN8 CN8 34.53 110.10 22.53 2.179 ! HN8 CN8 HN8 35.5 109.00 5.40 1.802 ! HN7 CN7 HN7 35.5 109.00 5.40 1.802 ! !@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@ !@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@ CN7 ON6B CN7B 110.0 115.0 ! From CN7 ON6 CN7B CN7 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6 ON6B CN7B CN7B 90.0 106.0 ! 030998 CN7B CN7B CN7 110.0 96.0 ! CN7B CN7 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4' HN7 CN7 ON6B 45.2 107.24 ! HN7 CN7B ON6B 45.2 107.24 ! CN7B CN7B HN7 33.4 110.10 22.53 2.179 ! following terms directly HN7 CN7B HN7 35.5 109.00 5.40 1.802 ! !@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@ !@@@@@@@@@ Beginning of endocyclic valence angles for arabinose @@@@@@@ ON6 CN7B CN7C 90.0 102.0 ! NF, 11/97, C4'O4'C1' CN7B CN7C CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3' CN7C CN7 CN7 60.00 102.0 8.00 2.561 !NF, 11/97, C2'C3'C4' CN7B CN7C HN7 33.4 110.10 22.53 2.179 ! following terms directly CN7C CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes HN7 CN7 CN7C 34.5 110.1 22.53 2.179 ! HN7 CN7C CN7 34.53 110.10 22.53 2.179 ! HN7 CN7C HN7 35.5 109.00 5.40 1.802 ! !@@@@@@@@@ End of endocyclic valence angles for arabinose @@@@@@@ !@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@ ON6 CN7 CN8B 90.0 108.2 !NF, 11/97, O4'C4'C5' CN7 CN7 CN8B 45.0 110.0 !NF, 11/97, C3'C4'C5' CN7 CN8B ON2 70.0 108.4 !NF, 11/97, C4'C5'O5' CN7 CN7 ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' CN7B CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH CN7 CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH CN8 CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3' CN8B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P CN7 ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P CN7B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH ! sugar HN7 CN7 CN8B 34.5 110.1 22.53 2.179 ! From HN7 CN7 CN8 HN8 CN8B ON2 60.0 109.5 ! From HN7 CN8 ON2 HN5 ON5 CN8B 57.5 106.0 ! From HN5 ON5 CN8 HN8 CN8B HN8 35.5 109.0 5.40 1.802 ! Alkanes, sacred HN8 CN8B CN7 34.53 110.1 22.53 2.179 ! Alkanes, sacred HN7 CN7 ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2 HN7 CN7B ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2, for NADPH !===== For 5ter patch: CN7 CN8B ON5 75.7 110.10 ! From CN7 CN8B ON5 HN8 CN8B ON5 45.9 108.89 ! From HN7 CN8 ON5 !===== For 3ter patch: ON5 CN7 CN8 75.7 110.0 ! from CHARMM22 ON5 CN7 CN7 75.7 110.1 ! HN7 CN7 ON5 60.0 109.5 ! HN5 ON5 CN7 57.5 109.0 ! !@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@ !@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@ !O4'-C4'-C5' ON6B CN7 CN8B 90.0 108.2 ! !O3'-C3'-C2' ON2 CN7 CN7B 90.0 110.0 ! ON5 CN7 CN7B 90.0 110.0 ! From ON5 CN7 CN8 !O2'-C2'-C1' ON5 CN7B CN7B 80.0 108.4 ! !O2'-C2'-C3' ON5 CN7B CN7 90.0 108.0 ! HN7 CN7B ON5 60.0 109.5 ! HN5 ON5 CN7B 57.5 109.0 ! HN7 CN7B CN7 34.53 110.10 22.53 2.179 HN7 CN7 CN7B 34.53 110.10 22.53 2.179 !@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@ CN7C CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3' !===== For 3ter patch: !From DNA: ON5 CN7 CN7C 75.7 110.0 ! from CHARMM22 !From RNA: ON5 CN7C CN7B 80.0 108.4 ! From ON5 CN7B CN7B !O2'-C2'-C3' ON5 CN7C CN7 90.0 108.0 ! From ON5 CN7B CN7 HN7 CN7C ON5 60.0 109.5 ! HN5 ON5 CN7C 57.5 109.0 ! 032598 !@@@@@@@@@ Beginning of exocyclic valence angles for arabinose @@@@@@@ !@@@@@@@@@ End of exocyclic valence angles for arabinose @@@@@@@ !@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@ CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, adm jr. !@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@ ON2 P ON3 98.9 111.6 !DMP, adm jr. ON3 P ON3 120.0 120.0 !DMP, adm jr. HN8 CN8 ON2 60.0 109.5 !DMP, adm jr. ON5 P ON3 98.9 111.6 ! From ON2 P ON3 !-- For imidazole, from imidazole alone: !-- and for link between sugar and imidazole ON6 CN7B NR1 140.0 108.00 ! k guessed, theta from ribo./desox. xtal (NF) ON6B CN7B NR1 140.0 108.00 ! RNUS CN8 CN7B NR1 140.0 113.70 ! k guessed, theta from ribo./desox. xtal (NF) CN7B CN7B NR1 140.0 113.70 ! RNUS CN7B NR1 CPH2 130.0 127.00 ! k guessed, theta from A/G xtal (NF) CN7B NR1 CPH1 130.0 126.00 ! k guessed, theta from A/G xtal (NF) HN7 CN7B NR1 30.0 106.3 ! k guessed, theta from ai (NF) !CPH2 NR1 CPH1 130.0 107.0000 ! From imidazole (NF), modified for 360 deg. condition !CPH2 NR2 CPH1 130.0 104.0000 ! From imidazole (NF) !NR1 CPH1 CPH1 130.0 106.0000 ! From imidazole (NF) !NR1 CPH2 NR2 130.0 112.5000 ! From imidazole !NR2 CPH1 CPH1 130.0 110.0000 ! From imidazole (NF) !NR1 CPH2 HR1 25.0 122.50 20.00 2.14000 ! From imidazole (NF) !NR2 CPH2 HR1 25.0 125.00 20.00 2.12000 ! From imidazole (NF) !HR3 CPH1 CPH1 25.0 130.00 20.00 2.20000 ! From imidazole (NF) !NR1 CPH1 HR3 25.0 124.00 20.00 2.14000 ! From imidazole (NF) !NR2 CPH1 HR3 25.0 120.00 20.00 2.14000 ! From imidazole (NF) !------------------------ For water ------------------- !HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY !------------------------ added for arao ----------------------- !------------------------ added for araim ---------------------- ON6 CN7B CN7 120.0 106.25 ! CN7B CN7 CN8 58.35 113.6 11.16 2.561 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c CE1 CE1 CT3 HA 0.0300 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT2 CT3 0.5000 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT2 HA 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT3 HA 0.0500 3 180.00 ! ! for propene, yin/adm jr., 12/95 CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI ! ethylbenzene ethyl rotation, adm jr. 3/7/92 CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP ! from CT2 C NH1 CT2, adm jr. 10/21/96 CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP ! from CT2 C NH1 CT2, adm jr. 10/21/96 CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 toluene and ethylbenzene CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! from CT2 CT1 NH1 C, for lactams, adm jr. CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO !JWK CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP ! for acetylated GLY N-terminus, adm jr. CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! for acetylated GLY N-terminus, adm jr. CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! toluene, adm jr., 3/7/92 CT3 CE1 CE2 HE2 5.2000 2 180.00 ! ! for propene, yin/adm jr., 12/95 CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI ! ethylbenzene ethyl rotation, adm jr. 3/7/92 CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION ! DTN 8/24/90 CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP ! from H NH1 CT2 CT3, for lactams, adm jr. H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/20/89 H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA H NY CA CY 0.8000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO ! adm jr., 10/02/89 HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO ! ADM JR., 10/02/89 HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! TRP (JES) HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO ! JWK HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO ! JWK HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA NY H 1.