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top_all_glyco.lib
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top_all_glyco.lib
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* Added glycan topology files from CHARMM Update
* toppar_all36_glycopeptide.str & top_all36_carb.rtf
*>>>>>>>> Developmental Residue Topology File for Proteins <<<<<
*>>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>> May 1993 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
* These files are a beta release; additional parameter development
* and testing may lead to alteration of the contents.
*
*
*
*
* Original file: top_all22_prot_b5.inp.
*
* IMPROPER dihedrals, some from toph19.inp, were added to this library to
* make it more useful for MODELLER (Andrej Sali). Note that this is
* only necessary when MODELLER's non-hydrogen topology is used;
* presumably, the H-related energy terms in the all-hydrogen topology
* would restrain peptide bonds, ring planarities, and chiralities (?)
* sufficiently and would obviate the need for these impropers.
*
* Specifically, the following impropers were added:
*
* IMPR CA N C CB for mainchain of all residues but GLY;
* ring impropers for Phe, Tyr, Hsd (His on 1/25/03), Hsp, Hse, and Trp.
*
* the chirality constraints for the chiral and pro-chiral
* centers in sidechains of ILE, LEU, THR, VAL; note that
* the toph19.inp IMPR for LEU had to be changed to allow
* for the swapped CD1/CD2 LEU labels (that was changed back on 1/25/03).
*
* IMPR NE CD CZ HE for ARG.
*
* Trp appeared to have too many improper dih restraints so the optimizer
* got caught in a deep local minimum too easily. I made them sparser
* relative to toph19 and also introduced two new 180 degree impropers
* across the two rings.
*
* The IC entries added to allow amino-acid residue creation without patches:
*
* IC N CA C O 1.4592 114.4400 0.0000 122.5200 1.2297
* IC HN N CA C 0.9996 115.4200 0.0000 114.4400 1.5390
*
* Only the 20 standard residue types were modified.
*
* No changes were done for cis/trans prolines.
*
* PA, PB, and UNDF atom types were added.
*
* GDP and GTP residue types were added.
*
* Pro pucker is enforced by an additional explicit CP1 CP2 CP2 CP3 term.
*
*
* This file was obtained by editing the H naming conventions in top.lib
* (1/25/03) to conform to those of PDB, which now conforms to IUPAC. In
* addition, the models.lib file had to be edited, and the source code changed
* in iupac_model.F90. I ran program PDB-H/conver-top on
* the original top.lib and edited special cases manually as follows:
* DECL HN --> H
* RESI ASX copied to be the same as ASN
* RESI GLX copied to be the same as GLN
* RESI CYS old HG1 is non-conforming, renamed to HG per PDB
* RESI CSS was edited manually based on the new CYS (copy CYS, delete all
* references to HG)
* PRES DISU, edit lots of H names to match the new CYS, CSS.
* RESI UNK is like GLY, so copy GLY to it.
* RESI ILE: edit HD1/2/3 to 1HD1/2/3
* RESI SER: HG1 -> HG
* RESI HSE: keep it as edited by the program thinking it is HIS,
* even though HE2 is undefined in PDB (keep it as HE2)
* RESI HSP: the same as HSE
* PRES NTER, GLYP, PROP: all these N-terminals are edited manually into 1H,
* 2H, 3H
* PRES ASPP edited to reflect new ASP (HB1 and HB2 into 1HB and 2HB)
* PRES GLUP the same as ASPP
* PRES HS2 not edited, won't work, so it was just deleted
*
* While renaming the hydrogens, I also renamed here a few other atoms to make
* them conform to PDB and simplify the source code (dihedral_routines.F90,
* atom_residue_routines.F90, iupac_model.F90):
* RESI ILE CD --> CD1; and resdih.lib was changed accordingly
* RESI LEU CD1 and CD2 were swapped back (in the IMPR entry), and
* resdih.lib was changed accordingly.
* RESI HSD --> HIS, to conform to PDB; (restyp and resdih libs changed
* accordingly).
