Charmm22 All-Hydrogen Topology File for Proteins >>>>>>>>>>>>>>>>>>> and Nucleic Acids



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*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<< *>>>>>>>>>>>>>>>>>>>> and Nucleic Acids <<<<<<<<<<<<<<<<<<<<<<<<< *>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< *>>>>>>>>>>>>>>>>>>>>>> July, 2004 <<<<<<<<<<<<<<<<<<<<<<<<<< * All comments to ADM jr. via the CHARMM web site: www.charmm.org * parameter set discussion forum * 31 1 ! references ! !PROTEINS ! !MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the !treatment of backbone energetics in protein force fields: limitations !of gas-phase quantum mechanics in reproducing protein conformational !distributions in molecular dynamics simulations, Journal of !Computational Chemistry, 25: 1400-1415, 2004. ! !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. ! !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. 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. 2000, 21: 105-120. ! MASS 1 H 1.00800 H ! polar H MASS 2 HC 1.00800 H ! N-ter H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 H ! aromatic H MASS 6 HB 1.00800 H ! backbone H MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 H ! (+) his HE1 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 MASS 10 HS 1.00800 H ! thiol hydrogen MASS 11 HE1 1.00800 H ! for alkene; RHC=CR MASS 12 HE2 1.00800 H ! for alkene; H2C=CR MASS 13 HA1 1.00800 H ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 14 HA2 1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 15 HA3 1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 16 HF1 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) MASS 17 HF2 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) MASS 20 C 12.01100 C ! carbonyl C, peptide backbone MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons MASS 26 CPH2 12.01100 C ! his CE1 carbon MASS 27 CPT 12.01100 C ! trp C between rings MASS 28 CY 12.01100 C ! TRP C in pyrrole ring MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 MASS 34 CPA 12.01100 C ! heme alpha-C MASS 35 CPB 12.01100 C ! heme beta-C MASS 36 CPM 12.01100 C ! heme meso-C MASS 37 CM 12.01100 C ! heme CO carbon MASS 38 CS 12.01100 C ! thiolate carbon MASS 39 CE1 12.01100 C ! for alkene; RHC=CR MASS 40 CE2 12.01100 C ! for alkene; H2C=CR MASS 41 CST 12.01100 C ! CO2 carbon MASS 42 CT 12.01100 C ! aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str) MASS 43 CT1x 12.01100 C ! aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 44 CT2x 12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 45 CT3x 12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 46 CN 12.01100 C ! C for cyano group (see toppar_all22_prot_pyridines.str) MASS 47 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 48 COA 12.01100 C ! carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 49 C3 12.01100 C ! cyclopropyl carbon MASS 50 N 14.00700 N ! proline N MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen MASS 53 NR3 14.00700 N ! charged his ring nitrogen MASS 54 NH1 14.00700 N ! peptide nitrogen MASS 55 NH2 14.00700 N ! amide nitrogen MASS 56 NH3 14.00700 N ! ammonium nitrogen MASS 57 NC2 14.00700 N ! guanidinium nitroogen MASS 58 NY 14.00700 N ! TRP N in pyrrole ring MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) MASS 60 NPH 14.00700 N ! heme pyrrole N MASS 61 NC 14.00700 N ! N for cyano group (see toppar_all22_prot_pyridines.str) MASS 70 O 15.99900 O ! carbonyl oxygen MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid MASS 72 OC 15.99900 O ! carboxylate oxygen MASS 73 OH1 15.99900 O ! hydroxyl oxygen MASS 74 OS 15.99940 O ! ester oxygen MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS 76 OM 15.99900 O ! heme CO/O2 oxygen MASS 77 OST 15.99900 O ! CO2 oxygen MASS 78 OCA 15.99900 O ! carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 81 S 32.06000 S ! sulphur MASS 82 SM 32.06000 S ! sulfur C-S-S-C type MASS 83 SS 32.06000 S ! thiolate sulfur MASS 85 HE 4.00260 HE ! helium MASS 86 NE 20.17970 NE ! neon MASS 87 CF1 12.01100 C ! monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 88 CF2 12.01100 C ! difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 89 CF3 12.01100 C ! trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 90 FE 55.84700 Fe ! heme iron 56 MASS 91 CLAL 35.45300 CL ! Chlorine Atom (see toppar_all22_prot_aldehydes.str) MASS 92 FA 18.99800 F ! aromatic flourine (see toppar_all22_prot_pyridines.str) MASS 93 F1 18.99800 F ! Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 94 F2 18.99800 F ! Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 95 F3 18.99800 F ! Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 99 DUM 0.00000 H ! dummy atom !see NA section !MASS 100 SOD 22.989770 NA ! Sodium Ion !MASS 101 MG 24.305000 MG ! Magnesium Ion !MASS 102 POT 39.102000 K ! Potassium Ion! check masses !MASS 103 CES 132.900000 CS ! Cesium Ion !MASS 104 CAL 40.080000 CA ! Calcium Ion !MASS 105 CLA 35.450000 CL ! Chloride Ion !MASS 106 ZN 65.370000 ZN ! zinc (II) cation !NA section !MASS 101 HT 1.008000 H ! TIPS3P WATER HYDROGEN MASS 102 HN1 1.008000 H ! Nucleic acid amine proton MASS 103 HN2 1.008000 H ! Nucleic acid ring nitrogen proton MASS 104 HN3 1.008000 H ! Nucleic acid aromatic carbon proton MASS 105 HN3B 1.008000 H ! NAD+ aromatic hydrogen MASS 106 HN3C 1.008000 H ! Standard aromatic hydrogen (as in benzene) MASS 107 HNP 1.008000 H ! pure aromatic H MASS 108 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 109 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton MASS 110 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton MASS 111 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) MASS 112 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds MASS 113 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds MASS 114 HNE1 1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha) MASS 115 HNE2 1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha) MASS 120 CN1 12.011000 C ! Nucleic acid carbonyl carbon MASS 121 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon MASS 122 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2) MASS 123 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide MASS 124 CN3 12.011000 C ! Nucleic acid aromatic carbon MASS 125 CN3A 12.011000 C ! NAD+ aromatic carbon MASS 126 CN3B 12.011000 C ! NAD+ aromatic carbon MASS 127 CN3C 12.011000 C ! NADH aromatic carbon MASS 128 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC MASS 129 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5 MASS 130 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 MASS 131 CN5 12.011000 C ! Nucleic acid purine C4 and C5 MASS 132 CN5G 12.011000 C ! Nucleic acid guanine C5 MASS 133 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) MASS 134 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1' MASS 135 CN7C 12.011000 C ! C2' in arabinose MASS 136 CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives MASS 137 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 138 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 139 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) MASS 140 CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha) MASS 141 CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha) MASS 142 CNA 12.011000 C ! pure aromatic carbon MASS 143 CNA2 12.011000 C ! pure aromatic carbon bound to F MASS 144 CN6 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str) MASS 145 CN7E 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str) MASS 150 NN1 14.007000 N ! Nucleic acid amide nitrogen MASS 151 NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha) MASS 152 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen MASS 153 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE MASS 154 NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha) MASS 155 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 MASS 156 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 MASS 157 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen MASS 158 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 MASS 159 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 MASS 160 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3 MASS 161 NN4 14.007000 N ! Nucleic acid purine N7 MASS 162 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen MASS 163 NN6 14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) !MASS 170 OT 15.999400 O ! TIPS3P WATER OXYGEN MASS 171 ON1 15.999400 O ! Nucleic acid carbonyl oxygen MASS 172 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 MASS 173 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 174 ON3 15.999400 O ! Nucleic acid =O in phosphate MASS 175 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 176 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen MASS 177 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen MASS 178 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen MASS 179 ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str) MASS 180 FN1 18.998400 F ! Fluorine for sugar derivatives (NF) MASS 181 FNA 18.998400 F ! Aromatic fluorine MASS 182 P 30.974000 P ! phosphorus MASS 183 P2 30.974000 P ! pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) MASS 184 P3 30.974000 P ! protonated pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) MASS 190 SOD 22.989770 NA ! Sodium Ion MASS 191 MG 24.305000 MG ! Magnesium Ion MASS 192 POT 39.102000 K ! Potassium Ion! check masses MASS 193 CES 132.900000 CS ! Cesium Ion MASS 194 CAL 40.080000 CA ! Calcium Ion MASS 195 CLA 35.450000 CL ! Chloride Ion MASS 196 ZN 65.370000 ZN ! zinc (II) cation !MASS 199 DUM 0.001 H ! dummy atom !the following masses must be added to the parent RTF for retinol/al MASS 212 CC1A 12.01100 C ! alkene conjugation MASS 213 CC1B 12.01100 C ! alkene conjugation MASS 214 CC2 12.01100 C ! alkene conjugation MASS 220 NS1 14.00700 N ! N for deprotonated Schiff's base MASS 221 NS2 14.00700 N ! N for protonated Schiff's base ! SAM requires mixed protein/NA topology parameter set MASS 222 SP 32.06000 S ! positive Sulphur, S-adenosylmethionine (SAM) DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA !nucleic acid section DECL +P DECL +O1P DECL +O2P DECL +O5' DECL -O3' DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 RESI ARG 1.00 GROUP ATOM N NH1 -0.47 ! | HH11 ATOM HN H 0.31 ! HN-N | ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12 ATOM HA HB 0.09 ! | | | | | //(+) GROUP ! HA-CA--CB--CG--CD--NE--CZ ATOM CB CT2 -0.18 ! | | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22 ATOM HB2 HA 0.09 ! O=C | GROUP ! | HH21 ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 0.20 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 ATOM NE NC2 -0.70 ATOM HE HC 0.44 ATOM CZ C 0.64 ATOM NH1 NC2 -0.80 ATOM HH11 HC 0.46 ATOM HH12 HC 0.46 ATOM NH2 NC2 -0.80 ATOM HH21 HC 0.46 ATOM HH22 HC 0.46 