# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 07:32:37 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: L-gamma-glutamyl-S-[(9S,10S)-10-hydroxy-9,10-dihydrophenanthren-9-yl]-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CS[C@@H]1[C@@H](O)c2ccccc2c3ccccc13)C(=O)NCC(O)=O)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
 GPS  GPS  L-gamma-glutamyl-S-[(9S,10S)-10-hydroxy-9,10-dihydrophenanthren-9-yl]-L-cysteinylglycine  ligand  60  35  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GPS
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
 GPS  C1    C  C      0   0.386  13.6081  17.1372  25.7832
 GPS  N1    N  NH2    0  -0.804  14.6510  15.0416  24.9352
 GPS  C2    C  C      0   0.565  17.0692  15.8522  32.7226
 GPS  N2    N  NH1    0  -0.652  16.1834  16.7172  30.5697
 GPS  C3    C  C      0   0.401  17.3395  12.6860  33.1904
 GPS  O5    O  OH1    0  -0.650  21.3937  19.2125  30.9709
 GPS  O11   O  O      0  -0.600  13.9281  17.6738  24.7058
 GPS  O12   O  OC    -1  -0.612  12.8196  17.5924  26.6388
 GPS  O31   O  O      0  -0.595  18.0817  12.8580  32.2100
 GPS  O32   O  OC    -1  -0.613  17.3824  11.7783  34.0422
 GPS  CA1   C  CH1    0  -0.165  14.2645  15.7801  26.1324
 GPS  CA2   C  CH1    0  -0.202  17.1769  16.8822  31.5934
 GPS  CA3   C  CH2    0  -0.441  16.1809  13.6961  33.3950
 GPS  CA4   C  CH1    0  -0.544  19.1239  19.3232  30.3819
 GPS  CA5   C  CH1    0  -0.006  20.1381  19.6183  31.4754
 GPS  CB1   C  CH2    0  -0.422  15.5266  15.9900  26.9769
 GPS  CB2   C  CH2    0  -0.588  17.1624  18.2969  32.1759
 GPS  CB4   C  CR6    0   0.104  19.3246  20.2295  29.2022
 GPS  CB5   C  CR6    0   0.052  20.1271  21.0859  31.8137
 GPS  CD1   C  C      0   0.581  16.4741  16.5735  29.2535
 GPS  CD4   C  CR16   0  -0.258  19.2471  20.6019  26.8209
 GPS  CD5   C  CR16   0  -0.257  20.3579  22.8603  33.4327
 GPS  OE1   O  O      0  -0.482  17.6157  16.4366  28.8418
 GPS  CE4   C  CR16   0  -0.243  19.6864  21.9050  27.0153
 GPS  CE5   C  CR16   0  -0.243  20.1834  23.7958  32.4233
 GPS  CG1   C  CH2    0  -0.594  15.2634  16.5915  28.3487
 GPS  SG2   S  S2     0   0.030  17.4060  19.5982  30.9413
 GPS  CG4   C  CR16   0  -0.297  19.0688  19.7711  27.9162
 GPS  CG5   C  CR16   0  -0.313  20.3250  21.5079  33.1199
 GPS  CH4   C  CR6    0   0.132  19.7416  21.5502  29.4098
 GPS  CH5   C  CR6    0   0.103  19.9644  22.0253  30.7875
 GPS  CZ4   C  CR16   0  -0.333  19.9311  22.3714  28.2969
 GPS  CZ5   C  CR16   0  -0.331  19.9838  23.3805  31.1146
 GPS  HN1   H  HNH2   0   0.329  14.8827  14.0914  25.1995
 GPS  HN1A  H  HNH2   0   0.332  13.8594  14.9669  24.3091
 GPS  HN2   H  HNH1   0   0.404  15.2277  16.9329  30.8156
 GPS  HN3   H  HNH1   0   0.396  15.7969  14.7590  31.6138
 GPS  HO5   H  HOH1   0   0.452  22.0589  19.3793  31.6469
 GPS  HA1   H  HCH1   0   0.176  13.5435  15.2243  26.7523