* PRES CTER OT1 and OT2 were changed to O and OXT, respectively, to conform
* to PDB
* RESI TIP3, OH2 --> O, to conform to PDB
*
* Additionally modified 08/25/2008 to conform to remediated PDB (v3):
* new atom naming for nucleic acids, NAD, GDP, GTP, ions. New deoxy nucleic
* acid types DADE, DCYT, DGUA, DTHY, DURA. All hydrogen names now start
* with H, not a digit.
*
* Modified 09/18/2008 to add elements to MASS lines, to conform to newer
* CHARMM format and to allow writing out new-style PDB output.
*
* MODELLER topology.submodel = 1
22 1
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 HA1 1.00800 H ! for alkene; RHC=CR
MASS 12 HA2 1.00800 H ! for alkene; H2C=CR
MASS 13 C 12.01100 C ! carbonyl C, peptide backbone
MASS 14 CA 12.01100 C ! aromatic C
MASS 15 CT1 12.01100 C ! aliphatic sp3 C for CH
MASS 16 CT2 12.01100 C ! aliphatic sp3 C for CH2
MASS 17 CT3 12.01100 C ! aliphatic sp3 C for CH3
MASS 18 CPH1 12.01100 C ! his CG and CD2 carbons
MASS 19 CPH2 12.01100 C ! his CE1 carbon
MASS 20 CPT 12.01100 C ! trp C between rings
MASS 21 CY 12.01100 C ! TRP C in pyrrole ring
MASS 22 CP1 12.01100 C ! tetrahedral C (proline CA)
MASS 23 CP2 12.01100 C ! tetrahedral C (proline CB/CG)
MASS 24 CP3 12.01100 C ! tetrahedral C (proline CD)
MASS 25 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS 26 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1
MASS 27 CPA 12.01100 C ! heme alpha-C
MASS 28 CPB 12.01100 C ! heme beta-C
MASS 29 CPM 12.01100 C ! heme meso-C
MASS 30 CM 12.01100 C ! heme CO carbon
MASS 31 CS 12.01100 C ! thiolate carbon
MASS 32 CE1 12.01100 C ! for alkene; RHC=CR
MASS 33 CE2 12.01100 C ! for alkene; H2C=CR
MASS 34 N 14.00700 N ! proline N
MASS 35 NR1 14.00700 N ! neutral his protonated ring nitrogen
MASS 36 NR2 14.00700 N ! neutral his unprotonated ring nitrogen
MASS 37 NR3 14.00700 N ! charged his ring nitrogen
MASS 38 NH1 14.00700 N ! peptide nitrogen
MASS 39 NH2 14.00700 N ! amide nitrogen
MASS 40 NH3 14.00700 N ! ammonium nitrogen
MASS 41 NC2 14.00700 N ! guanidinium nitroogen
MASS 42 NY 14.00700 N ! TRP N in pyrrole ring
MASS 43 NP 14.00700 N ! Proline ring NH2+ (N-terminal)
MASS 44 NPH 14.00700 N ! heme pyrrole N
MASS 45 NP1 14.00700 N ! heme pyrrole N ! Roberto
MASS 46 PA 15.00000 P ! PA ! Andrej
MASS 47 PB 15.00000 P ! PB ! Andrej
MASS 48 O 15.99900 O ! carbonyl oxygen
MASS 49 OB 15.99900 O ! carbonyl oxygen in acetic acid
MASS 50 OC 15.99900 O ! carboxylate oxygen
MASS 51 OH1 15.99900 O ! hydroxyl oxygen
MASS 52 OS 15.99940 O ! ester oxygen
MASS 53 OT 15.99940 O ! TIPS3P WATER OXYGEN
MASS 54 OM 15.99900 O ! heme CO/O2 oxygen
MASS 55 S 32.06000 S ! sulphur
MASS 56 SM 32.06000 S ! sulfur C-S-S-C type
MASS 57 SS 32.06000 S ! thiolate sulfur
MASS 58 HE 4.00260 HE ! helium
MASS 59 NE 20.17970 NE ! neon
MASS 60 CAL 40.08000 CA ! calcium 2+
MASS 61 ZN 65.37000 ZN ! zinc (II) cation
MASS 62 FE 55.84700 FE ! heme iron 56