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE CD CZ NE BOND NH2 CZ N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 DOUBLE O C CZ NH1 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N IMPR CZ NH1 NH2 NE DONOR HN N DONOR HE NE DONOR HH11 NH1 DONOR HH12 NH1 DONOR HH21 NH2 DONOR HH22 NH2 ACCEPTOR O C IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 RESI ASN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1) ATOM HA HB 0.09 ! | | || / GROUP ! HA-CA--CB--CG--ND2 ATOM CB CT2 -0.18 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CC 0.55 ATOM OD1 O -0.55 GROUP ATOM ND2 NH2 -0.62 ATOM HD21 H 0.32 ATOM HD22 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 DOUBLE C O CG OD1 IMPR N -C CA HN C CA +N O IMPR CG ND2 CB OD1 CG CB ND2 OD1 IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 CMAP -C N CA C N CA C +N DONOR HN N DONOR HD21 ND2 DONOR HD22 ND2 ACCEPTOR OD1 CG ACCEPTOR O C IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 RESI ASP -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 OD1 ATOM HA HB 0.09 ! | | // GROUP ! HA-CA--CB--CG ATOM CB CT2 -0.28 ! | | \ ATOM HB1 HA 0.09 ! | HB2 OD2(-) ATOM HB2 HA 0.09 ! O=C ATOM CG CC 0.62 ! | ATOM OD1 OC -0.76 ATOM OD2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB OD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 DOUBLE O C CG OD1 IMPR N -C CA HN C CA +N O !IMPR OD1 CB OD2 CG IMPR CG CB OD2 OD1 CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR OD1 CG ACCEPTOR OD2 CG ACCEPTOR O C IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 RESI CYS 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--SG ATOM CB CT2 -0.11 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HG1 ATOM HB2 HA 0.09 ! O=C ATOM SG S -0.23 ! | ATOM HG1 HS 0.16 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA SG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 SG HG1 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HG1 SG ACCEPTOR O C IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 RESI GLN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) ATOM HA HB 0.09 ! | | | || / GROUP ! HA-CA--CB--CG--CD--NE2 ATOM CB CT2 -0.18 ! | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CC 0.55 ATOM OE1 O -0.55 GROUP ATOM NE2 NH2 -0.62 ATOM HE21 H 0.32 ATOM HE22 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 NE2 HE21 NE2 HE22 DOUBLE O C CD OE1 IMPR N -C CA HN C CA +N O IMPR CD NE2 CG OE1 CD CG NE2 OE1 IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 CMAP -C N CA C N CA C +N DONOR HN N DONOR HE21 NE2 DONOR HE22 NE2 ACCEPTOR OE1 CD ACCEPTOR O C IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 RESI GLU -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 OE1 ATOM HA HB 0.09 ! | | | // GROUP ! HA-CA--CB--CG--CD ATOM CB CT2 -0.18 ! | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.28 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 ATOM CD CC 0.62 ATOM OE1 OC -0.76 ATOM OE2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG OE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 DOUBLE O C CD OE1 IMPR N -C CA HN C CA +N O IMPR CD CG OE2 OE1 CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR OE1 CD ACCEPTOR OE2 CD ACCEPTOR O C IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 RESI GLY 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! N-H ATOM CA CT2 -0.02 ! | ATOM HA1 HB 0.09 ! | ATOM HA2 HB 0.09 ! HA1-CA-HA2 GROUP ! | ATOM C C 0.51 ! | ATOM O O -0.51 ! C=O ! | BOND N HN N CA C CA BOND C +N CA HA1 CA HA2 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 PATCHING FIRS GLYP RESI HSD 0.00 ! neutral HIS, proton on ND1 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / || GROUP ! HA-CA--CB--CG || ATOM CB CT2 -0.09 ! | | \\ || ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 ATOM HB2 HA 0.09 ! O=C | ATOM ND1 NR1 -0.36 ! | HD2 ATOM HD1 H 0.32 ATOM CG CPH1 -0.05 GROUP ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 ATOM NE2 NR2 -0.70 ATOM CD2 CPH1 0.22 ATOM HD2 HR3 0.10 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CE1 ND1 BOND NE2 CD2 N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 DOUBLE O C CG CD2 CE1 NE2 IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HD1 ND1 ACCEPTOR NE2 ACCEPTOR O C IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 RESI HSE 0.00 ! neutral His, proton on NE2 GROUP ATOM N NH1 -0.47 ! | HE1 ATOM HN H 0.31 ! HN-N __ / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / | GROUP ! HA-CA--CB--CG | ATOM CB CT2 -0.08 ! | | \\ | ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 ATOM HB2 HA 0.09 ! O=C | \ ATOM ND1 NR2 -0.70 ! | HD2 HE2 ATOM CG CPH1 0.22 ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 GROUP ATOM NE2 NR1 -0.36 ATOM HE2 H 0.32 ATOM CD2 CPH1 -0.05 ATOM HD2 HR3 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG BOND NE2 CD2 N HN N CA BOND C CA C +N NE2 CE1 CA HA CB HB1 BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 DOUBLE O C CD2 CG CE1 ND1 IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HE2 NE2 ACCEPTOR ND1 ACCEPTOR O C IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 RESI HSP 1.00 ! Protonated His GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / || GROUP ! HA-CA--CB--CG || ATOM CB CT2 -0.05 ! | | \\ || ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+) ATOM HB2 HA 0.09 ! O=C | \ ATOM CD2 CPH1 0.19 ! | HD2 HE2 ATOM HD2 HR1 0.13 ATOM CG CPH1 0.19 GROUP ATOM NE2 NR3 -0.51 ATOM HE2 H 0.44 ATOM ND1 NR3 -0.51 ATOM HD1 H 0.44 