# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 17:19:17 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: L-gamma-glutamyl-S-benzyl-N-[(R)-carboxy(phenyl)methyl]-L-cysteinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSCc1ccccc1)C(=O)N[C@@H](C(O)=O)c2ccccc2)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VWW  VWW  L-gamma-glutamyl-S-benzyl-N-[(R)-carboxy(phenyl)methyl]-L-cysteinamide  peptide  58  33  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_VWW
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VWW  N     N  NH2    0  -0.805  14.5670  10.4279  23.1903
 VWW  CA    C  CH1    0  -0.161  14.6380   9.9698  24.5735
 VWW  C     C  C      0   0.386  15.9602   9.2163  24.8594
 VWW  O     O  O      0  -0.613  16.3714   9.2738  26.0379
 VWW  CB    C  CH2    0  -0.422  13.4296   9.0604  24.8220
 VWW  CG    C  CH2    0  -0.595  13.2537   8.6411  26.2717
 VWW  CD    C  C      0   0.565  11.9886   7.8471  26.5264
 VWW  OE1   O  O      0  -0.490  11.2139   7.5155  25.6416
 VWW  OXT   O  OC    -1  -0.600  16.4910   8.6006  23.9158
 VWW  N1    N  NH1    0  -0.625  11.7941   7.5333  27.8248
 VWW  CA1   C  CH1    0  -0.210  10.6893   6.7593  28.3084
 VWW  CB1   C  CH2    0  -0.571  11.1288   5.3738  28.8004
 VWW  SG    S  S2     0   0.006  11.8002   4.3093  27.5052
 VWW  CD1   C  CH2    0  -0.661  10.3104   3.9940  26.5009
 VWW  CE    C  CR6    0   0.136   9.1620   3.4496  27.2968
 VWW  CZ1   C  CR16   0  -0.318   8.0013   4.1990  27.4627
 VWW  CZ2   C  CR16   0  -0.280   9.2430   2.1983  27.9065
 VWW  CT1   C  CR16   0  -0.234   6.9451   3.7187  28.2289
 VWW  CT2   C  CR16   0  -0.240   8.1886   1.7123  28.6637
 VWW  CH    C  CR16   0  -0.270   7.0372   2.4743  28.8333
 VWW  C1    C  C      0   0.555  10.0001   7.4830  29.4671
 VWW  O1    O  O      0  -0.490  10.6307   8.1891  30.2401
 VWW  N2    N  NH1    0  -0.624   8.6990   7.2054  29.5942
 VWW  CA2   C  CH1    0  -0.245   7.8640   7.7817  30.6266
 VWW  CB2   C  CR6    0   0.102   6.6267   6.9256  30.7629
 VWW  CG1   C  CR16   0  -0.280   5.5935   7.0210  29.8320
 VWW  CD11  C  CR16   0  -0.241   4.4752   6.2053  29.9277
 VWW  CE1   C  CR16   0  -0.267   4.3744   5.2762  30.9558
 VWW  CD2   C  CR16   0  -0.239   5.3998   5.1703  31.8851
 VWW  CG2   C  CR16   0  -0.315   6.5177   5.9892  31.7858
 VWW  C2    C  C      0   0.404   7.4793   9.2701  30.3655
 VWW  O2    O  O      0  -0.592   6.9686   9.8402  31.3462
 VWW  OXT1  O  OC    -1  -0.588   7.6845   9.7265  29.2296
 VWW  H     H  HNH2   0   0.329  13.7792  11.0580  23.0951
 VWW  H2    H  HNH2   0   0.332  15.3861  10.9806  22.9708
 VWW  HA    H  HCH1   0   0.174  14.5800  10.8029  25.2916
 VWW  HB2   H  HCH2   0   0.219  12.5311   9.5927  24.4943
 VWW  HB3   H  HCH2   0   0.215  13.5145   8.1798  24.1796
 VWW  HG2   H  HCH2   0   0.268  14.1021   8.0401  26.6077