 GPS  HA2   H  HCH1   0   0.298  18.1496  16.6928  31.1333
 GPS  HA3   H  HCH2   0   0.249  15.2330  13.1815  33.2236
 GPS  HA3A  H  HCH2   0   0.238  16.1665  14.0274  34.4342
 GPS  HA4   H  HCH1   0   0.309  19.2199  18.2833  30.0616
 GPS  HA5   H  HCH1   0   0.238  19.8826  19.0449  32.3752
 GPS  HB1   H  HCH2   0   0.221  16.0127  15.0167  27.1010
 GPS  HB1A  H  HCH2   0   0.218  16.2272  16.6135  26.4155
 GPS  HB2   H  HCH2   0   0.295  16.1834  18.5130  32.6123
 GPS  HB2A  H  HCH2   0   0.289  17.8928  18.3868  32.9773
 GPS  HD4   H  HCR6   0   0.256  19.0522  20.2330  25.8224
 GPS  HD5   H  HCR6   0   0.255  20.5093  23.1796  34.4555
 GPS  HE4   H  HCR6   0   0.257  19.8433  22.5594  26.1677
 GPS  HE5   H  HCR6   0   0.257  20.1917  24.8533  32.6533
 GPS  HG1   H  HCH2   0   0.274  14.9364  17.6312  28.2598
 GPS  HG1A  H  HCH2   0   0.250  14.4402  16.0676  28.8430
 GPS  HG4   H  HCR6   0   0.256  18.7311  18.7509  27.7756
 GPS  HG5   H  HCR6   0   0.255  20.4473  20.7684  33.9033
 GPS  HZ4   H  HCR6   0   0.250  20.2872  23.3857  28.4223
 GPS  HZ5   H  HCR6   0   0.250  19.8221  24.1296  30.3503
 GPS  O2    O  O      0  -0.500  17.7437  15.9898  33.7351
 GPS  N3    N  NH1    0  -0.612  16.2222  14.8414  32.5230

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
 GPS  O11  C1    deloc     1.246  0.020  1.246
 GPS  C1   CA1   single    1.547  0.020  1.547
 GPS  C1   O12   deloc     1.249  0.020  1.249
 GPS  N1   CA1   single    1.459  0.020  1.459
 GPS  N1   HN1   single    0.890  0.020  1.040
 GPS  N1   HN1A  single    0.890  0.020  1.040
 GPS  CA2  C2    single    1.532  0.020  1.532
 GPS  C2   N3    single    1.334  0.020  1.334
 GPS  C2   O2    double    1.224  0.020  1.224
 GPS  CD1  N2    single    1.356  0.020  1.356
 GPS  N2   CA2   single    1.436  0.020  1.436
 GPS  N2   HN2   single    0.860  0.020  1.020
 GPS  O31  C3    deloc     1.242  0.020  1.242
 GPS  CA3  C3    single    1.551  0.020  1.551
 GPS  C3   O32   deloc     1.246  0.020  1.246
 GPS  N3   CA3   single    1.440  0.020  1.440
 GPS  N3   HN3   single    0.860  0.020  1.020
 GPS  O5   CA5   single    1.413  0.020  1.413
 GPS  O5   HO5   single    0.850  0.020  0.980
 GPS  CA1  CB1   single    1.533  0.020  1.533
 GPS  CA1  HA1   single    0.970  0.020  1.090
 GPS  CA2  CB2   single    1.530  0.020  1.530
 GPS  CA2  HA2   single    0.970  0.020  1.090
 GPS  CA3  HA3   single    0.970  0.020  1.090
 GPS  CA3  HA3A  single    0.970  0.020  1.090
 GPS  CB4  CA4   single    1.501  0.020  1.501
 GPS  CA4  SG2   single    1.827  0.020  1.827
 GPS  CA4  CA5   single    1.520  0.020  1.520
 GPS  CA4  HA4   single    0.970  0.020  1.090
 GPS  CA5  CB5   single    1.506  0.020  1.506
 GPS  CA5  HA5   single    0.970  0.020  1.090
 GPS  CB1  CG1   single    1.521  0.020  1.521
 GPS  CB1  HB1   single    0.970  0.020  1.090