ATOM CE1 CPH2 0.32 ATOM HE1 HR2 0.18 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CE1 ND1 BOND NE2 CD2 N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 DOUBLE O C CD2 CG NE2 CE1 IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HD1 ND1 DONOR HE2 NE2 ACCEPTOR O C IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 RESI ILE 0.00 GROUP ATOM N NH1 -0.47 ! | HG21 HG22 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | CG2--HG23 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB HD1 ATOM CB CT1 -0.09 ! | \ / ATOM HB HA 0.09 ! | CG1--CD--HD2 GROUP ! O=C / \ \ ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM CG1 CT2 -0.18 ATOM HG11 HA 0.09 ATOM HG12 HA 0.09 GROUP ATOM CD CT3 -0.27 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 ATOM HD3 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB CD CG1 BOND N HN N CA C CA C +N BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 RESI LEU 0.00 GROUP ATOM N NH1 -0.47 ! | HD11 HD12 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 CD1--HD13 ATOM HA HB 0.09 ! | | / GROUP ! HA-CA--CB--CG-HG ATOM CB CT2 -0.18 ! | | \ ATOM HB1 HA 0.09 ! | HB2 CD2--HD23 ATOM HB2 HA 0.09 ! O=C | \ GROUP ! | HD21 HD22 ATOM CG CT1 -0.09 ATOM HG HA 0.09 GROUP ATOM CD1 CT3 -0.27 ATOM HD11 HA 0.09 ATOM HD12 HA 0.09 ATOM HD13 HA 0.09 GROUP ATOM CD2 CT3 -0.27 ATOM HD21 HA 0.09 ATOM HD22 HA 0.09 ATOM HD23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD1 CG CD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360 IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 RESI LYS 1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 ATOM HA HB 0.09 ! | | | | | / GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 ATOM CB CT2 -0.18 ! | | | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 -0.18 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 GROUP ATOM CE CT2 0.21 ATOM HE1 HA 0.05 ATOM HE2 HA 0.05 ATOM NZ NH3 -0.30 ATOM HZ1 HC 0.33 ATOM HZ2 HC 0.33 ATOM HZ3 HC 0.33 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG CE CD NZ CE BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 DOUBLE O C BOND NZ HZ1 NZ HZ2 NZ HZ3 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HZ1 NZ DONOR HZ2 NZ DONOR HZ3 NZ ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 RESI MET 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 HE1 ATOM HA HB 0.09 ! | | | | GROUP ! HA-CA--CB--CG--SD--CE--HE3 ATOM CB CT2 -0.18 ! | | | | ATOM HB1 HA 0.09 ! | HB2 HG2 HE2 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.14 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 ATOM SD S -0.09 ATOM CE CT3 -0.22 ATOM HE1 HA 0.09 ATOM HE2 HA 0.09 ATOM HE3 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB SD CG CE SD BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 BOND CE HE1 CE HE2 CE HE3 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 RESI PHE 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | | ATOM CA CT1 0.07 ! | HB1 CD1--CE1 ATOM HA HB 0.09 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--HZ ATOM CB CT2 -0.18 ! | | \ __ / ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CZ CA -0.115 ATOM HZ HP 0.115 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 N HN BOND N CA C CA C +N CA HA BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 DOUBLE O C CD1 CG CZ CE1 CE2 CD2 BOND CE2 HE2 CZ HZ IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 RESI PRO 0.00 GROUP ! HD1 HD2 ATOM N N -0.29 ! | \ / ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 ATOM HD1 HA 0.09 ! | \ / ATOM HD2 HA 0.09 ! | CG ATOM CA CP1 0.02 ! | / \ ATOM HA HB 0.09 ! HA-CA--CB HG2 GROUP ! | / \ ATOM CB CP2 -0.18 ! | HB1 HB2 ATOM HB1 HA 0.09 ! O=C ATOM HB2 HA 0.09 ! | GROUP ATOM CG CP2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND C CA C +N BOND N CA CA CB CB CG CG CD N CD BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB DOUBLE O C IMPR N -C CA CD IMPR C CA +N O CMAP -C N CA C N CA C +N ACCEPTOR O C IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 PATCHING FIRS PROP RESI SER 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--OG ATOM CB CT2 0.05 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HG1 ATOM HB2 HA 0.09 ! O=C ATOM OG OH1 -0.66 ! | ATOM HG1 H 0.43 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 OG HG1 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HG1 OG ACCEPTOR OG ACCEPTOR O C IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 RESI THR 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | OG1--HG1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 0.14 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 ATOM OG1 OH1 -0.66 ! O=C / \ ATOM HG1 H 0.43 ! | HG21 HG22 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HG1 OG1 ACCEPTOR OG1 ACCEPTOR O C IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 RESI TRP 0.00 GROUP ATOM N NH1 -0.47 ! | HE3 ATOM HN H 0.31 ! HN-N | ATOM CA CT1 0.07 ! | HB1 CE3 ATOM HA HB 0.09 ! | | / \\ GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 ATOM CB CT2 -0.18 ! | | || || | ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2 ATOM HB2 HA 0.09 ! O=C / \ / \ // GROUP ! | HD1 NE1 CZ2 ATOM CG CY -0.03 ! | | ATOM CD1 CA 0.035 ! HE1 HZ2 ATOM HD1 HP 0.115 ATOM NE1 NY -0.61 ATOM HE1 H 0.38 ATOM CE2 CPT 0.13 ATOM CD2 CPT -0.02 GROUP ATOM CE3 CA -0.115 ATOM HE3 HP 0.115 GROUP ATOM CZ3 CA -0.115 ATOM HZ3 HP 0.115 GROUP ATOM CZ2 CA -0.115 ATOM HZ2 HP 0.115 GROUP ATOM CH2 CA -0.115 ATOM