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ! adm jr. 4/10/91, acetamide update HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO ! JWK HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO ! JWK HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HE1 CE1 CE2 HE2 5.2000 2 180.00 ! ! for propene, yin/adm jr., 12/95 HE1 CE1 CT2 HA 0.8700 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE1 CE1 CT2 CT3 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE1 CE1 CT3 HA 0.3400 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE2 CE2 CE1 CT2 5.2000 2 180.00 ! ! for butene, yin/adm jr., 12/95 HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HC NH2 CT2 HB 0.1100 3 0.00 !from X CT3 NH2 X, neutral glycine, adm jr. HC NH2 CT2 CD 0.1100 3 0.00 !from X CT3 NH2 X, neutral glycine, adm jr. HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 toluene and ethylbenzene HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO ! toluene, adm jr., 3/7/92 HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA NY H 0.4000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90, his HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90, YES, 0.0 HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP ! from NH1 C CT1 CT2, for lactams, adm jr. NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO ! adm jr. 3/24/92, for PRES GLYP NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO ! HIS CB-CG TORSION, NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO ! HIS CB-CG TORSION, NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO ! HIS CB-CG TORSION, NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO ! JWK NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO ! Backbone parameter set made complete RLD 8/8/90 O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP ! from O C CT1 CT2, for lactams, adm jr. O C CT2 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO ! Backbone parameter set made complete RLD 8/8/90 O C CT3 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations O C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O C NH1 H 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! adm jr. 8/27/91, phenoxide OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO ! adm jr. 8/27/91, phenoxide OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 phenol OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 phenol S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 X C C X 4.0000 2 180.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO ! 9.0->2.25 GUANIDINIUM (KK) X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CE1 CE1 X 5.2000 2 180.00 ! ! for butene, yin/adm jr., 12/95 X CE2 CE2 X 4.9000 2 180.00 ! ! for ethene, yin/adm jr., 12/95 X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP ! changed to 0.0 RLD 5/19/92 X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) X CPB C X 3.0000 2 180.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI ! rotation barrier in Ethane (SF) X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X FE CM X 0.0500 4 0.00 ! ALLOW HEM ! Heme (6-liganded): ligands (KK 05/13/91) X FE NPH X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) X FE OM X 0.0000 4 0.00 ! ALLOW HEM ! Heme (6-liganded): ligands (KK 05/13/91) X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) CA CA CA ON2b 3.10 2 180.0 !phenol phosphate, 6/94, adm jr. HP CA CA ON2b 4.20 2 180.0 !phenol phosphate, 6/94, adm jr. CA CA ON2b P 1.40 2 180.0 !phenol phosphate, 6/94, adm jr. CA CA ON2b P 0.20 3 180.0 !phenol phosphate, 6/94, adm jr. CA ON2b P ON4 0.95 2 0.0 !phenol phosphate, 6/94, adm jr. CA ON2b P ON4 0.50 3 0.0 !phenol phosphate, 6/94, adm jr. CA ON2b P ON3 0.10 3 0.0 !phenol phosphate, 6/94, adm jr. !nucleic acid section ! PHOSPHATE ON2 P ON2 CN7 1.20 1 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN7 0.10 2 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN7 0.10 3 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN7 0.00 6 0.0 !10/97, DMP, adm jr. ON2 P ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr. ! Added when C5' defined as CN8B (NF 041497): ON2 P ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr. ON2 P ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr. ON2 P ON2 CN9 1.20 1 180.0 !dmp ON2 P ON2 CN9 0.10 2 180.0 !dmp ON2 P ON2 CN9 0.10 3 180.0 !dmp ON2 P ON2 CN9 0.00 6 0.0 !dmp ! ON3 P ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3' ON3 P ON2 CN7B 0.10 3 0.0 !for NADPH ON3 P ON2 CN8 0.10 3 0.0 !dmp ON3 P ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5' ON3 P ON2 CN9 0.10 3 0.0 !dmp ! terminal phosphate terms, adm jr. ON4 P ON2 CN7 0.95 2 0.0 !MP_1, adm jr. ON4 P ON2 CN7 0.50 3 0.0 !MP_1, adm jr. ON4 P ON2 CN7B 0.95 2 0.0 !for NADPH ON4 P ON2 CN7B 0.50 3 0.0 !for NADPH ON4 P ON2 CN8 0.95 2 0.0 !MP_1, adm jr. ON4 P ON2 CN8 0.50 3 0.0 !MP_1, adm jr. ON4 P ON2 CN8B 0.95 2 0.0 !MP_1, adm jr. ON4 P ON2 CN8B 0.50 3 0.0 !MP_1, adm jr. ON4 P ON2 CN9 0.95 2 0.0 !MP_1, adm jr. ON4 P ON2 CN9 0.50 3 0.0 !MP_1, adm jr. X ON4 P X 0.30 3 0.0 !MP_1, adm jr. ! When O5' is ON2 (phosphodiester linkage): P ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P P ON2 CN7B HN7 0.000 3 0.0 !for NADPH P ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P P ON2 CN8 HN8 0.000 3 0.0 !dmp P ON2 CN9 HN9 0.000 3 0.0 !dmp ! butane gauche terms cn9 cn8 cn8 cn9 0.15 1 0.0 cn9 cn8 cn8 cn8 0.15 1 0.0 ! BASES ! Uracil NN2B CN1T NN2U CN1 1.5 2 180.0 ! adm jr. 11/97 CN1T NN2U CN1 CN3 1.5 2 180.0 ! adm jr. 11/97 NN2U CN1 CN3 CN3 1.5 2 180.0 ! adm jr. 11/97 CN1 CN3 CN3 NN2B 6.0 2 180.0 ! adm jr. 11/97 CN3 CN3 NN2B CN1T 1.5 2 180.0 ! adm jr. 11/97 CN3 NN2B CN1T NN2U 1.5 2 180.0 ! adm jr. 11/97 HN3 CN3 CN3 HN3 3.0 2 180.0 ! adm jr. 11/97 HN3 CN3 CN1 ON1 6.0 2 180.0 ! adm jr. 11/97 ON1 CN1T NN2B HN2 0.0 2 180.0 ! adm jr. 11/97 ON1 CN1 NN2U HN2 0.0 2 180.0 ! adm jr. 11/97 ON1 CN1T NN2U