 GPS  CB1  HB1A  single    0.970  0.020  1.090
 GPS  SG2  CB2   single    1.810  0.020  1.810
 GPS  CB2  HB2   single    0.970  0.020  1.090
 GPS  CB2  HB2A  single    0.970  0.020  1.090
 GPS  CG4  CB4   aromatic  1.389  0.020  1.389
 GPS  CB4  CH4   aromatic  1.400  0.020  1.400
 GPS  CH5  CB5   aromatic  1.401  0.020  1.401
 GPS  CB5  CG5   aromatic  1.387  0.020  1.387
 GPS  CG1  CD1   single    1.512  0.020  1.512
 GPS  OE1  CD1   double    1.221  0.020  1.221
 GPS  CD4  CG4   aromatic  1.386  0.020  1.386
 GPS  CD4  CE4   aromatic  1.389  0.020  1.389
 GPS  CD4  HD4   single    0.930  0.020  1.080
 GPS  CG5  CD5   aromatic  1.388  0.020  1.388
 GPS  CE5  CD5   aromatic  1.387  0.020  1.387
 GPS  CD5  HD5   single    0.930  0.020  1.080
 GPS  CE4  CZ4   aromatic  1.386  0.020  1.386
 GPS  CE4  HE4   single    0.930  0.020  1.080
 GPS  CZ5  CE5   aromatic  1.387  0.020  1.387
 GPS  CE5  HE5   single    0.930  0.020  1.080
 GPS  CG1  HG1   single    0.970  0.020  1.090
 GPS  CG1  HG1A  single    0.970  0.020  1.090
 GPS  CG4  HG4   single    0.930  0.020  1.080
 GPS  CG5  HG5   single    0.930  0.020  1.080
 GPS  CZ4  CH4   aromatic  1.396  0.020  1.396
 GPS  CH4  CH5   aromatic  1.474  0.020  1.474
 GPS  CH5  CZ5   aromatic  1.394  0.020  1.394
 GPS  CZ4  HZ4   single    0.930  0.020  1.080
 GPS  CZ5  HZ5   single    0.930  0.020  1.080

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
 GPS  CA1   C1   O12  115.64  3.000
 GPS  O12   C1   O11  126.70  3.000
 GPS  CA1   C1   O11  117.65  3.000
 GPS  HN1A  N1   HN1  105.72  3.000
 GPS  HN1A  N1   CA1  109.75  3.000
 GPS  HN1   N1   CA1  108.75  3.000
 GPS  CA2   C2   N3   116.35  3.000
 GPS  N3    C2   O2   123.97  3.000
 GPS  CA2   C2   O2   119.68  3.000
 GPS  HN2   N2   CD1  117.52  3.000
 GPS  HN2   N2   CA2  117.16  3.000
 GPS  CD1   N2   CA2  123.77  3.000
 GPS  CA3   C3   O32  114.22  3.000
 GPS  O32   C3   O31  128.34  3.000
 GPS  CA3   C3   O31  117.42  3.000
 GPS  HO5   O5   CA5  108.28  3.000
 GPS  HA1   CA1  CB1  107.34  3.000
 GPS  HA1   CA1  N1   112.33  3.000
 GPS  CB1   CA1  N1   107.65  3.000
 GPS  HA1   CA1  C1   106.97  3.000
 GPS  CB1   CA1  C1   110.70  3.000
 GPS  N1    CA1  C1   111.79  3.000
 GPS  HA2   CA2  CB2  109.22  3.000
 GPS  HA2   CA2  N2   107.21  3.000
 GPS  CB2   CA2  N2   111.79  3.000
 GPS  HA2   CA2  C2   104.86  3.000
 GPS  CB2   CA2  C2   109.90  3.000
 GPS  N2    CA2  C2   113.54  3.000
 GPS  HA3A  CA3  HA3  106.33  3.000
 GPS  HA3A  CA3  N3   109.61  3.000
 GPS  HA3   CA3  N3   107.73  3.000
 GPS  HA3A  CA3  C3   109.48  3.000
 GPS  HA3   CA3  C3   108.71  3.000
 GPS  N3    CA3  C3   114.63  3.000
 GPS  HA4   CA4  SG2  108.40  3.000
 GPS  HA4   CA4  CB4  109.43  3.000
 GPS  SG2   CA4  CB4  105.99  3.000
 GPS  HA4   CA4  CA5  109.69  3.000
 GPS  SG2   CA4  CA5  112.19  3.000