HH2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG NE1 CD1 BOND CZ2 CE2 BOND N HN N CA C CA C +N BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 BOND CZ3 HZ3 CH2 HH2 DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HE1 NE1 ACCEPTOR O C IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 RESI TYR 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | | ATOM CA CT1 0.07 ! | HB1 CD1--CE1 ATOM HA HB 0.09 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--OH ATOM CB CT2 -0.18 ! | | \ __ / \ ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CZ CA 0.11 ATOM OH OH1 -0.54 ATOM HH H 0.43 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 OH CZ BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 OH HH DOUBLE O C CD1 CG CE1 CZ CE2 CD2 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N DONOR HH OH ACCEPTOR OH ACCEPTOR O C IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 RESI VAL 0.00 GROUP ATOM N NH1 -0.47 ! | HG11 HG12 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | CG1--HG13 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 -0.09 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 GROUP ! O=C / \ ATOM CG1 CT3 -0.27 ! | HG21 HG22 ATOM HG11 HA 0.09 ATOM HG12 HA 0.09 ATOM HG13 HA 0.09 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 BOND CG2 HG22 CG2 HG23 DOUBLE O C IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 RESI ALAD 0.00 ! Alanine dipeptide, with CMAP term GROUP ATOM CL CT3 -0.27 ATOM HL1 HA 0.09 ATOM HL2 HA 0.09 ATOM HL3 HA 0.09 GROUP ATOM CLP C 0.51 ATOM OL O -0.51 GROUP ATOM NL NH1 -0.47 ATOM HL H 0.31 ATOM CA CT1 0.07 ATOM HA HB 0.09 GROUP ATOM CB CT3 -0.27 ! HL1 OL OR HR1 ATOM HB1 HA 0.09 ! \ || HL HA || HR / ATOM HB2 HA 0.09 ! \ || | | || | / ATOM HB3 HA 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 GROUP ! / | \ ATOM CRP C 0.51 ! / HB1--CB--HB3 \ ATOM OR O -0.51 ! HL3 | HR3 GROUP ! HB2 ATOM NR NH1 -0.47 ATOM HR H 0.31 ATOM CR CT3 -0.11 ATOM HR1 HA 0.09 ATOM HR2 HA 0.09 ATOM HR3 HA 0.09 BOND CL CLP CLP NL NL CA BOND CA CRP CRP NR NR CR DOUBLE CLP OL CRP OR BOND NL HL NR HR BOND CA HA CA CB BOND CL HL1 CL HL2 CL HL3 BOND CB HB1 CB HB2 CB HB3 BOND CR HR1 CR HR2 CR HR3 IMPR CLP CL NL OL NL CLP CA HL IMPR CRP CA NR OR NR CRP CR HR CMAP CLP NL CA CRP NL CA CRP NR ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0 ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0 ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 patch first none last none RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 !H1 H2 ! the last bond is needed for shake ANGLE H1 OH2 H2 ! required ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p GROUP ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p ANGLE H1 OH2 H2 ! required ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE ! Ion parameters from Benoit Roux and Coworkers ! As of 8/98 no NBFIX terms required ! RESI SOD 1.00 ! Sodium Ion GROUP ATOM SOD SOD 1.00 PATCHING FIRST NONE LAST NONE RESI MG 2.00 ! Magnesium Ion GROUP ATOM MG MG 2.00 PATCHING FIRST NONE LAST NONE RESI POT 1.00 ! Potassium Ion GROUP ATOM POT POT 1.00 PATCHING FIRST NONE LAST NONE RESI CES 1.00 ! Cesium Ion GROUP ATOM CES CES 1.00 PATCHING FIRST NONE LAST NONE RESI CAL 2.00 ! Calcium Ion GROUP ATOM CAL CAL 2.00 PATCHING FIRST NONE LAST NONE RESI CLA -1.00 ! Chloride Ion GROUP ATOM CLA CLA -1.00 PATCHING FIRST NONE LAST NONE RESI ZN2 2.00 ! Zinc ion, Roland Stote GROUP ATOM ZN ZN 2.00 PATCHING FIRST NONE LAST NONE PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! (+)/ ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES GLYP 1.00 ! Glycine N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HA1 HT1 ATOM HT2 HC 0.33 ! | (+)/ ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT2 0.13 ! | \ ATOM HA1 HB 0.09 ! HA2 HT3 ATOM HA2 HB 0.09 ! DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES PROP 1.00 ! Proline N-Terminal GROUP ! use in generate statement ATOM N NP -0.07 ! HA ATOM HN1 HC 0.24 ! | ATOM HN2 HC 0.24 ! -CA HN1 ATOM CD CP3 0.16 ! / \ / ATOM HD1 HA 0.09 ! N(+) ATOM HD2 HA 0.09 ! / \ ATOM CA CP1 0.16 ! -CD HN2 ATOM HA HB 0.09 ! | \ BOND HN1 N HN2 N ! HD1 HD2 DONOR HN1 N DONOR HN2 N IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 PRES ACE 0.00 ! acetylated N-terminus ! do NOT use to create dipeptides, see ACED GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY N OY IMPR N CY CA HN CMAP CY N CA C N CA C +N ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ACED 0.00 ! acetylated N-terminus (to create dipeptide) GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY N OY IMPR N CY CA HN CMAP CY N CA C N CA C NT ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ACP 0.00 ! acetylated N-terminus ! NOT for proline dipeptide, see ACPD GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY N OY IMPR N CY CA CD CMAP CY N CA C N CA C +N ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ACPD 0.00 ! acetylated N-terminus (for proline dipeptide) GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY N OY IMPR N CY CA CD CMAP CY N CA C N CA C NT ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES NNEU 0.00 ! neutral N-terminus; charges from LSN GROUP ! use in generate statement ATOM N NH2 -0.96 ! ATOM HT1 H 0.34 ! HT1 ATOM HT2 H 0.34 ! / ! --CA--N--HT2 ATOM CA CT1 0.19 ! | ! change to CT2 for neutral N terminal glycine ATOM HA HB 0.09 ! HA ! change to HA1 and HB2 and add HA2 atom for N terminal glycine DELETE ATOM HN BOND HT1 N HT2 N DONOR HT1 N DONOR HT2 