MASS 63 UNDF 55.84700 X ! undefined Andrej
! nucleic acid section
!MASS 104 HT 1.008000 H ! TIPS3P WATER HYDROGEN
MASS 64 HN1 1.008000 H ! Nucleic acid amine proton
MASS 65 HN2 1.008000 H ! Nucleic acid ring nitrogen proton
MASS 66 HN3 1.008000 H ! Nucleic acid aromatic carbon proton
MASS 67 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton
MASS 68 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton
MASS 69 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton
MASS 70 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA)
MASS 71 HN3B 1.008000 H ! NAD+ aromatic hydrogen
MASS 72 CN1 12.011000 C ! Nucleic acid carbonyl carbon
MASS 73 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide
MASS 74 CN3 12.011000 C ! Nucleic acid aromatic carbon
MASS 75 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2
MASS 76 CN5 12.011000 C ! Nucleic acid purine C4 and C5
MASS 77 CN6 12.011000 C ! Nucleic acid sp3 ribose ring carbon
MASS 78 CN6B 12.011000 C ! Nucleic acid sp3 ribose ring carbon, C1'
MASS 79 CN6C 12.011000 C ! Nucleic acid sp3 deoxyribose ring carbon, C2'
MASS 80 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1)
MASS 81 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS 82 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3)
MASS 83 CN3A 12.011000 C ! NAD+ aromatic carbon
MASS 84 CN3B 12.011000 C ! NAD+ aromatic carbon
MASS 85 CN3C 12.011000 C ! NADH aromatic carbon
MASS 86 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC
MASS 87 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon
MASS 88 NN1 14.007000 N ! Nucleic acid amide nitrogen
MASS 89 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen
MASS 90 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
MASS 91 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
MASS 92 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen
MASS 93 NN4 14.007000 N ! Nucleic acid purine N7
MASS 94 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen
MASS 95 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
MASS 96 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3
!MASS 164 OT 15.999400 O ! TIPS3P WATER OXYGEN
MASS 97 ON1 15.999400 O ! Nucleic acid carbonyl oxygen
MASS 98 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2
MASS 99 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen
MASS 100 ON3 15.999400 O ! Nucleic acid =O in phosphate
MASS 101 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
MASS 102 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen
MASS 103 ON6 15.999400 O ! Nucleic acid ribose ring oxygen
MASS 104 ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen, tyr-phosphate
MASS 105 P 30.974000 P ! phosphorus
MASS 106 P2 30.974000 P ! pyrophosphate phosphorus
MASS 107 SOD 22.989770 NA ! Sodium Ion
MASS 108 MG 24.305000 MG ! Magnesium Ion
MASS 109 DUM 0.001 X ! dummy atom
!Added glycan mass entries, guttman
! C6H12O6 pyranose monosaccharide atom types