HN2 0.0 2 180.0 ! adm jr. 11/97 HN2 NN2B CN3 HN3 1.5 2 180.0 ! adm jr. 11/97 NN2B CN1T NN2U HN2 3.8 2 180.0 ! adm jr. 11/97 CN3 CN1 NN2U HN2 3.8 2 180.0 ! adm jr. 11/97 CN3 CN3 NN2B HN2 1.6 2 180.0 ! adm jr. 11/97 NN2U CN1T NN2B HN2 1.6 2 180.0 ! adm jr. 11/97 !Thymine CN1T NN2B CN3 CN3T 1.8 2 180.0 ! adm jr. 11/97 NN2U CN1 CN3T CN3 1.8 2 180.0 ! adm jr. 11/97 CN1 CN3T CN3 NN2B 3.0 2 180.0 ! adm jr. 11/97 NN2B CN1 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97 NN2B CN3 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97 CN1 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97 CN3 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97 CN3T CN1 NN2U HN2 4.8 2 180.0 ! adm jr. 11/97 ! Cytosine CN3 NN2 CN1 NN3 0.6 2 180.0 ! adm jr. 11/97 NN2 CN1 NN3 CN2 0.6 2 180.0 ! adm jr. 11/97 CN1 NN3 CN2 CN3 6.0 2 180.0 ! adm jr. 11/97 NN3 CN2 CN3 CN3 0.6 2 180.0 ! adm jr. 11/97 CN2 CN3 CN3 NN2 6.0 2 180.0 ! adm jr. 11/97 CN3 CN3 NN2 CN1 0.6 2 180.0 ! adm jr. 11/97 NN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97 CN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97 NN1 CN2 NN3 CN1 2.0 2 180.0 ! adm jr. 11/97 NN1 CN2 CN3 CN3 2.0 2 180.0 ! adm jr. 11/97 NN1 CN2 CN3 HN3 2.0 2 180.0 ! adm jr. 11/97 ON1C CN1 NN2 HN2 3.0 2 180.0 ! adm jr. 11/97 ON1C CN1 NN3 CN2 1.6 2 180.0 ! adm jr. 11/97 ON1C CN1 NN2 CN3 1.6 2 180.0 ! adm jr. 11/97 NN3 CN2 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97 NN2 CN3 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97 CN2 CN3 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97 CN1 NN2 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97 X CN2 NN3 X 2.0 2 180.0 ! adm jr. 11/97 ! 5-methylcytosine NN2 CN3 CN3D CN2 3.0 2 180.0 !5mc, adm jr. 9/9/93 CN3 CN3D CN2 NN3 1.0 2 180.0 !5mc, adm jr. 9/9/93 CN3D CN2 NN3 CN1 10.0 2 180.0 !5mc, adm jr. 9/9/93 CN3D CN3 NN2 CN1 1.0 2 180.0 !5mc, adm jr. 9/9/93 CN3D CN2 NN1 HN1 2.0 2 180.0 !5mc, adm jr. 9/9/93 NN1 CN2 CN3D CN3 0.0 2 180.0 !5mc, adm jr. 9/9/93 NN1 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr. 9/9/93 NN2 CN3 CN3D CN9 4.0 2 180.0 !5mc, adm jr. 9/9/93 NN3 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr. 9/9/93 CN3 CN3D CN9 HN9 0.0 3 0.0 !5mc, adm jr. 9/9/93 CN2 CN3D CN9 HN9 0.35 3 0.0 !5mc, adm jr. 9/9/93 CN2 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr. 9/9/93 CN9 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr. 9/9/93 ! Adenine CN2 NN3A CN4 NN3A 1.8 2 180.0 ! adm jr. 11/97, 6-mem NN3A CN4 NN3A CN5 2.0 2 180.0 ! CN4 NN3A CN5 CN5 1.8 2 180.0 ! NN3A CN5 CN5 CN2 2.0 2 180.0 ! treated 2x CN5 CN5 CN2 NN3A 1.8 2 180.0 ! CN5 CN2 NN3A CN4 10.0 2 180.0 ! CN5 CN5 NN4 CN4 6.0 2 180.0 ! 5-mem CN5 NN4 CN4 NN2 14.0 2 180.0 ! NN4 CN4 NN2 CN5 6.0 2 180.0 ! CN4 NN2 CN5 CN5 6.0 2 180.0 ! NN2 CN5 CN5 NN4 14.0 2 180.0 ! treated 2x CN2 NN3A CN4 HN3 8.5 2 180.0 ! H2 CN5 NN3A CN4 HN3 8.5 2 180.0 ! H2 CN5 NN4 CN4 HN3 5.2 2 180.0 ! H8 CN5 NN2 CN4 HN3 5.2 2 180.0 ! H8 CN5 CN5 NN2 HN2 1.2 2 180.0 ! H9 NN4 CN4 NN2 HN2 1.2 2 180.0 ! H9 HN2 NN2 CN4 HN3 0.0 2 180.0 ! H8-C-N-H9 CN4 NN3A CN2 NN1 4.0 2 180.0 ! N6 CN5 CN5 CN2 NN1 4.0 2 180.0 ! N6 NN4 CN5 CN2 NN1 0.0 2 180.0 ! N6 CN5 CN2 NN1 HN1 0.5 2 180.0 ! 6-NH2 NN3A CN2 NN1 HN1 0.5 2 180.0 ! ! Butterfly motion NN3A CN5 CN5 NN4 7.0 2 180.0 !A, adm jr. 11/97 CN2 CN5 CN5 NN2 7.0 2 180.0 !A NN3A CN2 CN5 NN4 2.0 2 180.0 !A CN2 CN5 NN4 CN4 2.0 2 180.0 !A CN4 NN3A CN5 NN2 2.0 2 180.0 !A NN3A CN5 NN2 CN4 2.0 2 180.0 !A ! Guanine CN1 NN2G CN2 NN3G 0.2 2 180.0 !adm jr. 11/97, 6-mem NN2G CN2 NN3G CN5 2.0 2 180.0 ! CN2 NN3G CN5 CN5G 0.2 2 180.0 ! NN3G CN5 CN5G CN1 2.0 2 180.0 ! CN5 CN5G CN1 NN2G 0.2 2 180.0 ! CN5G CN1 NN2G CN2 0.2 2 180.0 ! CN5 CN5G NN4 CN4 6.0 2 180.0 !5-mem CN5G NN4 CN4 NN2B 16.0 2 180.0 ! NN4 CN4 NN2B CN5 6.0 2 180.0 ! CN4 NN2B CN5 CN5G 6.0 2 180.0 ! NN2B CN5 CN5G NN4 10.0 2 180.0 ! ! substitutents ON1 CN1 CN5G CN5 14.0 2 180.0 !G, O6 ON1 CN1 CN5G NN4 0.0 2 180.0 ! ON1 CN1 NN2G CN2 14.0 2 180.0 ! ON1 CN1 NN2G HN2 0.0 2 180.0 ! NN1 CN2 NN2G CN1 4.0 2 180.0 !G, N2 NN1 CN2 NN3G CN5 4.0 2 180.0 ! NN1 CN2 NN2G HN2 0.0 2 180.0 ! NN2G CN2 NN1 HN1 1.2 2 180.0 ! NN3G CN2 NN1 HN1 1.2 2 180.0 ! HN2 NN2G CN1 CN5G 3.6 2 180.0 !G, H1 HN2 NN2G CN2 NN3G 3.6 2 180.0 ! HN3 CN4 NN4 CN5G 5.6 2 180.0 !G, H8 HN3 CN4 NN2B CN5 5.6 2 180.0 ! HN3 CN4 NN2B HN2 0.0 2 180.0 ! HN2 NN2B CN5 CN5G 1.2 2 180.0 !G, H9 HN2 NN2B CN5 NN3G 1.2 2 180.0 ! HN2 NN2B CN4 NN4 1.2 2 180.0 ! ! Butterfly motion NN3G CN5 CN5G NN4 10.0 2 180.0 !adm jr. 11/97 CN1 CN5G CN5 NN2 10.0 2 180.0 ! NN2G CN1 CN5G NN4 2.0 2 180.0 ! CN1 CN5G NN4 CN4 2.0 2 180.0 ! CN2 NN3G CN5 NN2B 2.0 2 180.0 ! NN3G CN5 NN2B CN4 2.0 2 180.0 ! ! inosine, adm jr. 2/94 CN5 CN5 NN3I CN4 6.0 2 180.0 NN2G CN4 NN3I CN5 6.0 2 180.0 NN3I CN4 NN2G HN2 1.5 2 180.0 NN3I CN4 NN2G CN1 1.5 2 180.0 HN3 CN4 NN2G HN2 1.5 2 180.0 HN3 CN4 NN2G CN1 1.5 2 180.0 ! Wild cards for inosine X CN4 NN3I X 3.5 2 180.0 X CN5 NN3I X 1.0 2 180.0 ! Wild cards for uracil, thymine and cytosine X CN1 NN3 X 1.0 2 180.0 ! c22 X CN1 NN2 X 0.9 2 180.0 ! c22 X CN1T NN2B X 0.9 2 180.0 ! From X CN1 NN2 X, for thymines X CN1 NN2G X 0.9 2 180.0 ! c22 X CN1 NN2U X 0.9 2 180.0 ! c22 X CN1T NN2U X 0.9 2 180.0 ! c22 X CN3 NN2 X 1.0 2 180.0 ! c22 X CN3 NN2B X 1.0 2 180.0 ! From X CN3 NN2 X, for thymines X CN3 CN3 X 1.0 2 180.0 ! c22 X CN3 CN3T X 1.0 2 180.0 !T, adm jr. 11/97 X CN1 CN3 X 1.0 2 180.0 ! c22 X CN1 CN3T X 1.0 2 180.0 !T, adm jr. 11/97 X CN2 CN3 X 0.8 2 180.0 ! c22 ! Wild cards for adenine and guanine X CN1 CN5G X 1.0 2 180.0 ! adm jr. 11/97 X CN2 NN2G X 1.0 2 180.0 ! X CN2 CN5 X 1.0 2 180.0 ! X CN4 NN2 X 1.5 2 180.0 ! X CN4 NN2B X 1.5 2 180.0 ! From X CN4 NN2 X X CN4 NN3A X 3.5 2 180.0 ! X CN4 NN4 X 2.0 2 180.0 ! A,G X CN5 CN5 X 0.0 2 180.0 ! X CN5G CN5 X 0.0 2 180.0 ! adm jr. 11/97 X CN5 NN2 X 1.5 2 180.0 ! X CN5 NN2B X 1.5 2 180.0 ! From X CN5 NN2 X X CN5 NN3A X 1.0 2 180.0 ! X CN5 NN3G X 1.0 2 180.0 ! adm jr. 11/97 X CN5 NN4 X 1.0 2 180.0 ! X CN5G NN4 X 1.0 2 180.0 ! adm jr. 11/97 X CN2 NN3A X 1.0 2 180.0 ! X CN2 NN3G X 1.0 2 180.0 ! adm jr. 11/97 ! MISC. CN1 NN2 CN9 HN9 0.19 3 0.0 ! 1-M-C CN3 NN2 CN9 HN9 0.00 3 0.0 ! 1-M-C CN4 NN2 CN9 HN9 0.00 3 0.0 ! 9-M-A CN5 NN2 CN9 HN9 0.19 3 0.0 ! 9-M-A CN1 NN2B CN9 HN9 0.19 3 0.0 ! 1-M-U CN1T NN2B CN9 HN9 0.19 3 0.0 ! 1-M-T CN3 NN2B CN9 HN9 0.00 3 0.0 ! 1-M-T/U CN4 NN2B CN9 HN9 0.00 3 0.0 ! 9-M-G CN5 NN2B CN9 HN9 0.19 3 0.0 ! 9-M-G CN4 NN2B CN8 HN8 0.00 3 0.0 ! 9-E-G CN5 NN2B CN8 HN8 0.19 3 0.0 ! 9-E-G CN4 NN2B CN8 CN9 0.00 3 0.0 ! 9-E-G CN5 NN2B CN8 CN9 0.19 3 0.0 ! 