 VWW  HG3   H  HCH2   0   0.256  13.2490   9.5221  26.9218
 VWW  H1    H  HNH1   0   0.395  12.4666   7.8503  28.5062
 VWW  HA1   H  HCH1   0   0.283   9.9826   6.6445  27.4860
 VWW  HB21  H  HCH2   0   0.293  11.9264   5.4807  29.5388
 VWW  HB31  H  HCH2   0   0.282  10.3005   4.8632  29.2952
 VWW  HD2   H  HCH2   0   0.285  10.0241   4.9054  25.9752
 VWW  HD3   H  HCH2   0   0.301  10.6433   3.2789  25.7460
 VWW  HZ1   H  HCR6   0   0.258   7.9181   5.1688  26.9836
 VWW  HZ2   H  HCR6   0   0.250  10.1414   1.6031  27.7912
 VWW  HT1   H  HCR6   0   0.262   6.0556   4.3222  28.3573
 VWW  HT2   H  HCR6   0   0.254   8.2652   0.7373  29.1279
 VWW  HH    H  HCR6   0   0.253   6.2181   2.0980  29.4326
 VWW  H3    H  HNH1   0   0.404   8.2399   6.6958  28.8557
 VWW  HA2   H  HCH1   0   0.253   8.4169   7.7406  31.5683
 VWW  HG1   H  HCR6   0   0.248   5.6604   7.7420  29.0254
 VWW  HD1   H  HCR6   0   0.254   3.6806   6.2963  29.1982
 VWW  HE    H  HCR6   0   0.253   3.5014   4.6408  31.0319
 VWW  HD21  H  HCR6   0   0.253   5.3311   4.4490  32.6895
 VWW  HG21  H  HCR6   0   0.249   7.3144   5.8970  32.5145

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VWW  N     CA    single    1.458  0.019  1.458
 VWW  N     H     single    0.860  0.020  0.860
 VWW  N     H2    single    0.890  0.020  1.040
 VWW  CA    C     single    1.525  0.021  1.525
 VWW  CA    CB    single    1.521  0.033  1.521
 VWW  CA    HA    single    0.970  0.020  0.970
 VWW  C     O     deloc     1.231  0.020  1.231
 VWW  C     OXT   deloc     1.246  0.020  1.246
 VWW  CB    CG    single    1.519  0.020  1.519
 VWW  CB    HB2   single    0.970  0.020  1.090
 VWW  CB    HB3   single    0.970  0.020  1.090
 VWW  CG    CD    single    1.515  0.020  1.515
 VWW  CG    HG2   single    0.970  0.020  1.090
 VWW  CG    HG3   single    0.970  0.020  1.090
 VWW  CD    OE1   double    1.222  0.020  1.222
 VWW  N1    CA1   single    1.433  0.020  1.433
 VWW  N1    H1    single    0.860  0.020  1.020
 VWW  CA1   CB1   single    1.535  0.020  1.535
 VWW  CA1   C1    single    1.530  0.020  1.530
 VWW  CA1   HA1   single    0.970  0.020  1.090
 VWW  CB1   SG    single    1.806  0.020  1.806
 VWW  CB1   HB21  single    0.970  0.020  1.090
 VWW  CB1   HB31  single    0.970  0.020  1.090
 VWW  SG    CD1   single    1.824  0.020  1.824
 VWW  CD1   CE    single    1.500  0.020  1.500
 VWW  CD1   HD2   single    0.970  0.020  1.090
 VWW  CD1   HD3   single    0.970  0.020  1.090
 VWW  CE    CZ1   aromatic  1.392  0.020  1.392
 VWW  CE    CZ2   aromatic  1.394  0.020  1.394
 VWW  CZ1   CT1   aromatic  1.390  0.020  1.390
 VWW  CZ1   HZ1   single    0.930  0.020  1.080
 VWW  CZ2   CT2   aromatic  1.386  0.020  1.386
 VWW  CZ2   HZ2   single    0.930  0.020  1.080
 VWW  CT1   CH    aromatic  1.387  0.020  1.387
