# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 13:09:16 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: L-gamma-glutamyl-S-{(1S)-2-hydroxy-1-[(4-nitrophenoxy)methyl]ethyl}-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CS[C@@H](CO)COc1ccc(cc1)[N+]([O-])=O)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
 EPY  EPY  L-gamma-glutamyl-S-{(1S)-2-hydroxy-1-[(4-nitrophenoxy)methyl]ethyl}-L-cysteinylglycine  ligand  60  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EPY
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
 EPY  S     S  S2     0   0.022  88.7200  58.1990  45.8776
 EPY  C2A   C  CH1    0  -0.209  91.4534  57.8410  46.2070
 EPY  C3A   C  C      0   0.568  92.5555  57.0857  46.9454
 EPY  N4A   N  NH1    0  -0.616  93.3963  57.7899  47.7241
 EPY  C1A   C  CH2    0  -0.580  90.0904  57.3042  46.6458
 EPY  C5A   C  CH2    0  -0.456  93.4288  59.2102  47.9413
 EPY  C6A   C  C      0   0.540  92.4072  59.7714  48.9127
 EPY  O6A   O  OH1    0  -0.579  91.5454  58.8681  49.3518
 EPY  O3A   O  O      0  -0.479  92.6479  55.8756  46.8136
 EPY  O7A   O  O      0  -0.432  92.3909  60.9317  49.2308
 EPY  C6B   C  C      0   0.551  91.1055  59.2467  39.4217
 EPY  O7B   O  O      0  -0.454  90.0295  58.9362  39.8729
 EPY  C5B   C  CH1    0  -0.225  92.4465  59.0271  40.1305
 EPY  N5B   N  NH2    0  -0.840  93.4610  59.7532  39.3741
 EPY  C4B   C  CH2    0  -0.451  92.4141  59.3851  41.6186
 EPY  C3B   C  CH2    0  -0.592  91.6409  58.4006  42.4851
 EPY  O2B   O  O      0  -0.489  91.7349  59.9155  44.3452
 EPY  N1B   N  NH1    0  -0.627  91.6462  57.7016  44.7894
 EPY  C1C   C  CH1    0  -0.448  88.8265  59.7839  46.7686
 EPY  C3C   C  CH2    0  -0.126  88.2518  60.8424  45.8373
 EPY  O2C   O  OH1    0  -0.659  88.2101  62.0718  46.5154
 EPY  C2C   C  CH2    0  -0.164  88.1106  59.6791  48.1087
 EPY  O3C   O  O2     0  -0.453  88.6984  60.6254  48.9931
 EPY  C4C   C  CR6    0   0.413  88.1993  60.7862  50.2174
 EPY  C9C   C  CR16   0  -0.345  88.8845  61.6860  51.0441
 EPY  C8C   C  CR16   0  -0.251  88.4451  61.9276  52.3248
 EPY  C7C   C  CR6    0   0.227  87.3134  61.2658  52.7955
 EPY  C6C   C  CR16   0  -0.251  86.6313  60.3643  51.9918
 EPY  C5C   C  CR16   0  -0.373  87.0720  60.1207  50.7044
 EPY  N8C   N  N      1   0.328  86.8470  61.5192  54.1379
 EPY  O8C   O  O     -1  -0.390  87.4574  62.3165  54.8146
 EPY  O9C   O  O      0  -0.390  85.8657  60.9257  54.5266
 EPY  H3A1  H  HCH1   0   0.271  91.4961  58.9064  46.4155
 EPY  HNA4  H  HNH1   0   0.411  94.0880  57.2454  48.2194
 EPY  H1A1  H  HCH2   0   0.289  89.9950  57.3401  47.7322
 EPY  H1A2  H  HCH2   0   0.304  89.9769  56.2608  46.3488
 EPY  H5A1  H  HCH2   0   0.335  94.4132  59.4628  48.3359