9-E-G X CN8 CN8 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) X CN8 CN9 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) ! nicotinamide adenine dinucleotide CN3 NN2 CN3B HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 HN2 NN2 CN3B HN3B 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 HN3B CN3 CN3A HN3B 2.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 HN3B CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 NN2 CN3B CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN1A CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3A HN3B 5.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN1A CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3 HN3 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN1A NN1 0.35 1 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A NN1 0.35 1 0.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A CN3 CN1A 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A CN3 CN3B 6.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 NN2 CN3B CN3 CN3A 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B NN2 CN3B CN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN3A X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN8 X 1.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95 X NN1 CN1A X 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X NN2 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 ! nicotinamide adenine dinucleotide hydride, nadh CN8 CN3 CN1A ON1 1.00 2 180.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A ON1 1.00 3 0.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A ON1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A NN1 0.50 2 180.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A NN1 0.35 3 180.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A NN1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A ON1 0.30 1 0.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A ON1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A NN1 1.10 1 180.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A NN1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95 HN2 NN2 CN3C HN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 NN2 CN3C HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 NN2 CN3C CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN8 CN3 CN3C NN2 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 CN8 CN3 4.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3C NN2 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X NN2 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN3C CN3 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 ! pyrophosphate (ppi) P2 ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 !for nadp/nadph, adm jr. HN7 CN7 CN7B ON5 0.195 3 0.0 HN7 CN7 CN7 CN7 0.195 3 0.0 HN7 CN7 CN7 CN7B 0.195 3 0.0 HN7 CN7B CN7 CN7 0.195 3 0.0 HN7 CN7B NN2 CN3B 0.195 3 0.0 HN7 CN7B NN2 CN3C 0.195 3 0.0 HN7 CN7 CN7B HN7 0.195 3 0.0 HN7 CN7 CN7B ON6 0.195 3 0.0 HN7 CN7 CN7B ON2 0.195 3 0.0 HN7 CN7B CN7B ON2 0.195 3 0.0 HN7 CN7 CN7B NN2 0.195 3 0.0 ! it conflicts with a term transfered from rna to dna: !CN7B CN7 ON5 HN5 0.0 3 0.0 !ON5 CN7 CN7B HN7 0.195 3 0.0 !HN7 CN7B CN7 ON2 0.195 3 0.0 !P ON2 CN7 CN7B 0.0 3 0.0 ON6 CN7B CN7 ON5 3.4 1 180.0 !gam CN7 CN7B NN2 CN3B 0.0 3 0.0 CN7B CN7B NN2 CN3B 0.0 3 0.0 ! for NADPH ON6 CN7B NN2 CN3B 0.0 3 0.0 ! ON6B CN7B NN2 CN3B 0.0 3 0.0 ! for NADPH CN7 CN7B NN2 CN3C 0.0 3 0.0 CN7B CN7B NN2 CN3C 0.0 3 0.0 ! for NADPH ON6 CN7B NN2 CN3C 0.0 3 0.0 ! ON6B CN7B NN2 CN3C 0.0 3 0.0 ! for NADPH CN7 CN7 CN7B NN2 0.0 3 0.0 CN7 CN7B NN2 CN5 0.3 3 0.0 ! NF CN7 CN7B NN2 CN4 0.0 3 180.0 ! NF ON2 CN7 CN7B NN2 0.0 3 0.0 ON2 CN7B CN7B NN2 0.0 3 0.0 !for NADPH ON5 CN7 CN7B NN2 0.0 3 0.0 ! sugar, replace with ribose terms 021998 CN7 CN7B ON6 CN7 0.6 6 180.0 CN7B CN7 CN7 CN7 0.4 6 0.0 ! good for amplitudes CN7 CN7 CN7 ON6 0.6 6 0.0 CN7 CN7 CN7B ON6 0.6 6 0.0 ON2 CN7 CN7 CN7 0.8 6 0.0 ! ON2 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right ON2 CN7 CN7 CN7 2.0 3 180.0 ! ! for ndph ON2 CN7B CN7 CN7 0.8 6 0.0 ! ON2 CN7B CN7 CN7 0.4 5 0.0 ! Moves the barrier right ON2 CN7B CN7 CN7 2.0 3 180.0 ! ! ON5 CN7 CN7 CN7 0.8 6 0.0 ! ON5 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right ON5 CN7 CN7 CN7 2.0 3 180.0 ! ON5 CN7 CN7 ON5 0.0 3 0.0 ! ON5 CN7 CN7 ON2 0.0 3 0.0 ! ON2 CN7 CN7B ON6 0.5 6 0.0 !good for amplitudes ON2 CN7 CN7B ON6 0.3 5 0.0 !impact on amplitudes ON2 CN7 CN7B ON6 0.6 4 180.0 !increases c2'endo ON2 CN7 CN7B ON6 0.2 3 0.0 ! CN7 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg. !============ new parameters for sugar model compounds =============== !---------------- added for thf-imidazole ------------------ !-- For link between base and sugar: CN7B NR1 CPH1 HR3 0.0 2 180.0 !NF CN7B NR1 CPH1 CPH1 0.0 1 0.0 ! CN7B NR1 CPH2 HR1 0.0 2 180.0 ! CN7B NR1 CPH2 NR2 0.0 2 180.0 ! !-- For chi: ON6 CN7B NR1 CPH1 0.2 3 0.0 ! ON6 CN7B NR1 CPH1 0.5 2 -70.0 ! ON6 CN7B NR1 CPH1 0.6 1 180.0 ! ON6 CN7B NR1 CPH2 0.3 1 0.0 ! ON6B CN7B NR1 CPH1 0.2 3 0.0 ! RNUS ON6B CN7B NR1 CPH1 0.5 2 -70.0 ! RNUS ON6B CN7B NR1 CPH1 0.6 1 180.0 ! RNUS ON6B CN7B NR1 CPH2 0.3 1 0.0 ! RNUS CN8 CN7B NR1 CPH1 0.2 4 0.0 ! CN8 CN7B NR1 CPH2 0.1 3 180.0 ! CN8 CN7B NR1 CPH2 0.3 2 0.0 ! CN8 CN7B NR1 CPH2 0.0 1 180.0 ! CN7B CN7B NR1 CPH1 0.2 4 0.0 ! RNUS CN7B CN7B NR1 CPH2 0.1 3 180.0 ! RNUS CN7B CN7B NR1 CPH2 0.3 2 0.0 ! RNUS CN7B CN7B NR1 CPH2 0.0 1 180.0 ! RNUS HN7 CN7B NR1 CPH1 0.0 3 0.0 ! HN7 CN7B NR1 CPH2 0.195 3 0.0 ! CN8 CN8 CN7B NR1 0.0 3 0.0 CN7 CN7B CN7B NR1 0.0 3 0.0 ! RNUS CN8 ON6 CN7B NR1 0.0 3 0.0 HN8 CN8 CN7B NR1 0.0 3 0.0 HN7 CN7B CN7B NR1 0.0 3 0.0 ! RNUS NR1 CN7B CN7B ON5 0.0 3 0.0 ! RNUS !-- For imidazole, transferred from imidazole alone: !CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! From imidazole (NF) !CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! From imidazole (NF) !NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! From imidazole (NF) !NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! From imidazole (NF) !NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! From imidazole (NF) !NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! From imidazole (NF) !HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! From imidazole (NF) !HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! From imidazole (NF) !HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! From imidazole (NF) !HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! From imidazole (NF) !HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! From imidazole (NF) !NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! From imidazole (NF) !