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2(-) ATOM OT1 OC -0.67 ! / ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT2 ! OT1 DOUBLE C OT1 IMPR C CA OT2 OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT1 0.00 ! methylated C-terminus from methyl acetate GROUP ! use in generate statement ATOM N NH1 -0.47 ! ATOM HN H 0.31 ! OT1 ATOM CA CT1 0.17 ! | // ATOM HA HB 0.09 ! -N--CA--C HT1 ATOM C CD 0.63 ! | | \ / ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2 ATOM OT2 OS -0.34 ! \ ATOM CT CT3 -0.14 ! HT3 ATOM HT1 HA 0.09 ! ATOM HT2 HA 0.09 ! ATOM HT3 HA 0.09 ! DELETE ATOM O BOND C OT2 OT2 CT BOND CT HT1 CT HT2 CT HT3 DOUBLE C OT1 IMPR C CA OT2 OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 PRES CT2 0.00 ! amidated C-terminus GROUP ! use in generate statement ATOM C CC 0.55 ! ATOM O O -0.55 ! | GROUP ! O=C ATOM NT NH2 -0.62 ! | ATOM HT1 H 0.32 ! NT ATOM HT2 H 0.30 ! / \ BOND C NT ! HT1 HT2 (HT1 is cis to O) BOND NT HT1 NT HT2 ! IMPR C NT CA O C CA NT O IMPR NT C HT1 HT2 NT C HT2 HT1 DONOR HT1 NT DONOR HT2 NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT3 0.00 ! N-Methylamide C-terminus GROUP ! use in generate statement ATOM C C 0.51 ! ATOM O O -0.51 ! | GROUP ! C=O ATOM NT NH1 -0.47 ! | ATOM HNT H 0.31 ! NT-HNT ATOM CAT CT3 -0.11 ! | ATOM HT1 HA 0.09 ! HT1-CAT-HT3 ATOM HT2 HA 0.09 ! | ATOM HT3 HA 0.09 ! HT2 ! BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 IMPR NT C CAT HNT C CA NT O CMAP -C N CA C N CA C NT DONOR HNT NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES CNEU 0.00 ! neutral C-terminus; charges from ASPP GROUP ! use in generate statement; C reduced to balance ATOM C CD 0.72 ! OT2-HT2 ATOM OT1 OB -0.55 ! / ATOM OT2 OH1 -0.61 ! -C ATOM HT2 H 0.44 ! \\ DELETE ATOM O ! OT1 BOND C OT2 ! BOND OT2 HT2 DOUBLE C OT1 IMPR C CA OT2 OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000 PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 GROUP ! via acetic acid, use in a patch statementand ! follow with AUTOgenerate ANGLes DIHEdrals command ATOM CB CT2 -0.21 ! ATOM HB1 HA 0.09 ! HB1 OD1 ATOM HB2 HA 0.09 ! | // ATOM CG CD 0.75 ! -CB--CG ATOM OD1 OB -0.55 ! | \ ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2 ATOM HD2 H 0.44 ! BOND OD2 HD2 DONOR HD2 OD2 IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 GROUP ! via acetic acid, use in a patch statement and ! follow with AUTOgenerate ANGLes DIHEdrals command ATOM CG CT2 -0.21 ! ATOM HG1 HA 0.09 ! HG1 OE1 ATOM HG2 HA 0.09 ! | // ATOM CD CD 0.75 ! -CG--CD ATOM OE1 OB -0.55 ! | \ ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2 ATOM HE2 H 0.44 ! BOND OE2 HE2 DONOR HE2 OE2 IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES LSN 0.00 ! patch for neutral lysine based on methylamine ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command !delete atom and reassign charges DELETE ATOM HZ3 GROUP ATOM CE CT2 0.13 ATOM HE1 HA 0.075 ATOM HE2 HA 0.075 ATOM NZ NH2 -0.96 ATOM HZ1 HC 0.34 ATOM HZ2 HC 0.34 PRES LINK 0.00 ! linkage for IMAGES or for joining segments ! 1 refers to previous (N terminal) ! 2 refers to next (C terminal) ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N !the need for the explicit specification of angles and dihedrals in !patches linking images has not been tested !ANGLE 1C 2N 2CA 1CA 1C 2N !ANGLE 1O 1C 2N 1C 2N 2HN !DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB !DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N !DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA !DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command GROUP ATOM 1CB CT2 -0.10 ! ATOM 1SG SM -0.08 ! 2SG--2CB-- GROUP ! / ATOM 2SG SM -0.08 ! -1CB--1SG ATOM 2CB CT2 -0.10 ! DELETE ATOM 1HG1 DELETE ATOM 2HG1 BOND 1SG 2SG IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command GROUP ATOM CE1 CPH2 0.25 ! HE1 ATOM HE1 HR1 0.13 ! / ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1 ATOM CG CPH1 0.22 ! | / | ATOM CB CT2 -0.08 ! -CB--CG | ATOM HB1 HA 0.09 ! | \ | ATOM HB2 HA 0.09 ! HB2 CD2--NE2 GROUP ! | \ ATOM NE2 NR1 -0.36 ! HD2 HE2 ATOM HE2 H 0.32 ATOM CD2 CPH1 -0.05 ATOM HD2 HR3 0.09 DELETE ATOM HD1 DELETE ACCE NE2 BOND NE2 HE2 IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 DONOR HE2 NE2 ACCEPTOR ND1 IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 ! patches for cyclic peptides PRES LIG1 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus which is a glycine ! 2 refers to the N terminus ! use in a patch statement, perform initial ! generation using first NONE last NONE ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES LIG2 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus ! 2 refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES LIG3 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus which is a glycine ! 