MASS 171 C301 12.01100 C ! aliphatic C, no H's
MASS 172 C311 12.01100 C ! generic acyclic CH carbon
MASS 173 C312 12.01100 C ! CH carbon in linear polyols
MASS 174 3161 12.01100 C ! C2, C3, C4 CH bound to OH
MASS 175 3162 12.01100 C ! C1 (anomeric) CH bound to OH
MASS 176 3163 12.01100 C ! C5 CH bound to exocylic CH2OH
MASS 177 C321 12.01100 C ! generic acyclic CH2 carbon (hexopyranose C6)
MASS 178 C322 12.01100 C ! CH2 carbon in linear polyols erh
MASS 179 3263 12.01100 C ! C5 in xylose
MASS 180 C331 12.01100 C ! generic acyclic CH3 carbon (xyl C6, glcna/galna CT)
MASS 181 C2O1 12.01100 C ! sp2 carbon in amides, aldoses
MASS 182 C2O2 12.01100 C ! sp2 carbon in carboxylates
MASS 183 C2O3 12.01100 C ! sp2 carbon in acetone, ketoses
MASS 184 C2O4 12.01100 C ! c22 CD
MASS 185 HCA1 1.00800 H ! aliphatic proton, CH
MASS 186 HCA2 1.00800 H ! aliphatic proton, CH2
MASS 187 HCA3 1.00800 H ! aliphatic proton, CH3
MASS 188 HCP1 1.00800 H ! polar H
MASS 189 HCR1 1.00800 H ! c22 HR1
MASS 191 O311 15.99940 O ! hydroxyl oxygen
MASS 192 OC61 15.99940 O ! ether in six membered ring
MASS 193 O301 15.99940 O ! generic linear ether
MASS 194 O302 15.99940 O ! linear ether in 1-1 glycosidic linkage
MASS 195 O2D1 15.99940 O ! sp2 oxygen in amides, aldoses
MASS 196 O2D2 15.99940 O ! sp2 oxygen in carboxylates
MASS 197 O2D3 15.99940 O ! sp2 oxygen in acetone, ketoses
MASS 198 O2D4 15.99940 O ! par22 O
MASS 200 NC2D 14.00700 N ! peptide, NMA, IPAA nitrogen (C=NHR)
! model compound atom types
MASS 201 321C 12.01100 C ! cyclohexane, thp CH2
MASS 202 HC3M 1.00800 H ! alcohol aliphatic proton, CH3
MASS 203 HC1M 1.00800 H ! EGLY hydroxyl H
MASS 204 311M 15.99940 O ! MEOH, ETOH, PRO2, EGLY hydroxyl O
MASS 205 312D 12.01100 C ! cyclohexane, thp CH2 model for 1-1 linkage
MASS 206 311C 12.01100 C ! patch C1 in model compound
MASS 207 311D 12.01100 C ! patch C1 in model compound
! THF atom types
MASS 208 3C5M 15.99940 O ! thf ring oxygen
MASS 209 322C 12.01100 C ! cyclopentane, thf CH2
MASS 210 A2C2 1.00800 H ! cyclopentane, thp aliphatic proton, CH2
MASS 211 312C 12.01100 C ! tf2m CH1
MASS 212 A1C2 1.00800 H ! tf2m aliphatic proton, CH1
! Furanose atom types; erh 10/24/07
MASS 213 3C51 15.99940 O ! furan ring oxygen
MASS 214 3152 12.01100 C ! furan ring carbon
MASS 215 3153 12.01100 C ! furan ring carbon
MASS 216 2151 12.01100 C ! furan ring carbon; C2 deoxy
MASS 217 3151 12.01100 C ! furan ring carbon
MASS 218 3051 12.01100 C ! furan ring carbon; C2 fructose
! pyranose derivatives
MASS 219 3062 12.01100 C ! C2 on NE5AC
MASS 220 3261 12.01100 C ! C3 on NE5AC
!dummy atom
!MASS 99 DUM 1.00800 H ! dummy atom
!Added by sai for modelling phosphate
MASS 221 O312 15.99940 O ! OH in PO3H (phosphate) || OHL in top_all27_lipid.rtf
MASS 222 O30P 15.99940 O ! ester O in PO3H (phosphate) || OSL in top_all27_lipid.rtf
MASS 223 O2DP 15.99940 O ! =0 in P03H (phosphate) || O2L in top_all27_lipid.rtf