 GPS  CB4   CA4  CA5  111.03  3.000
 GPS  HA5   CA5  CB5  108.86  3.000
 GPS  HA5   CA5  CA4  109.46  3.000
 GPS  CB5   CA5  CA4  110.23  3.000
 GPS  HA5   CA5  O5   110.47  3.000
 GPS  CB5   CA5  O5   111.51  3.000
 GPS  CA4   CA5  O5   106.28  3.000
 GPS  HB1A  CB1  HB1  106.30  3.000
 GPS  HB1A  CB1  CG1  110.40  3.000
 GPS  HB1   CB1  CG1  109.03  3.000
 GPS  HB1A  CB1  CA1  108.84  3.000
 GPS  HB1   CB1  CA1  107.83  3.000
 GPS  CG1   CB1  CA1  114.11  3.000
 GPS  HB2A  CB2  HB2  106.91  3.000
 GPS  HB2A  CB2  SG2  110.64  3.000
 GPS  HB2   CB2  SG2  104.51  3.000
 GPS  HB2A  CB2  CA2  110.52  3.000
 GPS  HB2   CB2  CA2  110.07  3.000
 GPS  SG2   CB2  CA2  113.81  3.000
 GPS  CH4   CB4  CG4  120.22  3.000
 GPS  CH4   CB4  CA4  119.52  3.000
 GPS  CG4   CB4  CA4  120.25  3.000
 GPS  CH5   CB5  CG5  120.17  3.000
 GPS  CG5   CB5  CA5  120.47  3.000
 GPS  CH5   CB5  CA5  119.33  3.000
 GPS  CG1   CD1  OE1  123.25  3.000
 GPS  OE1   CD1  N2   122.66  3.000
 GPS  CG1   CD1  N2   114.09  3.000
 GPS  HD4   CD4  CG4  120.11  3.000
 GPS  HD4   CD4  CE4  120.39  3.000
 GPS  CG4   CD4  CE4  119.50  3.000
 GPS  HD5   CD5  CG5  120.24  3.000
 GPS  HD5   CD5  CE5  120.42  3.000
 GPS  CG5   CD5  CE5  119.34  3.000
 GPS  HE4   CE4  CZ4  119.69  3.000
 GPS  HE4   CE4  CD4  120.24  3.000
 GPS  CZ4   CE4  CD4  120.07  3.000
 GPS  HE5   CE5  CZ5  119.60  3.000
 GPS  HE5   CE5  CD5  120.22  3.000
 GPS  CZ5   CE5  CD5  120.17  3.000
 GPS  HG1A  CG1  HG1  105.49  3.000
 GPS  HG1A  CG1  CD1  109.06  3.000
 GPS  HG1   CG1  CD1  107.42  3.000
 GPS  HG1A  CG1  CB1  110.40  3.000
 GPS  HG1   CG1  CB1  110.76  3.000
 GPS  CD1   CG1  CB1  113.37  3.000
 GPS  CB2   SG2  CA4  103.13  3.000
 GPS  HG4   CG4  CD4  120.12  3.000
 GPS  HG4   CG4  CB4  119.22  3.000
 GPS  CD4   CG4  CB4  120.67  3.000
 GPS  HG5   CG5  CD5  119.93  3.000
 GPS  HG5   CG5  CB5  119.28  3.000
 GPS  CD5   CG5  CB5  120.79  3.000
 GPS  CZ4   CH4  CH5  122.34  3.000
 GPS  CH5   CH4  CB4  119.17  3.000
 GPS  CZ4   CH4  CB4  118.49  3.000
 GPS  CZ5   CH5  CH4  122.31  3.000
 GPS  CZ5   CH5  CB5  118.58  3.000
 GPS  CH4   CH5  CB5  119.08  3.000
 GPS  HZ4   CZ4  CH4  120.24  3.000
 GPS  HZ4   CZ4  CE4  118.73  3.000
 GPS  CH4   CZ4  CE4  121.03  3.000
 GPS  HZ5   CZ5  CH5  120.33  3.000
 GPS  HZ5   CZ5  CE5  118.72  3.000
 GPS  CH5   CZ5  CE5  120.94  3.000
 GPS  HN3   N3   CA3  118.00  3.000
 GPS  HN3   N3   C2   117.72  3.000
 GPS  CA3   N3   C2   122.03  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
 GPS  CONST_01  CE4  CD4  CG4  CB4     0.00   0.0  0
 GPS  CONST_02  CE4  CZ4  CH4  CB4     0.00   0.0  0
 GPS  CONST_06  CE5  CZ5  CH5  CB5     0.00   0.0  0
 GPS  CONST_07  CE5  CD5  CG5  CB5     0.00   0.0  0
 GPS  CONST_08  CH4  CB4  CG4  CD4     0.00   0.0  0
 GPS  CONST_09  CH4  CZ4  CE4  CD4     0.00   0.0  0
 GPS  CONST_10  CH5  CB5  CG5  CD5     0.00   0.0  0
