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top_all27_prot_na.rtf
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*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
*>>>>>>> CHARMM22 Proteins and CHARMM27 Nucleic Acids <<<<<<<<<<
*from
*>>>> CHARMM22 All-Hydrogen Topology 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 Topology 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
*
27 1
! AMENDMENTS TO DOWNLOADED FILE:
!
! SML. Feb. 7, 2003. Acetylated N-terminus.
! Changed CHARMM default PRES ACE patch to PRES PACE, and
! added RESI ACE, acetylated N-terminus, used as a residue.
! It was created starting from PRES ACE, the patch, and
! renaming (CAY, CY, OY) to (CA, C, O). Also, there is 1
! improper and 2 IC entries that are not needed because
! they will be in the next residue.
!
! SML. Feb. 7, 2003. Protonated Asp's and Glu's
! NOTE: Default use should be with residues!
! Added RESI AS2, RESI AS1, RESI GL2, RESI GL1
! Added PRES PAS2, PRES PAS1, PRES PGL2, PRES PGL1
! Param22 provides patches PRES ASPP and PRES GLUP, which
! protonate on OD2, OE2, respectively. However, also need
! option to protonate on OD1, OD2. Therefore, created the
! 2 new patches to do so, and renamed the originals to be
! consistent/clear. PRES PGL2 == PRES GLUP and PRES PAS2 ==
! PRES ASPP, only renamed. PRES PGL1 and PRES PAS1 created.
! Note that to create PGL1 and PAS1 correctly, redefinition of
! 1 improper was needed. Redefined the BOND, DOUBLE as well.
! The IC table should be left alone to keep the default build
! to have the O1 and O2 in the same place.
!
! SML. Feb. 7, 2003. pro-chirality of LEU CD1 CD2
! Fixed the pro-chirality. Corrected 2 impropers
! Commented out original as WRONG. Added in new as RIGHT
!IC CD1 CB *CG CD2 1.5361 110.4800 123.7500 112.5700 1.5360 !RIGHT
!IC CD1 CD2 *CG HG 1.5361 110.2600 116.6300 108.0200 1.1168 !RIGHT
!!IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 WRONG
!!IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 WRONG
!
! SML. Feb. 10, 2003. Commented out second identical occurence of RESI CAL.
!
! SML. Feb. 10, 2003. Water.
! Added RESI OH2, a copy of RESI TIP3
! General use in lab should be OH2.
! It is a tip3p water model (i.e. 3 bonds and 1 angle)
! Generate using noangle nodihedral
! You should probably have your water residue names and atom types
! renamed from your default PDB convention to match this CHARMM default.
! For example: PDB residue HOH should get changed to OH2
! PDB atom name O should get changed to OH2
!
! SML. Feb. 10, 2003. Commented out second identical occurence of RESI DUM.
!
! SML. Feb. 10, 2003. N-Methylamide C-terminus (PRES CT3 and RESI NMA).
! The existing patch, PRES CT3, had an error in the IC table, such that
! building from scratch would incorrectly rotate 180 degrees about
! final CA-C bond. An "O" was incorrectly in place of an "NT",
! which can be understood when comparing to a normal residue and
! the IC entries which call ahead to the next residue. I fixed this.
! Added RESI NMA. Equivalent to PRES CT3, but used as residue for
! cased when PDB file has it as a separate residue. Normally, use
! the patch PRES CT3.
!
! SML. Feb. 10, 2003. Histidines.
! Standard use should be residues HSE, HSD, and HSP.
! PRES PHSD and PRES PHSP were created, to patch from HSE to
! HSD and HSP, respectively. This may be useful for some future
! script for 'deciding' histidines, but general use should be the RESIs.
! Side-chain IC entries were used in both PRES's to make the default
! build identical between RESI HSD(P) and RESI HSE patched to HSD(P).
! NOTE: There is no HIS. An indecisive histidine should probably be
! made a HSE, the slighly energetically favorable form. But, in
! general, MAKE AN INTELLIGENT DECISION FOR YOUR HISTIDINES, and name
! them either HSE, HSD, or HSP for param22.
!
! SML. Feb. 11, 2003. Deprotonated cysteine.
! PRES CYSD was created in the past but is not supported. I write this
! here in case you need deprotonated cysteine, this MAY be what you
! want, but I'm not sure. What is immediately below is from Justin
! Caravella (JAC), Sep. 20, 1997.
! PRES CYSD -1.00 ! patch for deprotonated cysteine
! GROUP ! added by JAC 9/20/97
! ATOM CB CT2 -0.19 ! Charges on S, C from 6-31G** calculation
! ATOM HB1 HA 0.09 ! on CH3-S
! ATOM HB2 HA 0.09 !
! ATOM SG S -0.99 !
! DELETE ATOM HG1
!
! SML. Feb. 24, 2003. DIHE in PRES CT3
! Would add this dihedral because +N is now NT
! DIHE N CA C NT
! However this dihedral is not in RESI NMA and they should be the same.