------------------- added for thf-oh-ch3-im --------------------- CN7B ON6 CN7 CN9 0.0 3 0.0 CN7 ON6 CN7B NR1 0.0 3 0.0 CN7 ON6B CN7B NR1 0.0 3 0.0 ! RNUS NR1 CN7B CN8 CN7 0.0 3 0.0 !%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%% ! The following is for: THF3P (model for espilon), THFM3P (model for puckering), ! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue !@@@@@@ Begining of chi !============= added for torsion about chi in adenine ============ !For link from sugar to base: CN7B NN2 CN4 HN3 0.3 2 180.0 ! NF CN7B NN2 CN5 CN5 11.0 2 180.0 ! adm jr. CN7B NN2 CN4 NN4 11.0 2 180.0 ! adm jr. CN7B NN2 CN4 NN3A 11.0 2 180.0 ! adm jr. !For chi itself: !DNA: ON6 CN7B NN2 CN5 1.1 1 180.0 ! ON6 CN7B NN2 CN4 1.1 1 0.0 ! NF !RNA: ON6B CN7B NN2 CN5 1.1 1 180.0 ! ON6B CN7B NN2 CN4 1.1 1 0.0 ! !DNA: CN8 CN7B NN2 CN5 0.3 3 0.0 ! NF CN8 CN7B NN2 CN4 0.0 3 180.0 ! NF !RNA: CN7B CN7B NN2 CN5 0.3 3 0.0 ! NF CN7B CN7B NN2 CN4 0.0 3 180.0 ! NF !Arabinose: CN7C CN7B NN2 CN5 0.3 3 0.0 ! CN7C CN7B NN2 CN4 0.0 3 180.0 ! HN7 CN7B NN2 CN5 0.0 3 0.0 ! NF HN7 CN7B NN2 CN4 0.195 3 0.0 ! NF !@@@@@@ End of chi in adenines !============== terms for torsion about chi in cytosines =========== CN7B NN2 CN3 HN3 0.3 2 180.0 ! NF CN7B NN2 CN1 ON1C 11.0 2 180.0 ! adm jr. from A CN7B NN2 CN1 NN3 11.0 2 180.0 ! adm jr. CN7B NN2 CN3 CN3 11.0 2 180.0 ! adm jr. !DNA: ON6 CN7B NN2 CN1 0.0 3 0.0 ! ON6 CN7B NN2 CN3 1.0 1 0.0 ! NF !RNA: ON6B CN7B NN2 CN1 0.0 3 0.0 ! ON6B CN7B NN2 CN3 1.0 1 0.0 ! !DNA: CN8 CN7B NN2 CN1 1.0 3 0.0 ! CN8 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697 !RNA: CN7B CN7B NN2 CN1 1.0 3 0.0 ! CN7B CN7B NN2 CN3 0.0 3 180.0 ! !Arabinose: CN7C CN7B NN2 CN1 1.0 3 0.0 ! CN7C CN7B NN2 CN3 0.0 3 180.0 ! HN7 CN7B NN2 CN1 0.0 3 0.0 ! NF HN7 CN7B NN2 CN3 0.195 3 0.0 ! NF !@@@@@@ End of chi in cytosines !=========== terms for torsion about chi in uracils/thymines =========== CN7B NN2B CN3 HN3 0.3 2 180.0 ! NF CN7B NN2B CN1T ON1 11.0 2 180.0 ! adm jr. from A CN7B NN2B CN1T NN2U 11.0 2 180.0 ! adm jr. CN7B NN2B CN3 CN3T 11.0 2 180.0 ! adm jr. !DNA: ON6 CN7B NN2B CN1 0.0 3 0.0 ! ON6 CN7B NN2B CN1T 0.7 3 0.0 ! ON6 CN7B NN2B CN1T 0.8 1 180.0 ! ON6 CN7B NN2B CN3 0.9 1 0.0 ! NF !RNA: ON6B CN7B NN2B CN1 0.0 3 0.0 ! ON6B CN7B NN2B CN1T 0.7 3 0.0 ! ON6B CN7B NN2B CN1T 0.8 1 180.0 ! ON6B CN7B NN2B CN3 0.9 1 0.0 ! !DNA: CN8 CN7B NN2B CN1T 0.2 3 180.0 ! CN8 CN7B NN2B CN3 0.0 3 180.0 ! NF !RNA: CN7B CN7B NN2B CN1T 0.2 3 180.0 ! CN7B CN7B NN2B CN3 0.0 3 180.0 ! !Arabinose: CN7C CN7B NN2B CN1T 0.2 3 180.0 ! CN7C CN7B NN2B CN3 0.0 3 180.0 ! HN7 CN7B NN2B CN1T 0.0 3 0.0 ! NF HN7 CN7B NN2B CN3 0.195 3 0.0 ! NF !@@@@@@ End of chi in thymines !============= added for torsion about chi in guanine ============ CN7B NN2B CN4 HN3 0.3 2 180.0 ! NF CN7B NN2B CN4 NN4 11.0 2 180.0 ! adm jr. CN7B NN2B CN5 CN5G 11.0 2 180.0 ! adm jr. from U CN7B NN2B CN5 NN3G 11.0 2 180.0 ! adm jr. !DNA: ON6 CN7B NN2B CN5 0.2 3 0.0 ! ON6 CN7B NN2B CN5 1.1 1 180.0 ! ON6 CN7B NN2B CN4 1.4 1 0.0 ! NF !RNA: ON6B CN7B NN2B CN5 0.2 3 0.0 ! ON6B CN7B NN2B CN5 1.1 1 180.0 ! ON6B CN7B NN2B CN4 1.4 1 0.0 ! !DNA: CN8 CN7B NN2B CN5 0.0 3 0.0 ! NF CN8 CN7B NN2B CN4 0.0 3 180.0 ! NF 030697 !RNA: CN7B CN7B NN2B CN5 0.0 3 0.0 ! NF CN7B CN7B NN2B CN4 0.0 3 180.0 ! !Arabinose: CN7C CN7B NN2B CN5 0.0 3 0.0 ! CN7C CN7B NN2B CN4 0.0 3 180.0 ! HN7 CN7B NN2B CN5 0.0 3 0.0 ! NF HN7 CN7B NN2B CN4 0.195 3 0.0 ! NF !@@@@@@ End of chi in guanines !@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines: !DNA: CN7 ON6 CN7B NN2 0.0 3 0.0 CN7 ON6 CN7B NN2B 0.0 3 0.0 !RNA: CN7 ON6B CN7B NN2 0.0 3 0.0 CN7 ON6B CN7B NN2B 0.0 3 0.0 !DNA: CN7 CN8 CN7B NN2 0.0 3 0.0 CN7 CN8 CN7B NN2B 0.0 3 0.0 HN8 CN8 CN7B NN2 0.0 3 0.0 HN8 CN8 CN7B NN2B 0.0 3 0.0 !RNA: CN7 CN7B CN7B NN2 0.0 3 0.0 CN7 CN7B CN7B NN2B 0.0 3 0.0 !Arabinose: CN7 CN7C CN7B NN2 0.0 3 0.0 CN7 CN7C CN7B NN2B 0.0 3 0.0 !RNA HN7 CN7B CN7B NN2 0.0 3 0.0 HN7 CN7B CN7B NN2B 0.0 3 0.0 !Arabinose: HN7 CN7C CN7B NN2 0.0 3 0.0 HN7 CN7C CN7B NN2B 0.0 3 0.0 !@@@@@@ Begining of torsions involving exocyclic sugar atoms: !======= CN7 CN8B ON2 P = C4'-C5'-O5'-P CN7 CN8B ON2 P 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr. ! the following differ significantly from the alcohols ! in the protein (based on ethanol), they also differ from other ! NA C-C-OH-H parameters (see below) ! The two following terms have been replaced by their ethanol ! counterpart (NF, 083098) !CN7 CN8B ON5 HN5 0.5 3 0.0 !bet !CN7 CN8B ON5 HN5 1.0 1 0.0 !bet ! the following would be equivalent to the proteins CN7 CN8B ON5 HN5 1.3300 1 0.00 CN7 CN8B ON5 HN5 0.1800 2 0.00 CN7 CN8B ON5 HN5 0.3200 3 0.00 !======= HN8 CN8B ON2 P = H-C5'-O5'-P )beta HN8 CN8B ON5 HN5 0.0 3 0.0 !bet !======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5' ! When O5' is ON2 (phosphodiester linkage): CN7 CN7 CN8B ON2 0.20 4 180.0 !gam adm jr. CN7 CN7 CN8B ON2 0.80 3 180.0 !gam C3'-C4'-C5'-O5' CN7 CN7 CN8B ON2 0.40 2 0.0 !gam CN7 CN7 CN8B ON2 2.50 1 180.0 !gam ! When O5' is ON5 (5TER patch): CN7 CN7 CN8B ON5 0.20 4 180.0 !gam adm jr. CN7 CN7 CN8B ON5 0.80 3 180.0 !gam C3'-C4'-C5'-O5' CN7 CN7 CN8B ON5 0.40 2 0.0 !gam CN7 CN7 CN8B ON5 2.50 1 180.0 !gam !======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5' ! When O5' is ON2 (3'-5' phosphodiester linkage) ON6 CN7 CN8B ON2 3.4 1 180.0 !gam O4'-C4'-C5'-O5',influences +60 ON6B CN7 CN8B ON2 3.4 1 180.0 !gam, RNA ! When O5' is ON5 (5TER patch): ON6 CN7 CN8B ON5 3.4 1 180.0 !gam ON6B CN7 CN8B ON5 3.4 1 180.0 !gam, RNA !======== HN8 CN8B CN7 CN7 = H-C5'-C4'-H HN8 CN8B CN7 CN7 0.195 3 0.0 !gam,H-C5'-C4'-H !======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4' HN8 CN8B CN7 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4' HN8 CN8B CN7 ON6B 0.195 1 0.0 !gam, RNA !======== HN7 CN7 CN8B ON2 = H-C4'-C5'-O5' ! When O5' is ON2 (phosphodiester linkage): HN7 CN7 CN8B ON2 0.195 3 0.0 !gam H-C4'-C5'-O5' ! When O5' is ON5 (5TER patch): HN7 CN7 CN8B ON5 0.195 3 0.0 !gam HN8 CN8 CN8 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4' !======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5' ! This term is well suited to modify the puckering surfaces, in ! particular because it is present in THF5P CN8 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg. CN7B CN7 CN7 CN8B 0.2 4 180.0 !del, RNA CN7C CN7 CN7 CN8B 0.5 4 180.0 !del, arabinose !