MASS 224 PC 30.97400 P ! phosphorus || PL in top_all27_lipid.rtf
MASS 225 SC 32.06000 S ! Sulfate sulfur
!pram, furanosyl linkages
MASS 226 312D 12.01100 C ! from 322C ; THF anomeric carbon
MASS 227 O303 15.99940 O ! from OC301; linear ether in P1->F3 pyranose-furanose glycosidic linkage
DECL -CA
DECL -C
DECL -O
DECL +N
DECL +H
DECL +CA
DEFA FIRS NTER LAST CTER
AUTO ANGLES DIHE
RESI ALA 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! H-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 H N CA O C
BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
IMPR N -C CA H C CA +N O
IMPR CA N C CB
DONOR H N
ACCEPTOR O C
IC -C CA *N H 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
IC N CA C O 1.4300 107.0000 0.0000 122.5200 1.2297
IC H N CA C 0.9996 115.4200 0.0000 114.4400 1.4900
RESI ARG 1.00
GROUP
ATOM N NH1 -0.47 ! | HH11
ATOM H H 0.31 ! H-N |
ATOM CA CT1 0.07 ! | HB2 HG2 HD2 HE NH1-HH12
ATOM HA HB 0.09 ! | | | | | /
GROUP ! HA-CA--CB--CG--CD--NE--CZ
ATOM CB CT2 -0.18 ! | | | | \
ATOM HB3 HA 0.09 ! | HB3 HG3 HD3 NH2-HH21
ATOM HB2 HA 0.09 ! O=C |
GROUP ! | HH22
ATOM CG CT2 -0.18
ATOM HG3 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM CD CT2 0.20
ATOM HD3 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 NH1 CZ NH2 CZ N H N CA
BOND O C C CA C +N CA HA CB HB3
BOND CB HB2 CG HG3 CG HG2 CD HD3 CD HD2
BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22
IMPR N -C CA H C CA +N O
IMPR CZ NH1 NH2 NE
IMPR CA N C CB
IMPR NE CD CZ HE
DONOR H N
DONOR HE NE
DONOR HH11 NH1
DONOR HH12 NH1
DONOR HH21 NH2
DONOR HH22 NH2
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 HG3 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 HD3 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 H H 0.31 ! H-N
ATOM CA CT1 0.07 ! | HB2 OD1 HD21 (cis to OD1)
ATOM HA HB 0.09 ! | | || /
GROUP ! HA-CA--CB--CG--ND2
ATOM CB CT2 -0.18 ! | | \
ATOM HB3 HA 0.09 ! | HB3 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 HD22 H 0.32
ATOM HD21 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB OD1 CG ND2 CG
BOND N H N CA O C C CA C +N
BOND CA HA CB HB3 CB HB2 ND2 HD22 ND2 HD21
IMPR N -C CA H C CA +N O
IMPR CG ND2 CB OD1 CG CB ND2 OD1
IMPR ND2 CG HD22 HD21 ND2 CG HD21 HD22
IMPR CA N C CB
DONOR H N
DONOR HD22 ND2
DONOR HD21 ND2
ACCEPTOR OD1 CG
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 HD22 1.5319 116.1500 -179.2600 117.3500 0.9963
IC HD22 CG *ND2 HD21 0.9963 117.3500 178.0200 120.0500 0.9951
RESI ASX 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! H-N
ATOM CA CT1 0.07 ! | HB1 OD1 HD1 (cis to OD1)
ATOM HA HB 0.09 ! | | || /
GROUP ! HA-CA--CB--CG--ND2
ATOM CB CT2 -0.18 ! | | \
ATOM HB2 HA 0.09 ! | HB2 HD2 (trans to OD1)
ATOM HB1 HA 0.09 ! O=C
GROUP ! |
ATOM CG CC 0.55
ATOM OD1 O -0.55
GROUP
ATOM ND2 NH2 -0.62
ATOM HD2 H 0.32
ATOM HD1 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB OD1 CG ND2 CG
BOND N H N CA O C C CA C +N