 VWW  CT1   HT1   single    0.930  0.020  1.080
 VWW  CT2   CH    aromatic  1.391  0.020  1.391
 VWW  CT2   HT2   single    0.930  0.020  1.080
 VWW  CH    HH    single    0.930  0.020  1.080
 VWW  C1    O1    double    1.222  0.020  1.222
 VWW  N2    CA2   single    1.447  0.020  1.447
 VWW  N2    H3    single    0.860  0.020  1.020
 VWW  CA2   CB2   single    1.511  0.020  1.511
 VWW  CA2   C2    single    1.559  0.020  1.559
 VWW  CA2   HA2   single    0.970  0.020  1.090
 VWW  CB2   CG1   aromatic  1.394  0.020  1.394
 VWW  CB2   CG2   aromatic  1.391  0.020  1.391
 VWW  CG1   CD11  aromatic  1.387  0.020  1.387
 VWW  CG1   HG1   single    0.930  0.020  1.080
 VWW  CD11  CE1   aromatic  1.389  0.020  1.389
 VWW  CD11  HD1   single    0.930  0.020  1.080
 VWW  CE1   CD2   aromatic  1.388  0.020  1.388
 VWW  CE1   HE    single    0.930  0.020  1.080
 VWW  CD2   CG2   aromatic  1.389  0.020  1.389
 VWW  CD2   HD21  single    0.930  0.020  1.080
 VWW  CG2   HG21  single    0.930  0.020  1.080
 VWW  C2    O2    deloc     1.244  0.020  1.244
 VWW  C2    OXT1  deloc     1.241  0.020  1.241
 VWW  CD    N1    single    1.350  0.020  1.350
 VWW  C1    N2    single    1.336  0.020  1.336

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VWW  H2    N     H     105.62  3.000
 VWW  H2    N     CA    109.73  3.000
 VWW  H     N     CA    114.00  3.000
 VWW  HA    CA    CB    109.00  3.000
 VWW  HA    CA    C     110.00  3.000
 VWW  CB    CA    C     110.50  1.500
 VWW  HA    CA    N     110.00  3.000
 VWW  CB    CA    N     110.40  1.500
 VWW  C     CA    N     111.00  2.800
 VWW  OXT   C     O     126.66  3.000
 VWW  OXT   C     CA    120.80  1.700
 VWW  O     C     CA    120.80  1.700
 VWW  HB3   CB    HB2   106.23  3.000
 VWW  HB3   CB    CG    110.32  3.000
 VWW  HB2   CB    CG    108.96  3.000
 VWW  HB3   CB    CA    108.75  3.000
 VWW  HB2   CB    CA    108.07  3.000
 VWW  CG    CB    CA    114.19  3.000
 VWW  HG3   CG    HG2   105.27  3.000
 VWW  HG3   CG    CD    108.56  3.000
 VWW  HG2   CG    CD    107.97  3.000
 VWW  HG3   CG    CB    110.18  3.000
 VWW  HG2   CG    CB    110.81  3.000
 VWW  CD    CG    CB    113.68  3.000
 VWW  N1    CD    OE1   122.83  3.000
 VWW  N1    CD    CG    113.82  3.000
 VWW  OE1   CD    CG    123.35  3.000
 VWW  H1    N1    CA1   117.12  3.000
 VWW  H1    N1    CD    118.73  3.000
 VWW  CA1   N1    CD    124.15  3.000
 VWW  HA1   CA1   C1    109.21  3.000
 VWW  HA1   CA1   CB1   109.41  3.000
 VWW  C1    CA1   CB1   108.26  3.000
 VWW  HA1   CA1   N1    107.58  3.000
 VWW  C1    CA1   N1    110.33  3.000
 VWW  CB1   CA1   N1    112.02  3.000
 VWW  HB31  CB1   HB21  107.07  3.000
 VWW  HB31  CB1   SG    109.36  3.000
 VWW  HB21  CB1   SG    105.73  3.000
 VWW  HB31  CB1   CA1   110.50  3.000
 VWW  HB21  CB1   CA1   109.73  3.000
 VWW  SG    CB1   CA1   114.12  3.000