======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3' ! These terms affect the c2endo/c3endo energy difference ! When O3' is ON2 (3'-5' phosphodiester linkage) ON2 CN7 CN7 CN8B 0.2 4 0.0 !del ! the following term controls the location of the barrier at ~75 deg. ON2 CN7 CN7 CN8B 0.8 3 180.0 !del,decreases P [100,250] ! When O3' is ON5 (patch 3TER) ON5 CN7 CN7 CN8B 0.2 4 0.0 ! ON5 CN7 CN7 CN8B 0.8 3 180.0 ! !======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3' ! These terms contribute to delta ! These terms are present in THF3P and THFM3P but not in THF5P ! When O3' is ON2 (3'-5' phosphodiester linkage) ON2 CN7 CN7 ON6 0.5 6 0.0 !del, good for amplitudes ON2 CN7 CN7 ON6 0.3 5 0.0 !del, impact on amplitudes ON2 CN7 CN7 ON6 0.6 4 180.0 !del, increases c2'endo ON2 CN7 CN7 ON6 0.2 3 0.0 ! ON2 CN7 CN7 ON6B 0.4 6 0.0 !del, RNA, good for amplitudes ON2 CN7 CN7 ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes ON2 CN7 CN7 ON6B 0.0 4 180.0 !del, RNA, increases c2'endo ON2 CN7 CN7 ON6B 1.6 3 0.0 !del, RNA, increases C2'endo ! for ndph: make identical to ON2 CN7 CN7 ON6B ON2 CN7B CN7B ON6B 0.4 6 0.0 !del, RNA, good for amplitudes ON2 CN7B CN7B ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes ON2 CN7B CN7B ON6B 0.0 4 180.0 !del, RNA, increases c2'endo ON2 CN7B CN7B ON6B 1.6 3 0.0 !del, RNA, increases C2'endo ! When O3' is ON5 (patch 3TER) ON5 CN7 CN7 ON6 0.5 6 0.0 ! ON5 CN7 CN7 ON6 0.3 5 0.0 ! ON5 CN7 CN7 ON6 0.6 4 180.0 ! ON5 CN7 CN7 ON6 0.2 3 0.0 ! ON5 CN7 CN7 ON6B 0.4 6 0.0 !RNA ON5 CN7 CN7 ON6B 0.0 5 0.0 !RNA ON5 CN7 CN7 ON6B 0.0 4 180.0 !RNA ON5 CN7 CN7 ON6B 1.6 3 0.0 !RNA. increases c2'endo !======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1' ! This term can be used to adjust the c2'endo/c3'endo ! energy difference in THF5P CN7B ON6 CN7 CN8B 0.8 3 0.0 ! P [30,80] CN7B ON6B CN7 CN8B 2.0 3 0.0 ! To lower barrier in RNA !======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1' ! This term can be used to adjust the c2'endo/c3'endo ! When O3' is ON2 ON2 CN7 CN8 CN7B 0.8 6 0.0 ! ON2 CN7 CN8 CN7B 0.4 5 0.0 ! Moves the barrier right ON2 CN7 CN8 CN7B 2.0 3 180.0 ! ON2 CN7 CN7B CN7B 0.6 6 0.0 ! RNA ON2 CN7 CN7B CN7B 0.0 5 0.0 ! RNA c2/c3 endo in RNA ON2 CN7 CN7B CN7B 1.6 3 180.0 ! ON2 CN7 CN7C CN7B 0.8 6 0.0 ! Arabinose (from DNA) ON2 CN7 CN7C CN7B 0.4 5 0.0 ! ON2 CN7 CN7C CN7B 2.0 3 180.0 ! !When O3' is ON5 (patch 3TER) ON5 CN7 CN8 CN7B 0.8 6 0.0 ! ON5 CN7 CN8 CN7B 0.4 5 0.0 ! ON5 CN7 CN8 CN7B 2.0 3 180.0 ! ON5 CN7 CN7B CN7B 0.6 6 0.0 ! RNA, c2/c3 endo ON5 CN7 CN7B CN7B 0.0 5 0.0 ! RNA ON5 CN7 CN7B CN7B 1.6 3 180.0 ! RNA ON5 CN7 CN7C CN7B 0.8 6 0.0 ! Arabinose (from DNA) ON5 CN7 CN7C CN7B 0.4 5 0.0 ! Arabinose (from DNA) ON5 CN7 CN7C CN7B 2.0 3 180.0 ! Arabinose (from DNA) !======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H ON2 CN7 CN8 HN8 0.195 3 0.0 ! ON5 CN7 CN8 HN8 0.195 3 180.0 ! ON2 CN7 CN7B HN7 0.195 3 0.0 ! RNA ON5 CN7 CN7B HN7 0.195 3 180.0 ! RNA ON2 CN7 CN7C HN7 0.195 3 0.0 ! Arabinose (from DNA) ON5 CN7 CN7C HN7 0.195 3 180.0 ! Arabinose (from DNA) !======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3' HN7 CN7 CN7 ON2 0.195 3 0.0 HN7 CN7 CN7 ON5 0.195 3 0.0 !======== CN7 CN7 ON2 P = C4'-C3'-O3'-P CN7 CN7 ON2 P 0.6 5 0.0 !eps CN7 CN7 ON2 P 0.2 4 0.0 !eps, locat of 200 mimima CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE beteen minima CN7 CN7 ON2 P 0.4 2 0.0 !eps, relE of 200 vs 275 min CN7 CN7 ON2 P 1.9 1 180.0 !eps !======== CN8 CN7 ON2 P = C2'-C3'-O3'-P ! This term is involved in epsilon CN8 CN7 ON2 P 2.5 1 180.0 !eps CN7B CN7 ON2 P 2.5 1 180.0 !eps, RNA CN7B CN7B ON2 P 2.5 1 180.0 !eps, NADPH CN7 CN7B ON2 P 2.5 1 180.0 !eps, NADPH CN7C CN7 ON2 P 2.5 1 180.0 !eps, Arabinose (from DNA) ! base on thfalloh ! the following differ significantly from the protein based ! alcohol parameters (based on ethanol, see above) CN7 CN7 ON5 HN5 0.5 3 0.0 CN7 CN7 ON5 HN5 0.3 2 180.0 CN7 CN7 ON5 HN5 1.5 1 0.0 CN8 CN7 ON5 HN5 0.5 3 0.0 CN8 CN7 ON5 HN5 1.0 2 180.0 CN8 CN7 ON5 HN5 0.3 1 0.0 CN7B CN7 ON5 HN5 0.8 3 0.0 ! RNA CN7B CN7 ON5 HN5 0.5 1 0.0 ! RNA CN7C CN7 ON5 HN5 0.8 3 0.0 ! Arabinose (from DNA) CN7C CN7 ON5 HN5 0.5 1 0.0 ! Arabinose (from DNA) ! Was simply transfered from HN7 CN7 ON2 P ! adm jr. should convert to alcohol term (see ribose etc) HN7 CN7 ON5 HN5 0.0 3 0.0 HN7 CN7 CN8B HN8 0.195 3 0.0 !gam H-C4'-C5'-H HN7 CN7 CN7 CN8B 0.195 3 0.0 !gam H-C3'-C4'-C5' !@@@@@@ End of torsions involving exocyclic atoms: !@@@@@@ Begining of torsions for endocyclic atoms only: CN8 CN7B ON6 CN7 0.6 6 180.0 !C2'-C1'-O4'-C4' CN8 CN7 CN7 ON6 0.0 3 0.0 !C2'-C3'-C4'-O4' CN7B CN7B ON6B CN7 0.0 6 0.0 ! RNA, Lowers barrier CN7B CN7 CN7 ON6B 0.0 3 0.0 ! RNA CN7C CN7B ON6 CN7 0.6 6 180.0 ! Arabinose (from DNA) CN7C CN7 CN7 ON6 0.0 3 0.0 ! Arabinose (from DNA) !======== CN7 CN8 CN7B ON6 for nucleosides, transfered from ========= !======== CN7 CN8 CN8 ON6 from thfoh ============================== CN7 CN8 CN7B ON6 0.6 6 0.0 ! C3'-C2'-C1'-O4', adjust barrier CN7 CN7B CN7B ON6B 0.4 6 0.0 ! RNA CN7 CN7C CN7B ON6 0.6 6 0.0 ! Arabinose (from DNA) !======== C1'-C2'-C3'-C4' ======== CN7B CN8 CN7 CN7 0.4 6 0.0 ! good for amplitudes CN7B CN7B CN7 CN7 0.0 6 0.0 ! RNA CN7B CN7C CN7 CN7 0.4 6 0.0 ! Arabinose (from DNA) !======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ======== !======== CN7 CN7 ON6 CN8 from thfohch3 ============================ CN7 CN7 ON6 CN7B 0.6 6 180.0 ! C3'-C4'-O4'-C1' CN7 CN7 ON6B CN7B 0.0 6 180.0 ! RNA !======== Directly adjusted with TM3P HN7 CN7 CN7 CN8 0.0 3 0.0 !puc,H-C3'-C4'-C5' HN7 CN7 CN7 CN7C 0.0 3 0.0 ! Arabinose (from DNA) !======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4' HN7 CN7 CN8 CN7B 0.195 3 0.0 !H-C3'-C2'-C1' HN7 CN7B CN8 CN7 0.195 3 0.0 !H-C1'-C2'-C3' HN7 CN7 CN7 ON6 0.195 3 180.0 ! useful HN8 CN8 CN7B ON6 0.195 3 0.0 !H-C2'-C1'-O4' HN7 CN7 CN7 HN7 0.195 3 0.0 !H-C4'-C3'-H HN7 CN7B CN8 HN8 0.195 3 0.0 !H-C1'-C2'-H HN7 CN7 CN8 HN8 0.195 3 0.0 !H-C3'-C2'-H HN8 CN8 CN7 CN7 0.195 3 0.0 ! useful *cccc* HN7 CN7 ON6 CN7B 0.195 3 0.0 !H-C3'-C2'-C1' HN7 CN7B ON6 CN7 0.000 3 0.0 !H-C1'-O4'-C4' HN7 CN7 CN7 ON6B 0.195 3 180.0 ! RNA HN8 CN8 CN7B ON6B 0.195 3 0.0 ! RNA HN7 CN7B ON6B CN7 0.000 3 0.0 ! RNA HN7 CN7 ON6B CN7B 0.195 3 0.0 ! RNA HN7 CN7 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1' HN7 CN7B CN7B CN7 0.195 3 0.0 ! RNA, H-C1'-C2'-C3' HN7 CN7B CN7B ON6B 0.195 3 0.0 ! RNA, H-C2'-C1'-O4' HN7 CN7 CN7C CN7B 0.195 3 0.0 !Arabinose (from DNA), H-C3'-C2'-C1' HN7 CN7B CN7C CN7 0.195 3 0.0 !Arabinose (from DNA), H-C1'-C2'-C3' HN7 CN7C CN7B ON6 0.195 3 0.0 !Arabinose (from DNA), H-C2'-C1'-O4' HN7 CN7B CN7C HN7 0.195 3 0.0 !Arabinose (from DNA), H-C1'-C2'-H HN7 CN7 CN7C HN7 0.195 3 0.0 !Arabinose (from DNA), H-C3'-C2'-H HN7 CN7C CN7 CN7 0.195 3 0.0 !Arabinose (from DNA), useful *cccc* !