2 refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 !NA section RESI GUA -1.00 ! O6 ATOM P P 1.50 ! || ATOM O1P ON3 -0.78 ! C6 ATOM O2P ON3 -0.78 ! / \ ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\ ATOM C5' CN8B -0.08 ! | || C8-H8 ATOM H5' HN8 0.09 ! C2 C4--N9/ ATOM H5'' HN8 0.09 ! / \\ / \ GROUP ! H21-N2 N3 \ ATOM C4' CN7 0.16 ! | \ ATOM H4' HN7 0.09 ! H22 \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N9 NN2B -0.02 ! | | \ / \ ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1' ATOM N2 NN1 -0.68 ! / \ / \ ATOM H21 HN1 0.32 ! O3' H3' O2' H2'' ATOM H22 HN1 0.35 ! | | ATOM N3 NN3G -0.74 ! H2' ATOM C2 CN2 0.75 ATOM N1 NN2G -0.34 ATOM H1 HN2 0.26 ATOM C6 CN1 0.54 ATOM O6 ON1 -0.51 ATOM C5 CN5G 0.00 ATOM N7 NN4 -0.60 ATOM C8 CN4 0.25 ATOM H8 HN3 0.16 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 DONO H21 N2 DONO H22 N2 DONO H1 N1 DONO H2' O2' ACCE O6 C6 ACCE N3 ACCE N7 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! Chi and sugar-phosphate backbone in B-DNA like conformation BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI ADE -1.00 ! H61 H62! ATOM P P 1.50 ! \ / ATOM O1P ON3 -0.78 ! N6 ATOM O2P ON3 -0.78 ! | ATOM O5' ON2 -0.57 ! C6 ATOM C5' CN8B -0.08 ! // \ ATOM H5' HN8 0.09 ! N1 C5--N7\\ ATOM H5'' HN8 0.09 ! | || C8-H8 GROUP ! C2 C4--N9/ ATOM C4' CN7 0.16 ! / \\ / \ ATOM H4' HN7 0.09 ! H2 N3 \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! \ ATOM H1' HN7 0.09 ! \ GROUP ! O1P H5' H4' O4' \ ATOM N9 NN2 -0.05 ! | | \ / \ \ ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1' ATOM N7 NN4 -0.71 ! | | \ / \ ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1' ATOM H8 HN3 0.12 ! / \ / \ ATOM N1 NN3A -0.74 ! O3' H3' O2' H2'' ATOM C2 CN4 0.50 ! | | ATOM H2 HN3 0.13 ! H2' ATOM N3 NN3A -0.75 ATOM C4 CN5 0.43 ATOM C6 CN2 0.46 ATOM N6 NN1 -0.77 ATOM H61 HN1 0.38 ATOM H62 HN1 0.38 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI CYT -1.00 ATOM P P 1.50 ! ATOM O1P ON3 -0.78 ! H42 H41 ATOM O2P ON3 -0.78 ! \ / ATOM O5' ON2 -0.57 ! N4 ATOM C5' CN8B -0.08 ! | ATOM H5' HN8 0.09 ! C4 ATOM H5'' HN8 0.09 ! / \\ GROUP ! H5-C5 N3 ATOM C4' CN7 0.16 ! || | ATOM H4' HN7 0.09 ! H6-C6 C2 ATOM O4' ON6B -0.50 ! \ / \\ ATOM C1' CN7B 0.16 ! N1 O2 ATOM H1' HN7 0.09 ! \ GROUP ! \ ATOM N1 NN2 -0.13 ! \ ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \ ATOM H6 HN3 0.17 ! | | \ / \ \ ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1' ATOM H5 HN3 0.07 ! | | \ / \ ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1' ATOM O2 ON1C -0.49 ! / \ / \ ATOM N3 NN3 -0.66 ! O3' H3' O2' H2'' ATOM C4 CN2 0.65 ! | | ATOM N4 NN1 -0.75 ! H2' ATOM H41 HN1 0.37 ATOM H42 HN1 0.33 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 BOND C2 N3 C4 N4 N4 H41 N4 H42 BOND C4 C5 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR C2 N1 N3 O2 C4 N3 C5 N4 IMPR N4 C4 H41 H42 DONO H42 N4 DONO H2' O2' DONO H41 N4 ACCE O2 C2 ACCE N3 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI THY -1.00 ! H51 O4 ATOM P P 1.50 ! | || ATOM O1P ON3 -0.78 ! H52-C5M C4 H3 ATOM O2P ON3 -0.78 ! | \ / \ / ATOM O5' ON2 -0.57 ! H53 C5 N3 ATOM C5' CN8B -0.08 ! || | ATOM H5' HN8 0.09 ! H6-C6 C2 ATOM H5'' HN8 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN7 0.16 ! \ ATOM H4' HN7 0.09 ! \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2B -0.34 ! | | \ / \ ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1' ATOM H6 HN3 0.17 ! / \ / \ ATOM C2 CN1T 0.51 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.41 ! | | ATOM N3 NN2U -0.46 ! H2' ATOM H3 HN2 0.36 ! ATOM C4 CN1 0.50 ! ATOM O4 ON1 -0.45 ! ATOM C5 CN3T -0.15 ATOM C5M CN9 -0.11 ATOM H51 HN9 0.07 ATOM H52 HN9 0.07 ATOM H53 HN9 0.07 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M DONO H3 N3 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 RESI URA -1.00 ! O4 ATOM P P 1.50 ! || ATOM O1P ON3 -0.78 ! C4 H3 ATOM O2P ON3 -0.78 ! / \ / ATOM O5' ON2 -0.57 ! H5-C5 N3 ATOM C5' CN8B -0.08 ! || | ATOM H5' HN8 0.09 ! H6-C6 C2 ATOM H5'' HN8 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN7 0.16 ! \ ATOM H4' HN7 0.09 ! \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2B -0.34 ! | | \ / \ ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1' ATOM H6 HN3 0.14 ! / \ / \ ATOM C2 CN1T 0.55 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.45 ! | | ATOM N3 NN2U -0.46 ! H2' ATOM H3 HN2 0.36 ! ATOM C4 CN1 0.53 ! ATOM O4 ON1 -0.48 ! ATOM C5 CN3 -0.15 ! ATOM H5 HN3 0.10 ! GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 DONO H3 N3 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! NOTE the option to regenerate all angles and dihedrals allows ! the explicit inclusion of the THET and DIHE terms to be omitted ! even if the PRES is used in a PATCH statement. It is important to ! inspect the patches prior to use to determine if they should be used ! in a GENErate or PATCh statement and/or if the AUTOgeneration of ! angles and dihedrals is required. ! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the ! documentation PRES DEO1 0.000 ! Patch to make DEOXYribose in PYRIMIDINES DELETE ATOM O2' ! necessary due to auto-generate dihedrals GROUP ! To correct O4' atom type in DNA (NF) ATOM C4' CN7 0.16 ! ATOM H4' HN7 0.09 ! ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.16 ! ATOM H1' HN7 0.09 ! GROUP ATOM C2' CN8 -0.18 ATOM H2' HN8 0.09 ATOM H2'' HN8 0.09 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 PRES DEO2 0.000 ! Patch to make DEOXYribose in PURINES DELETE ATOM O2' ! necessary due to auto-generate dihedrals GROUP ! To correct O4' atom type in DNA (NF) ATOM C4' CN7 0.16 ! ATOM H4' HN7 0.09 ! ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.16 ! ATOM H1' HN7 0.09 ! GROUP ATOM C2' CN8 -0.18 ATOM H2' HN8 0.09 ATOM H2'' HN8 0.09 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH ! use in generate statement GROUP ATOM H5T HN5 0.43 ATOM O5' ON5 -0.66 ATOM C5' CN8B 0.05 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ! DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P ! BOND H5T O5' DONO H5T O5' BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 PRES 5MET 0.00 ! 