 VWW  CD1   SG    CB1   101.14  3.000
 VWW  HD3   CD1   HD2   107.11  3.000
 VWW  HD3   CD1   CE    111.27  3.000
 VWW  HD2   CD1   CE    111.00  3.000
 VWW  HD3   CD1   SG    104.17  3.000
 VWW  HD2   CD1   SG    109.60  3.000
 VWW  CE    CD1   SG    113.33  3.000
 VWW  CZ2   CE    CZ1   118.66  3.000
 VWW  CZ2   CE    CD1   120.89  3.000
 VWW  CZ1   CE    CD1   120.44  3.000
 VWW  HZ1   CZ1   CT1   119.60  3.000
 VWW  HZ1   CZ1   CE    119.52  3.000
 VWW  CT1   CZ1   CE    120.88  3.000
 VWW  HZ2   CZ2   CT2   119.74  3.000
 VWW  HZ2   CZ2   CE    119.64  3.000
 VWW  CT2   CZ2   CE    120.62  3.000
 VWW  HT1   CT1   CH    120.21  3.000
 VWW  HT1   CT1   CZ1   119.80  3.000
 VWW  CH    CT1   CZ1   119.99  3.000
 VWW  HT2   CT2   CH    119.97  3.000
 VWW  HT2   CT2   CZ2   119.75  3.000
 VWW  CH    CT2   CZ2   120.27  3.000
 VWW  HH    CH    CT2   120.23  3.000
 VWW  HH    CH    CT1   120.20  3.000
 VWW  CT2   CH    CT1   119.57  3.000
 VWW  N2    C1    O1    124.20  3.000
 VWW  N2    C1    CA1   114.35  3.000
 VWW  O1    C1    CA1   121.32  3.000
 VWW  H3    N2    CA2   117.46  3.000
 VWW  H3    N2    C1    118.61  3.000
 VWW  CA2   N2    C1    123.14  3.000
 VWW  HA2   CA2   C2    107.76  3.000
 VWW  HA2   CA2   CB2   108.37  3.000
 VWW  C2    CA2   CB2   110.73  3.000
 VWW  HA2   CA2   N2    107.93  3.000
 VWW  C2    CA2   N2    113.76  3.000
 VWW  CB2   CA2   N2    108.13  3.000
 VWW  CG2   CB2   CG1   118.63  3.000
 VWW  CG2   CB2   CA2   120.80  3.000
 VWW  CG1   CB2   CA2   120.53  3.000
 VWW  HG1   CG1   CD11  119.48  3.000
 VWW  HG1   CG1   CB2   119.79  3.000
 VWW  CD11  CG1   CB2   120.73  3.000
 VWW  HD1   CD11  CE1   120.10  3.000
 VWW  HD1   CD11  CG1   119.72  3.000
 VWW  CE1   CD11  CG1   120.18  3.000
 VWW  HE    CE1   CD2   120.27  3.000
 VWW  HE    CE1   CD11  120.21  3.000
 VWW  CD2   CE1   CD11  119.53  3.000
 VWW  HD21  CD2   CG2   119.80  3.000
 VWW  HD21  CD2   CE1   120.09  3.000
 VWW  CG2   CD2   CE1   120.11  3.000
 VWW  HG21  CG2   CD2   119.56  3.000
 VWW  HG21  CG2   CB2   119.61  3.000
 VWW  CD2   CG2   CB2   120.83  3.000
 VWW  OXT1  C2    O2    128.37  3.000
 VWW  OXT1  C2    CA2   117.61  3.000
 VWW  O2    C2    CA2   114.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VWW  CONST_01  CH    CT1   CZ1   CE      0.00   0.0  0
 VWW  CONST_02  CH    CT2   CZ2   CE      0.00   0.0  0
 VWW  CONST_03  CT2   CZ2   CE    CZ1     0.00   0.0  0
 VWW  CONST_04  CT2   CH    CT1   CZ1     0.00   0.0  0
 VWW  CONST_05  CT1   CZ1   CE    CZ2     0.00   0.0  0
 VWW  CONST_06  CT1   CH    CT2   CZ2     0.00   0.0  0
 VWW  CONST_07  CE1   CD11  CG1   CB2     0.00   0.0  0
 VWW  CONST_08  CE1   CD2   CG2   CB2     0.00   0.0  0
 VWW  CONST_09  CD2   CG2   CB2   CG1     0.00   0.0  0
 VWW  CONST_10  CD2   CE1   CD11  CG1     0.00   0.0  0
 VWW  CONST_11  CG2   CB2   CG1   CD11    0.00   0.0  0