BOND CA HA CB HB2 CB HB1 ND2 HD2 ND2 HD1
IMPR N -C CA H C CA +N O
IMPR CG ND2 CB OD1 CG CB ND2 OD1
IMPR ND2 CG HD2 HD1 ND2 CG HD1 HD2
IMPR CA N C CB
DONOR H N
DONOR HD2 ND2
DONOR HD2 ND2
ACCEPTOR OD1 CG
ACCEPTOR O C
IC -C CA *N H 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 HB2 1.5319 114.3000 119.1700 107.8200 1.1120
IC CG CA *CB HB1 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 HD2 1.5319 116.1500 -179.2600 117.3500 0.9963
IC HD2 CG *ND2 HD1 0.9963 117.3500 178.0200 120.0500 0.9951
RESI ASP -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! H-N
ATOM CA CT1 0.07 ! | HB2 OD1
ATOM HA HB 0.09 ! | | //
GROUP ! HA-CA--CB--CG
ATOM CB CT2 -0.28 ! | | \\
ATOM HB3 HA 0.09 ! | HB3 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 OD1 CG OD2 CG
BOND N H N CA O C C CA C +N
BOND CA HA CB HB3 CB HB2
IMPR N -C CA H C CA +N O
IMPR OD1 CB OD2 CG
IMPR CA N C CB
DONOR H N
ACCEPTOR OD1 CG
ACCEPTOR OD2 CG
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 H H 0.31 ! H-N
ATOM CA CT1 0.07 ! | HB2
ATOM HA HB 0.09 ! | |
GROUP ! HA-CA--CB--SG
ATOM CB CT2 -0.11 ! | | \
ATOM HB3 HA 0.09 ! | HB3 HG
ATOM HB2 HA 0.09 ! O=C
ATOM SG S -0.23 ! |
ATOM HG HS 0.16
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA SG CB N H N CA
BOND O C C CA C +N CA HA CB HB3
BOND CB HB2 SG HG
IMPR N -C CA H C CA +N O
IMPR CA N C CB
DONOR H N
DONOR HG SG
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 HG 1.5584 113.8700 176.9600 97.1500 1.3341
RESI CSS 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! H-N
ATOM CA CT1 0.07 ! | HB2
ATOM HA HB 0.09 ! | |
GROUP ! HA-CA--CB--SG
ATOM CB CT2 -0.11 ! | |
ATOM HB3 HA 0.09 ! | HB3
ATOM HB2 HA 0.09 ! O=C
ATOM SG S -0.23 ! |
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA SG CB N H N CA
BOND O C C CA C +N CA HA CB HB2
BOND CB HB3
IMPR N -C CA H C CA +N O
IMPR CA N C CB
DONOR H N
ACCEPTOR O C
IC -C CA *N H 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 HB3 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
RESI GLN 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! H-N
ATOM CA CT1 0.07 ! | HB2 HG2 OE1 HE21 (cis to OE1)
ATOM HA HB 0.09 ! | | | || /
GROUP ! HA-CA--CB--CG--CD--NE2
ATOM CB CT2 -0.18 ! | | | \
ATOM HB3 HA 0.09 ! | HB3 HG3 HE22 (trans to OE1)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.18
ATOM HG3 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 HE22 H 0.32
ATOM HE21 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG OE1 CD NE2 CD
BOND N H N CA O C C CA
BOND C +N CA HA CB HB3 CB HB2 CG HG3
BOND CG HG2 NE2 HE22 NE2 HE21
IMPR N -C CA H C CA +N O
IMPR CD NE2 CG OE1 CD CG NE2 OE1
IMPR NE2 CD HE22 HE21 NE2 CD HE21 HE22
IMPR CA N C CB
DONOR H N
DONOR HE22 NE2
DONOR HE21 NE2
ACCEPTOR OE1 CD
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 HG3 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 HE22 1.5320 116.8400 -179.7200 116.8600 0.9959
IC HE22 CD *NE2 HE21 0.9959 116.8600 -178.9100 119.8300 0.9943