5'-ribose METHYL patch ! use in generate statement GROUP ATOM C5' CN9 -0.27 ATOM H5' HN9 0.09 ATOM H5'' HN9 0.09 ATOM H53' HN9 0.09 ! Can't use ''' and avoid conflict with THY ! DELETE ATOM O5' DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P ! BOND C5' H53' IC C3' C4' C5' H53' 0.0000 0.00 180.00 0.00 0.0000 IC H53' C4' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000 IC H53' C4' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000 PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch ! use in generate statement GROUP ATOM C5' CN8B -0.08 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM P P 1.50 ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O5' ON2 -0.62 ATOM O5T ON4 -0.68 ATOM H5T HN4 0.34 BOND O5T P H5T O5T DONO H5T O5T ! Built in B-DNA-like conformation (NF) BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch ! use in generate statement GROUP ATOM C5' CN8B -0.08 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM P P 1.50 ATOM O1P ON3 -0.78 ATOM O2P ON3 -0.78 ATOM O5' ON2 -0.57 ATOM O5T ON2 -0.57 ATOM C5T CN9 -0.17 ATOM H5T1 HN9 0.09 ATOM H5T2 HN9 0.09 ATOM H5T3 HN9 0.09 BOND O5T P O5T C5T C5T H5T1 C5T H5T2 BOND C5T H5T3 !DONO H5T O5T ! Built in B-DNA-like conformation (NF) BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 BILD C5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000 BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000 BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000 PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH ! use in generate statement GROUP ATOM C3' CN7 0.14 ATOM H3' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H3T HN5 0.43 BOND O3' H3T DONO H3T O3' BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch ! use in generate statement GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM P3 P 1.50 ATOM O1P3 ON3 -0.82 ATOM O2P3 ON3 -0.82 ATOM O3' ON2 -0.62 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34 BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T DONO H3T O3T ACCE O3T ACCE O1P3 ACCE O2P3 ! Build in B-DNA-like conformation (NF) BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000 BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 PRES 3POM -1.00 ! 3'terminal Methyl Phosphate patch ! use in generate statement ! To build model compound with OPO3-CH3 at the 3' end (nicolas) GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM P3 P 1.50 ATOM O1P3 ON3 -0.78 ATOM O2P3 ON3 -0.78 ATOM O3' ON2 -0.57 ATOM O3T ON2 -0.57 ATOM C3T CN9 -0.17 ATOM H3T1 HN9 0.09 ATOM H3T2 HN9 0.09 ATOM H3T3 HN9 0.09 BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T C3T BOND C3T H3T1 C3T H3T2 C3T H3T3 ACCE O3' ACCE O5' ACCE O1P3 ACCE O2P3 BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 BILD C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000 BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 BILD C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 BILD H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000 BILD H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000 BILD H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000 PRES 3PO3 -2.00 ! 3'terminal PHOSPHATE patch ! use in generate statement ! Added by Nicolas, to be consistent with model componds GROUP ATOM C3' CN7 -0.09 ATOM H3' HN7 0.09 ATOM P3 P 1.10 ATOM O3' ON2 -0.40 ATOM O1P3 ON3 -0.90 ATOM O2P3 ON3 -0.90 ATOM O3P3 ON3 -0.90 BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3P3 ACCE O1P3 ACCE O2P3 ACCE O3P3 BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000 BILD C3' O3' P3 O3P3 0.0000 000.00 -39.52 000.00 0.0000 BILD O3P3 O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 BILD O3P3 O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 BILD O3' P3 O3P3 O3T 0.0000 000.00 180.00 000.00 0.0000 BILD P3 O3P3 O3T H3T 0.0000 000.00 180.00 000.00 0.0000 PRES DELB 0.00 ! patch to delete all possible base atoms ! of Cyt,Gua,Ade,Thy and Ura ! !note: error messages will be obtained due to atoms not present in !residue being "deleted" by this patch !cyt section DELE ATOM N1 DELE ATOM C6 DELE ATOM H6 DELE ATOM C2 DELE ATOM O2 DELE ATOM N3 DELE ATOM C4 DELE ATOM N4 DELE ATOM H41 DELE ATOM H42 DELE ATOM C5 DELE ATOM H5 !gua section DELE ATOM N9 DELE ATOM H1 DELE ATOM N2 DELE ATOM H21 DELE ATOM H22 DELE ATOM O6 DELE ATOM N7 DELE ATOM C8 DELE ATOM H8 !ade section DELE ATOM H2 DELE ATOM N6 DELE ATOM H61 DELE ATOM H62 !thy/ura section DELE ATOM H3 DELE ATOM O4 DELE ATOM C5M DELE ATOM H51 DELE ATOM H52 DELE ATOM H53 PRES CY35 0.0 ! patch to make a cyclic 3'-5' nucleotide ! use AUTOGEN ANGLE DIHE after this patch BOND O3' P ! but before water-generation PRES LKNA 0.0 ! Patch to join to nucleic acid segments (eg for IMAGES) ! eg: patch sega 10 segb 1 ! sega should have std 3' (gene sega ... last none) ! segb should have std 5' (gene segb ... first none) ! USE AUTOgen ANGL DIHE after this patch, ! but before water-generation BOND 1O3' 2P !following commented due to use of autogenerate !THET 1C3' 1O3' 2P !THET 1O3' 2P 2O5' !THET 1O3' 2P 2O1P !THET 1O3' 2P 2O2P !DIHE 1O3' 2P 2O5' 2C5' 1O3' 2P 2O5' 2C5' !DIHE 1C4' 1C3' 1O3' 2P !DIHE 1C3' 1O3' 2P 2O5' 1C3' 1O3' 2P 2O5' IC 1O3' 2P 2O5' 2C5' 1.6001 101.45 -39.25 119.00 1.4401 IC 1O3' 2O5' *2P 2O1P 1.6001 101.45 -115.82 109.74 1.4802 IC 1O3' 2O5' *2P 2O2P 1.6001 101.45 115.90 109.80 1.4801 IC 1C4' 1C3' 1O3' 2P 1.5284 111.92 159.13 119.05 1.6001 IC 1C3' 1O3' 2P 2O5' 1.4212 119.05 -98.86 101.45 1.5996 END


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