 VWW  CONST_12  CG2   CD2   CE1   CD11    0.00   0.0  0
 VWW  CONST_13  CT1   CZ1   CE    CD1   180.00   0.0  0
 VWW  CONST_14  CT2   CZ2   CE    CD1   180.00   0.0  0
 VWW  CONST_15  CD11  CG1   CB2   CA2   180.00   0.0  0
 VWW  CONST_16  CD2   CG2   CB2   CA2   180.00   0.0  0
 VWW  CONST_17  HT1   CT1   CZ1   CE    180.00   0.0  0
 VWW  CONST_18  HT2   CT2   CZ2   CE    180.00   0.0  0
 VWW  CONST_19  HZ2   CZ2   CE    CZ1   180.00   0.0  0
 VWW  CONST_20  HH    CH    CT1   CZ1   180.00   0.0  0
 VWW  CONST_21  HZ1   CZ1   CE    CZ2   180.00   0.0  0
 VWW  CONST_22  HD1   CD11  CG1   CB2   180.00   0.0  0
 VWW  CONST_23  HD21  CD2   CG2   CB2   180.00   0.0  0
 VWW  CONST_24  HG21  CG2   CB2   CG1   180.00   0.0  0
 VWW  CONST_25  HE    CE1   CD11  CG1   180.00   0.0  0
 VWW  CONST_26  HG1   CG1   CD11  CE1   180.00   0.0  0
 VWW  CONST_27  CA1   N1    CD    CG    180.00   0.0  0
 VWW  CONST_28  CA1   N1    CD    OE1     0.00   0.0  0
 VWW  CONST_29  CA2   N2    C1    CA1   180.00   0.0  0
 VWW  CONST_30  CA2   N2    C1    O1      0.00   0.0  0
 VWW  CONST_31  H1    N1    CD    CG      0.00   0.0  0
 VWW  CONST_32  H3    N2    C1    CA1     0.00   0.0  0
 VWW  Var_01    CZ1   CE    CD1   SG    113.99  30.0  2
 VWW  Var_02    CE    CD1   SG    CB1   -54.13  30.0  3
 VWW  Var_03    CD    CG    CB    CA    174.78  30.0  3
 VWW  Var_04    OE1   CD    CG    CB      3.47  30.0  3
 VWW  Var_05    HB21  CB1   SG    CD1   171.17  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VWW  chir_01  CA   N   C    CB  positiv
 VWW  chir_02  CA1  N1  CB1  C1  negativ
 VWW  chir_03  CA2  N2  CB2  C2  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VWW  plan-1  CD1   0.020
 VWW  plan-1  CE    0.020
 VWW  plan-1  CZ1   0.020
 VWW  plan-1  CZ2   0.020
 VWW  plan-1  CT1   0.020
 VWW  plan-1  CT2   0.020
 VWW  plan-1  CH    0.020
 VWW  plan-1  HZ1   0.020
 VWW  plan-1  HZ2   0.020
 VWW  plan-1  HT1   0.020
 VWW  plan-1  HT2   0.020
 VWW  plan-1  HH    0.020
 VWW  plan-2  CA2   0.020
 VWW  plan-2  CB2   0.020
 VWW  plan-2  CG1   0.020
 VWW  plan-2  CD11  0.020
 VWW  plan-2  CE1   0.020
 VWW  plan-2  CD2   0.020
 VWW  plan-2  CG2   0.020
 VWW  plan-2  HG1   0.020
 VWW  plan-2  HD1   0.020
 VWW  plan-2  HE    0.020
 VWW  plan-2  HD21  0.020
 VWW  plan-2  HG21  0.020
 VWW  plan-3  CG    0.020
 VWW  plan-3  CD    0.020
 VWW  plan-3  OE1   0.020
 VWW  plan-3  N1    0.020
 VWW  plan-3  CA1   0.020
 VWW  plan-3  H1    0.020
 VWW  plan-4  CA1   0.020
 VWW  plan-4  C1    0.020
 VWW  plan-4  O1    0.020
 VWW  plan-4  N2    0.020
 VWW  plan-4  CA2   0.020
 VWW  plan-4  H3    0.020
 VWW  plan-5  CA    0.020
 VWW  plan-5  C     0.020
 VWW  plan-5  O     0.020
 VWW  plan-5  OXT   0.020
 VWW  plan-6  CA2   0.020
 VWW  plan-6  C2    0.020
 VWW  plan-6  O2    0.020
 VWW  plan-6  OXT1  0.020