! Therefore, no changes made here.
!
! SML. Feb. 26, 2003. TRP IC Table - Chi Definition
! The default IC table for TRP has the dihedral CA CB CG CD2, NOT the
! standard chi2 of CA CB CG CD1. Two rows of the table were changed
! to have standard chi2 from a default build. Equivalent changes were
! made in param19 for TRP (and Histidines where they were needed also,
! but param22 already fixed them).
!
! END OF AMENDMENTS TO DOWNLOADED FILE.
!references
!
!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
!
!
!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)
!
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 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 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 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 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 90 CAL 40.08000 CA ! calcium 2+
MASS 91 ZN 65.37000 ZN ! zinc (II) cation
MASS 92 FE 55.84700 Fe ! heme iron 56
MASS 99 DUM 0.00000 H ! dummy atom
!nucleic acid section
!MASS 1 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 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 70 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)
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
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 94 CAL 40.080000 CA ! Calcium Ion
MASS 195 CLA 35.450000 CL ! Chloride Ion
!MASS 99 DUM 0.001 H ! dummy atom
!MASS 102 CPH1 12.011000 C ! For imidazole model compound (NF)
!MASS 103 CPH2 12.011000 C ! For imidazole model compound (NF)
!MASS 104 HR3 1.008000 H ! For imidazole model compound (NF)
!MASS 105 HR1 1.008000 H ! For imidazole model compound (NF)
!MASS 106 NR1 14.007000 H ! For nitrogen in imidazol (NF)
!MASS 107 NR2 14.007000 H ! For nitrogen in imidazol (NF)
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
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
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
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
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
! SML. Feb. 10, 2003. Added RESI AS2. See notes at top of file.
RESI AS2 0.00 ! residue for protonated aspartic acid, proton on od2
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 -0.21 ! | | \
ATOM HB1 HA 0.09 ! | HB2 OD2-HD2
ATOM HB2 HA 0.09 ! O=C
ATOM CG CD 0.75 ! |
ATOM OD1 OB -0.55
ATOM OD2 OH1 -0.61
ATOM HD2 H 0.44
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
BOND OD2 HD2
DOUBLE O C CG OD1
IMPR N -C CA HN C CA +N O
!IMPR OD1 CB OD2 CG
IMPR CG CB OD2 OD1
DONOR HN N
DONOR HD2 OD2
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
IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000
! End SML Feb. 10, 2003.
! SML. Feb. 10, 2003. Added RESI AS1. See notes at top of file.
RESI AS1 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 OD1-HD1
ATOM HA HB 0.09 ! | | /
GROUP ! HA-CA--CB--CG
ATOM CB CT2 -0.21 ! | | \\
ATOM HB1 HA 0.09 ! | HB2 OD2
ATOM HB2 HA 0.09 ! O=C
ATOM CG CD 0.75 ! |
ATOM OD2 OB -0.55
ATOM OD1 OH1 -0.61
ATOM HD1 H 0.44
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB OD1 CG
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2
BOND OD1 HD1
DOUBLE O C CG OD2
IMPR N -C CA HN C CA +N O
!IMPR OD2 CB OD1 CG
IMPR CG CB OD1 OD2
DONOR HN N
DONOR HD1 OD1
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
IC HD1 OD1 CG OD2 0.0000 0.0000 0.0000 0.0000 0.0000
! End SML Feb. 10, 2003.
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
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
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 OE1 CG OE2 CD
IMPR CD CG OE2 OE1
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
! SML. Feb. 7, 2003. Added residues for protonated Glu's. See top of file.
RESI GL2 0.00
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-HE2
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.21
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
ATOM CD CD 0.75
ATOM OE1 OB -0.55
ATOM OE2 OH1 -0.61
ATOM HE2 H 0.44
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
BOND OE2 HE2
DOUBLE O C CD OE1
IMPR N -C CA HN C CA +N O
!IMPR OE1 CG OE2 CD
IMPR CD CG OE2 OE1
DONOR HN N
DONOR HE2 OE2
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
IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000
! End SML Feb. 7, 2003.
! SML. Feb. 7, 2003. Added residues for protonated Glu's. See top of file.
RESI GL1 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 OE1-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 -0.21
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
ATOM CD CD 0.75
ATOM OE2 OB -0.55
ATOM OE1 OH1 -0.61
ATOM HE1 H 0.44
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG OE1 CD
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CG HG1
BOND CG HG2
BOND OE1 HE1
DOUBLE O C CD OE2
IMPR N -C CA HN C CA +N O
!IMPR OE1 CG OE2 CD
IMPR CD CG OE1 OE2
DONOR HN N
DONOR HE1 OE1
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
IC HE1 OE1 CD OE2 0.0000 0.0000 0.0000 0.0000 0.0000
! End SML Feb. 7, 2003.
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
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
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
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 ! | | / ||