RESI GLX 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! H-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 HB2 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1)
ATOM HB1 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.18
ATOM HG2 HA 0.09
ATOM HG1 HA 0.09
GROUP
ATOM CD CC 0.55
ATOM OE1 O -0.55
GROUP
ATOM NE2 NH2 -0.62
ATOM HE22 H 0.32
ATOM HE21 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG OE1 CD NE2 CD
BOND N H N CA O C C CA
BOND C +N CA HA CB HB2 CB HB1 CG HG2
BOND CG HG1 NE2 HE22 NE2 HE21
IMPR N -C CA H C CA +N O
IMPR CD NE2 CG OE1 CD CG NE2 OE1
IMPR NE2 CD HE22 HE21 NE2 CD HE21 HE22
IMPR CA N C CB
DONOR H N
DONOR HE22 NE2
DONOR HE21 NE2
ACCEPTOR OE1 CD
ACCEPTOR O C
IC -C CA *N H 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 HB2 1.5534 115.5200 120.9300 106.8000 1.1147
IC CG CA *CB HB1 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 HG2 1.5320 112.5000 118.6900 110.4100 1.1112
IC CD CB *CG HG1 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 HE22 1.5320 116.8400 -179.7200 116.8600 0.9959
IC HE22 CD *NE2 HE21 0.9959 116.8600 -178.9100 119.8300 0.9943
RESI GLU -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! H-N
ATOM CA CT1 0.07 ! | HB2 HG2 OE1
ATOM HA HB 0.09 ! | | | //
GROUP ! HA-CA--CB--CG--CD
ATOM CB CT2 -0.18 ! | | | \\
ATOM HB3 HA 0.09 ! | HB3 HG3 OE2
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.28
ATOM HG3 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 OE1 CD OE2 CD
BOND N H N CA O C C CA
BOND C +N CA HA CB HB3 CB HB2 CG HG3
BOND CG HG2
IMPR N -C CA H C CA +N O
IMPR OE1 CG OE2 CD
IMPR CA N C CB
DONOR H N
ACCEPTOR OE1 CD
ACCEPTOR OE2 CD
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 HG3 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 H H 0.31 ! N-H
ATOM CA CT2 -0.02 ! |
ATOM HA3 HB 0.09 ! |
ATOM HA2 HB 0.09 ! HA2-CA-HA3
GROUP ! |
ATOM C C 0.51 ! |
ATOM O O -0.51 ! C=O
! |
BOND N H N CA O C C CA
BOND C +N CA HA3 CA HA2
IMPR N -C CA H C CA +N O
DONOR H N
ACCEPTOR O C
IC -C CA *N H 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 HA3 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 UNK 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM H H 0.31 ! N-H
ATOM CA CT2 -0.02 ! |
ATOM HA3 HB 0.09 ! |
ATOM HA2 HB 0.09 ! HA2-CA-HA3
GROUP ! |
ATOM C C 0.51 ! |
ATOM O O -0.51 ! C=O
! |
BOND N H N CA O C C CA
BOND C +N CA HA3 CA HA2
IMPR N -C CA H C CA +N O
DONOR H N
ACCEPTOR O C
IC -C CA *N H 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 HA3 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 HIS 0.00 ! neutral HIS, proton on ND1
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM H H 0.31 ! H-N | /
ATOM CA CT1 0.07 ! | HB2 ND1--CE1
ATOM HA HB 0.09 ! | | / |
GROUP ! HA-CA--CB--CG |
ATOM ND1 NR1 -0.36 ! | | \ |
ATOM HD1 H 0.32 ! | HB3 CD2--NE2
ATOM CG CPH1 -0.05 ! O=C |
ATOM CB CT2 -0.09 ! | HD2
ATOM HB3 HA 0.09
ATOM HB2 HA 0.09