 GPS  CONST_11  CH5  CZ5  CE5  CD5     0.00   0.0  0
 GPS  CONST_12  CH5  CH4  CZ4  CE4   180.00   0.0  0
 GPS  CONST_13  CH4  CH5  CZ5  CE5   180.00   0.0  0
 GPS  CONST_14  CZ4  CH4  CB4  CG4     0.00   0.0  0
 GPS  CONST_15  CH5  CH4  CB4  CG4   180.00   0.0  0
 GPS  CONST_16  CZ4  CE4  CD4  CG4     0.00   0.0  0
 GPS  CONST_17  CH4  CH5  CB5  CG5   180.00   0.0  0
 GPS  CONST_18  CZ5  CH5  CB5  CG5     0.00   0.0  0
 GPS  CONST_19  CZ5  CE5  CD5  CG5     0.00   0.0  0
 GPS  CONST_21  HG4  CG4  CB4  CA4     0.00   0.0  0
 GPS  CONST_22  HG5  CG5  CB5  CA5     0.00   0.0  0
 GPS  CONST_23  HD4  CD4  CG4  CB4   180.00   0.0  0
 GPS  CONST_24  HZ4  CZ4  CH4  CB4   180.00   0.0  0
 GPS  CONST_25  HZ5  CZ5  CH5  CB5   180.00   0.0  0
 GPS  CONST_26  HD5  CD5  CG5  CB5   180.00   0.0  0
 GPS  CONST_27  HE4  CE4  CD4  CG4   180.00   0.0  0
 GPS  CONST_28  HE5  CE5  CD5  CG5   180.00   0.0  0
 GPS  CONST_29  CA3  N3   C2   O2      0.00   0.0  0
 GPS  CONST_30  CA3  N3   C2   CA2   180.00   0.0  0
 GPS  CONST_31  CG1  CD1  N2   CA2   180.00   0.0  0
 GPS  CONST_32  OE1  CD1  N2   CA2     0.00   0.0  0
 GPS  CONST_33  HN3  N3   C2   O2    180.00   0.0  0
 GPS  CONST_34  HN2  N2   CD1  OE1   180.00   0.0  0
 GPS  Var_01    HB2  CB2  SG2  CA4   173.46  30.0  3
 GPS  Var_02    C3   CA3  N3   C2    -76.33  30.0  3
 GPS  Var_03    CB1  CG1  CD1  N2   -161.13  30.0  2
 GPS  Var_04    O31  C3   CA3  N3     -8.79  30.0  3
 GPS  Var_05    CD1  CG1  CB1  CA1   170.14  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
 GPS  chir_01  CA1  C1   N1   CB1  negativ
 GPS  chir_02  CA2  N2   C2   CB2  positiv
 GPS  chir_03  CA4  SG2  CA5  CB4  positiv
 GPS  chir_04  CA5  O5   CA4  CB5  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
 GPS  plan-1  C2   0.020
 GPS  plan-1  CA2  0.020
 GPS  plan-1  CA3  0.020
 GPS  plan-1  HN3  0.020
 GPS  plan-1  O2   0.020
 GPS  plan-1  N3   0.020
 GPS  plan-2  CA4  0.020
 GPS  plan-2  CB4  0.020
 GPS  plan-2  CD4  0.020
 GPS  plan-2  CE4  0.020
 GPS  plan-2  CG4  0.020
 GPS  plan-2  CH4  0.020
 GPS  plan-2  CH5  0.020
 GPS  plan-2  CZ4  0.020
 GPS  plan-2  HD4  0.020
 GPS  plan-2  HE4  0.020
 GPS  plan-2  HG4  0.020
 GPS  plan-2  HZ4  0.020
 GPS  plan-3  CA5  0.020
 GPS  plan-3  CB5  0.020
 GPS  plan-3  CD5  0.020
 GPS  plan-3  CE5  0.020
 GPS  plan-3  CG5  0.020
 GPS  plan-3  CH4  0.020
 GPS  plan-3  CH5  0.020
 GPS  plan-3  CZ5  0.020
 GPS  plan-3  HD5  0.020
 GPS  plan-3  HE5  0.020
 GPS  plan-3  HG5  0.020
 GPS  plan-3  HZ5  0.020
 GPS  plan-4  N2   0.020
 GPS  plan-4  CA2  0.020
 GPS  plan-4  CD1  0.020
 GPS  plan-4  OE1  0.020
 GPS  plan-4  CG1  0.020
 GPS  plan-4  HN2  0.020
 GPS  plan-5  C1   0.020
 GPS  plan-5  O11  0.020
 GPS  plan-5  O12  0.020
 GPS  plan-5  CA1  0.020
 GPS  plan-6  C3   0.020
 GPS  plan-6  O31  0.020
 GPS  plan-6  O32  0.020
 GPS  plan-6  CA3  0.020