@@@@@@ End of torsions for endocyclic atoms only !@@@@@@ Begining of orsions specifically defined for RNA @@@@@@ ! N9-C1'-C2'-O2': NN2 CN7B CN7B ON5 0.000 3 0.0 ! Adenine and cytosine NN2B CN7B CN7B ON5 0.000 3 0.0 ! Guanine and uracil ON5 CN7B CN7B HN7 0.000 3 0.0 ! HN7 CN7B CN7B HN7 0.000 3 0.0 ! CN7 CN7 CN7B ON5 0.000 3 0.0 ON6B CN7B CN7B ON5 0.000 3 0.0 ON5 CN7B CN7 ON2 0.000 3 0.0 ! for ndph ON5 CN7 CN7B ON2 0.000 3 0.0 ON5 CN7B CN7 ON5 0.000 3 0.0 HN7 CN7B ON5 HN5 0.000 3 0.0 ! the following differ significantly from the protein based ! alcohol parameters (based on ethanol, see above) HN5 ON5 CN7B CN7B 0.000 6 180.0 ! HN5 ON5 CN7B CN7B 0.800 3 0.0 ! HN5 ON5 CN7B CN7B 0.000 2 180.0 ! HN5 ON5 CN7B CN7B 0.000 1 180.0 ! HN5 ON5 CN7B CN7 0.300 3 0.0 ! 030298 HN5 ON5 CN7B CN7 0.000 1 0.0 ! 030298 !@@@@@@ End of torsions specifically defined for RNA @@@@@@ !@@@@@@ Begining of torsions specifically defined for arabinose @@@@@@ ON6 CN7B CN7C ON5 0.000 3 0.0 ! the following differ significantly from the protein based ! alcohol parameters (based on ethanol, see above) CN7B CN7C ON5 HN5 0.000 3 0.0 CN7 CN7C ON5 HN5 0.000 3 0.0 HN7 CN7B CN7C ON5 0.000 3 0.0 CN7 CN7 CN7C ON5 0.000 3 0.0 HN7 CN7C ON5 HN5 0.000 3 0.0 ON5 CN7C CN7 HN7 0.000 3 0.0 ON5 CN7C CN7 ON2 0.000 3 0.0 !@@@@@@ End of torsions specifically defined for arabinose @@@@@@ IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB X X C 90.0000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK, from propene (JCS)) HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO ! Heme (6-liganded): substituents (KK 05/13/91) HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK, from propene (JCS)) HE2 HE2 CE2 CE2 3.0 0 0.00 ! ! for ethene, yin/adm jr., 12/95 HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO ! 5.75->40.0 GUANIDINIUM (KK) NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO ! NMA Vibrational Modes (LK) NH2 X X H 4.0000 0 0.0000 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO ! adm jr., 5/13/91, formamide geometry and vibrations O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 5/13/91, formamide geometry and vibrations O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO ! NMA Vibrational Modes (LK) OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL ! adm jr., 10/17/90, acetic acid vibrations OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK) CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK) CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK) CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK) !nucleic acid section ! HN2 X X NN2 1.0 0 0.0 !C, adm jr. 11/97 NN2B CN4 CN5 HN2 7.0 0 0.0 !G, adm jr. 11/97 NN2G CN4 CN1 HN2 0.8 0 0.0 !Inosine, adm jr. 2/94 HN1 X X NN1 4.0 0 0.0 !G, adm jr. 11/97 NN1 CN2 HN1 HN1 6.0 0 0.0 !A,C adm jr. 11/97 CN1 X X ON1 90.0 0 0.0 !U CN1T X X ON1 90.0 0 0.0 !U CN1 NN2G CN5G ON1 90.0 0 0.0 !G CN1T NN2B NN2U ON1 110.0 0 0.0 !T/O2, adm jr. 11/97 CN1 NN2U CN3T ON1 90.0 0 0.0 !T/O4, adm jr. 11/97 CN1 X X ON1C 80.0 0 0.0 !C, par_32, adm jr. 10/2/91 CN2 X X NN1 90.0 0 0.0 !C, CN2 NN3G NN2G NN1 40.0 0 0.0 !G CN2 NN3A CN5 NN1 40.0 0 0.0 !A CN2 NN3 CN3 NN1 60.0 0 0.0 !C, CN4 NN2G NN3I HN3 39.0 0 0.0 !Inosine, adm jr. 2/94 CN9 X X CN3T 14.0 0 0.0 !T, adm jr. 11/97 ! nicotinamide adenine dinucleotide CN3 CN3C CN8 HN6 15.0 0 0.0 !nich, jjp1/adm jr. HN3B X X CN3 15.0 0 0.0 !nad/ppi, jjp1/adm jr. HN3B X X CN3A 13.0 0 0.0 !nad/ppi, jjp1/adm jr. HN3B X X CN3B 13.0 0 0.0 !nad/ppi, jjp1/adm jr. HN2 CN3 CN3B NN2 50.0 0 0.0 !nad/ppi, jjp1/adm jr. HN1 HN1 CN1A NN1 -5.0 0 0.0 !nad/ppi, jjp1/adm jr. ON1 X X CN1A 40.0 0 0.0 !nad/ppi, jjp1/adm jr. HN3 X X CN3C 53.0 0 0.0 !nad/ppi, jjp1/adm jr. HN6 X X CN3C 53.0 0 0.0 !nich, adm jr. HN8 CN3 CN3 CN8 18.0 0 0.0 !nad/ppi, jjp1/adm jr. !================== new terms added for sugar model compounds ========= !----------------------- Added for imidazole -------------------- !HR1 NR1 NR2 CPH2 0.50 0 0.00 ! From imidazole (NF) !HR1 NR2 NR1 CPH2 0.50 0 0.00 ! From imidazole (NF) !HR3 CPH1 NR1 CPH1 0.50 0 0.00 ! From imidazole (NF) !HR3 CPH1 NR2 CPH1 0.50 0 0.00 ! From imidazole (NF) !HR3 NR1 CPH1 CPH1 0.50 0 0.00 ! From imidazole (NF) !HR3 NR2 CPH1 CPH1 0.50 0 0.00 ! From imidazole (NF) !NR1 CPH1 CPH2 CN7B 0.60 0 0.00 ! From imidazole (NF), k increased !NR1 CPH2 CPH1 CN7B 0.60 0 0.00 ! From imidazole (NF), k increased NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CA 0.000000 -0.070000 1.992400 ! ALLOW ARO ! benzene (JES) CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CD 0.000000 -0.070000 2.000000 ! ALLOW POL ! adm jr. 3/19/92, acetate a.i. and dH of solvation CE1 0.000000 -0.068000 2.090000 ! ! for propene, yin/adm jr., 12/95 CE2 0.000000 -0.064000 2.080000 ! ! for ethene, yin/adm jr., 12/95 CM 0.000000 -0.110000 2.100000 ! ALLOW HEM ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO ! benzene (JES) CS 0.000000 -0.110000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! propane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 CY 0.000000 -0.070000 1.992400 ! ALLOW ARO ! TRP, JWK 08/29/89 ! carbon wildcards, following atom order is essential for accurate results !C* 0.000000 -0.070000 2.000000 !CP% 0.000000 -0.090000 1.800000 !C%1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 !C%2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 !C%3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 !CPH+ 0.000000 -0.050000 1.800000 !C 0.000000 -0.110000 2.000000 !CA 0.000000 -0.070000 1.992400 !CE1 0.000000 -0.068000 2.090000 !CE2 0.000000 -0.064000 2.080000 !CM 0.000000 -0.110000 2.100000 !CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI !CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 !CS 0.000000 -0.110000 2.200000 !CY 0.000000 -0.070000 1.992400 H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HE1 0.000000 -0.031000 1.250000 ! ! for propene, yin/adm jr., 12/95 HE2 0.000000 -0.026000 1.260000 ! ! for ethene, yin/adm jr., 12/95 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO ! JES 8/25/89 values from Jorgensen fit to hydration energy HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO ! adm jr., 6/27/90, his HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO ! adm jr., 6/27/90, his HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS 0.000000 -0.100000 0.450000 ! ALLOW SUL ! methanethiol pure solvent, adm jr., 6/22/92 HT 0.000000 -0.046000 0.224500 ! ALLOW WAT !