GROUP
ATOM NE2 NR2 -0.70
ATOM CD2 CPH1 0.22
ATOM HD2 HR3 0.10
ATOM CE1 CPH2 0.25
ATOM HE1 HR1 0.13
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CD2 CG CE1 ND1
BOND NE2 CD2 N H N CA O C
BOND C CA C +N NE2 CE1 CA HA CB HB3
BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1
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 H C CA +N O
IMPR CA N C CB
IMPR CG ND1 CD2 CB CG ND1 CE1 NE2
IMPR ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1
IMPR CD2 CG ND1 CE1
DONOR H N
DONOR HD1 ND1
ACCEPTOR NE2
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 H H 0.31 ! H-N /
ATOM CA CT1 0.07 ! | HB2 ND1--CE1
ATOM HA HB 0.09 ! | | / |
GROUP ! HA-CA--CB--CG |
ATOM NE2 NR1 -0.36 ! | | \ |
ATOM HE2 H 0.32 ! | HB3 CD2--NE2
ATOM CD2 CPH1 -0.05 ! O=C | \
ATOM HD2 HR3 0.09 ! | HD2 HE2
GROUP
ATOM ND1 NR2 -0.70
ATOM CG CPH1 0.22
ATOM CE1 CPH2 0.25
ATOM HE1 HR1 0.13
ATOM CB CT2 -0.08
ATOM HB3 HA 0.09
ATOM HB2 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CD2 CG CE1 ND1
BOND NE2 CD2 N H N CA O C
BOND C CA C +N NE2 CE1 CA HA CB HB3
BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1
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 H C CA +N O
IMPR CA N C CB
IMPR CG ND1 CD2 CB CG ND1 CE1 NE2
IMPR ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1
IMPR CD2 CG ND1 CE1
DONOR H N
DONOR HE2 NE2
ACCEPTOR ND1
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 H H 0.31 ! H-N | /
ATOM CA CT1 0.07 ! | HB2 ND1--CE1
ATOM HA HB 0.09 ! | | / |
GROUP ! HA-CA--CB--CG |
ATOM ND1 NR3 -0.51 ! | | \ |
ATOM HD1 H 0.44 ! | HB3 CD2--NE2
ATOM NE2 NR3 -0.51 ! O=C | \
ATOM HE2 H 0.44 ! | HD2 HE2
ATOM CE1 CPH2 0.32
ATOM HE1 HR2 0.18
GROUP
ATOM CD2 CPH1 0.19
ATOM HD2 HR1 0.13
ATOM CG CPH1 0.19
ATOM CB CT2 -0.05
ATOM HB3 HA 0.09
ATOM HB2 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CD2 CG CE1 ND1
BOND NE2 CD2 N H N CA O C
BOND C CA C +N NE2 CE1 CA HA CB HB3
BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1
IMPR HD1 CG CE1 ND1
IMPR HD1 CE1 CG ND1
IMPR HE2 CD2 CE1 NE2 HE2 CE1 CD2 NE2
IMPR N -C CA H C CA +N O
IMPR CA N C CB
IMPR CG ND1 CD2 CB CG ND1 CE1 NE2
IMPR ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1
IMPR CD2 CG ND1 CE1
DONOR H N
DONOR HD1 ND1
DONOR HE2 NE2
ACCEPTOR O C
IC -C CA *N H 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 HB3 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 H H 0.31 ! H-N | /
ATOM CA CT1 0.07 ! | CG2--HG23
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB HD11
ATOM CB CT1 -0.09 ! | \ /
ATOM HB HA 0.09 ! | CG1--CD1--HD12
GROUP ! O=C / \ \
ATOM CG2 CT3 -0.27 ! | HG12 HG13 HD13
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM CG1 CT2 -0.18
ATOM HG13 HA 0.09
ATOM HG12 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 C C 0.51
ATOM O O -0.51
BOND CB CA CG1 CB CG2 CB CD1 CG1
BOND N H N CA O C C CA C +N
BOND CA HA CB HB CG1 HG13 CG1 HG12 CG2 HG21
BOND CG2 HG22 CG2 HG23 CD1 HD11 CD1 HD12 CD1 HD13