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete ! hydrogen wildcards !H* 0.000000 -0.046000 0.224500 !HA 0.000000 -0.022000 1.320000 !HE1 0.000000 -0.031000 1.250000 !HE2 0.000000 -0.026000 1.260000 !HB 0.000000 -0.022000 1.320000 !HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 !HR1 0.000000 -0.046000 0.900000 !HR2 0.000000 -0.046000 0.700000 !HR3 0.000000 -0.007800 1.468000 !HS 0.000000 -0.100000 0.450000 ! N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 0.000000 -0.200000 1.850000 ! ALLOW POL ! JG 8/27/89; note: NH1 in ARG was changed to NC2. NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH2 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. NP 0.000000 -0.200000 1.850000 ! ALLOW PRO ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NY 0.000000 -0.200000 1.850000 ! ALLOW ARO ! trp, JWK ! nitrogen wildcards !N* 0.000000 -0.200000 1.850000 !N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 !NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid carbonyl O OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) OM 0.000000 -0.120000 1.700000 ! ALLOW HEM ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO ! adm jr. 9/17/90, avoid O* wildcard OT 0.000000 -0.152100 1.768200 ! ALLOW WAT !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete ! oxygen wildcards !O* 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 !OC 0.000000 -0.120000 1.700000 !OH1 0.000000 -0.152100 1.770000 !OM 0.000000 -0.120000 1.700000 !OS 0.000000 -0.152100 1.770000 !OT 0.000000 -0.152100 1.768200 !CAL 0.000000 -0.120000 1.710000 ! ALLOW ION ! !Calcium (BP) FE 0.010000 0.000000 0.650000 ! ALLOW HEM ! Heme (6-liganded): Iron atom (KK 05/13/91) S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION ! adm jr., 3/3/92, dimethyldisulphide pure solvent SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 ZN 0.000000 -0.250000 1.090000 ! ALLOW ION ! RHS March 18, 1990 DUM 0.000000 -0.000000 0.000000 ! ! dummy atom HE 0.000000 -0.021270 1.4800 ! ! helium, experimental pot. energy surface, adm jr., 12/95 NE 0.000000 -0.086000 1.5300 ! neon, semiempirical pot. energy surface, adm jr., 12/95 !nucleic acid section !HT 0.0 -0.0460 0.2245 ! TIP3P HN1 0.0 -0.0460 0.2245 HN2 0.0 -0.0460 0.2245 HN3 0.0 -0.046 1.1000 !adm jr. aromatic Hvdw HNP 0.0 -0.03 1.3582 !JES 8/25/89 values from Jorgensen fit to hydration energy HN3B 0.0 -0.046 0.9000 !nad/ppi, jjp1/adm jr. HN3C 0.0 -0.03 1.3582 !check HN4 0.0 -0.0460 0.2245 HN5 0.0 -0.0460 0.2245 HN6 0.0 -0.0220 1.3200 HN7 0.0 -0.0220 1.3200 HN8 0.0 -0.0280 1.3400 ! Hydrogen bound to CN8 HN9 0.0 -0.0240 1.3400 ! Hydrogen bound to CN9 HNE1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95 HNE2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95 ! ! hydrogen wildcards !HN* 0.0 -0.0460 0.2245 ! HN1, HN2, HN4, HN5 !HN3 0.0 -0.0220 1.1000 !HN3B 0.0 -0.046 0.9000 ! nad/ppi, jjp1/adm jr. !HN6 0.0 -0.0220 1.3200 !HN7 0.0 -0.0220 1.3200 !HT 0.0 -0.0460 0.2245 ! TIP3P ! NN1 0.0 -0.20 1.85 NN1C 0.0 -0.20 1.85 NN2 0.0 -0.20 1.85 NN2B 0.0 -0.20 1.85 ! From NN2, for N9 in guanines NN2C 0.0 -0.20 1.85 ! NN2G 0.0 -0.20 1.85 NN2U 0.0 -0.20 1.85 NN3 0.0 -0.20 1.85 NN3A 0.0 -0.20 1.85 NN3G 0.0 -0.20 1.85 NN3I 0.0 -0.20 1.85 NN4 0.0 -0.20 1.85 NN5 0.0 -0.20 1.85 NN6 0.0 -0.20 1.85 ! ! nitrogen wildcards !NN* 0.0 -0.20 1.85 ! all nitrogens ! ON1 0.0 -0.1200 1.70 ON1C 0.0 -0.1200 1.70 ON2 0.0 -0.1521 1.77 ON2b 0.0 -0.1521 1.77 ON3 0.0 -0.1200 1.70 ON4 0.0 -0.1521 1.77 ON5 0.0 -0.1521 1.77 ON6 0.0 -0.1521 1.77 ON6B 0.0 -0.1521 1.77 !OT 0.0 -0.1521 1.7682 ! TIP3P ! ! oxygen wildcards !ON* 0.0 -0.1521 1.77 ! types ON2, ON4, ON5, ON6 and ON6B !ON1* 0.0 -0.1200 1.70 ! types ON1 and ON1C !ON3 0.0 -0.1200 1.70 !OT 0.0 -0.1521 1.7682 ! TIP3P ! ! base ring C vdw param, 11/14/97, adm jr CN1 0.0 -0.10 1.9000 CN1A 0.0 -0.07 2.0000 ! nad/ppi, jjp1/adm jr. (protein CC) CN1T 0.0 -0.10 1.9000 CN2 0.0 -0.10 1.9000 CN3 0.0 -0.09 1.9000 CN3A 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. CN3B 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. CN3C 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. CN3D 0.0 -0.09 1.9000 ! 5mc, adm jr. CN3T 0.0 -0.09 1.9000 ! T, adm jr. CN4 0.0 -0.075 1.9000 CN5 0.0 -0.075 1.9000 CN5G 0.0 -0.075 1.9000 CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 CN7C 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 CN7D 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1 ! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 ! CN8B 0.0 -0.0560 2.010 0.0 -0.01 1.90 ! CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 ! ! CNE1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95 CNE2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95 CNA 0.0 -0.07 1.9924 !benzene (JES) CNA2 0.0 -0.07 1.90 !dft, adm jr. ! ! carbon wildcards !CN* 0.0 -0.10 1.8000 ! CN1, CN2, !CN1A 0.0 -0.07 2.0000 ! nad/ppi, jjp1/adm jr. (protein CC) !CN3* 0.0 -0.09 1.8000 ! CN3, CN3A, CN3B, CN3C, CN3D !CN4 0.0 -0.075 1.8000 !CN5 0.0 -0.075 1.8000 !CN7* 0.0 -0.02 2.2750 0.0 -0.01 1.90 !equivalent to protein CT1 !CN8* 0.0 -0.0560 2.010 0.0 -0.01 1.90 ! !CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 ! ! FN1 0.0 -0.09 1.70 !aliphatic F for sugars, preliminary from !Yin Thesis FNA 0.0 -0.12 1.70 !aromatic F, 1,3-difluorobenzene pure solvent ! P 0.0 -0.585 2.15 P2 0.0 -0.585 2.15 ! nad/ppi, jjp1/adm jr. ! phosphate wildcards !P* 0.0 -0.585 2.15 ! P and P2 ! !-------------- for imidazole -------------- !CPH1 0.000000 -0.050000 1.800000 ! From imidazole (NF) !CPH2 0.000000 -0.050000 1.800000 ! From imidazole (NF) !NR1 0.000000 -0.200000 1.850000 ! From imidazole (NF) !NR2 0.000000 -0.200000 1.850000 ! From imidazole (NF) !HR3 0.000000 -0.007800 1.468000 ! From imidazole (NF) !HR1 0.000000 -0.046000 0.900000 ! From imidazole (NF) ! ! ions SOD 0.0 -0.0469 1.36375 ! sodium ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol POT 0.0 -0.0870 1.76375 ! potassium ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol CLA 0.0 -0.150 2.27 ! chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol CAL 0.0 -0.120 1.367 ! Calcium ! S. Marchand and B. Roux, dA = -384.8 kcal/mol MG 0.0 -0.0150 1.18500 ! Magnesium ! B. Roux dA = -441.65 CES 0.0 -0.1900 2.100 ! Cesium, so far untested. !DUM 0.0 -0.000 1.00 ! dummy atom ! HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use ! READ PARAM APPEND CARD ! to append hbond parameters from the file: par_hbond.inp END