 EPY  H5A2  H  HCH2   0   0.303  93.3462  59.7731  47.0082
 EPY  HOA6  H  HOH1   0   0.483  90.9189  59.2834  49.9635
 EPY  HOB6  H  HOH1   0   0.477  92.2153  59.9627  38.1563
 EPY  H5B1  H  HCH1   0   0.294  92.6602  57.9574  40.0287
 EPY  HN51  H  HNH2   0   0.386  94.3216  59.2285  39.3070
 EPY  HN52  H  HNH2   0   0.380  93.6808  60.6410  39.8094
 EPY  H4B1  H  HCH2   0   0.254  93.4530  59.4091  41.9562
 EPY  H4B2  H  HCH2   0   0.249  92.0218  60.3964  41.7460
 EPY  H3B1  H  HCH2   0   0.288  90.5875  58.3793  42.1977
 EPY  H3B2  H  HCH2   0   0.257  92.0185  57.3863  42.3312
 EPY  HNB1  H  HNH1   0   0.404  91.5813  56.7737  44.3991
 EPY  H1C1  H  HCH1   0   0.280  89.8819  60.0089  46.9449
 EPY  H3C1  H  HCH2   0   0.222  88.8833  60.8853  44.9423
 EPY  H3C2  H  HCH2   0   0.205  87.2494  60.5267  45.5156
 EPY  HOC2  H  HOH1   0   0.458  87.7772  62.7098  45.9406
 EPY  H2C1  H  HCH2   0   0.254  87.0397  59.8677  47.9797
 EPY  H2C2  H  HCH2   0   0.252  88.2224  58.6750  48.5299
 EPY  H9C1  H  HCR6   0   0.284  89.7661  62.1882  50.6674
 EPY  H8C1  H  HCR6   0   0.298  88.9839  62.6252  52.9488
 EPY  H6C1  H  HCR6   0   0.301  85.7560  59.8446  52.3535
 EPY  H5C1  H  HCR6   0   0.301  86.5283  59.4115  50.0975
 EPY  C2B   C  C      0   0.586  91.6874  58.7599  43.9514
 EPY  O6B   O  OH1    0  -0.595  91.2344  59.7945  38.2332

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
 EPY  S    C1A   single    1.808  0.020  1.808
 EPY  S    C1C   single    1.821  0.020  1.821
 EPY  C2A  C3A   single    1.527  0.020  1.527
 EPY  C2A  C1A   single    1.529  0.020  1.529
 EPY  C2A  N1B   single    1.438  0.020  1.438
 EPY  C2A  H3A1  single    0.970  0.020  1.090
 EPY  C3A  N4A   single    1.345  0.020  1.345
 EPY  C3A  O3A   double    1.221  0.020  1.221
 EPY  N4A  C5A   single    1.437  0.020  1.437
 EPY  N4A  HNA4  single    0.860  0.020  1.020
 EPY  C1A  H1A1  single    0.970  0.020  1.090
 EPY  C1A  H1A2  single    0.970  0.020  1.090
 EPY  C5A  C6A   single    1.517  0.020  1.517
 EPY  C5A  H5A1  single    0.970  0.020  1.090
 EPY  C5A  H5A2  single    0.970  0.020  1.090
 EPY  C6A  O6A   single    1.323  0.020  1.323
 EPY  C6A  O7A   double    1.203  0.020  1.203
 EPY  O6A  HOA6  single    0.850  0.020  0.980
 EPY  O6B  C6B   single    1.315  0.020  1.315
 EPY  O6B  HOB6  single    0.850  0.020  0.980
 EPY  C6B  O7B   double    1.207  0.020  1.207
 EPY  C6B  C5B   single    1.533  0.020  1.533
 EPY  C5B  N5B   single    1.459  0.020  1.459
 EPY  C5B  C4B   single    1.531  0.020  1.531
 EPY  C5B  H5B1  single    0.970  0.020  1.090
 EPY  N5B  HN51  single    0.890  0.020  1.040
 EPY  N5B  HN52  single    0.890  0.020  1.040
 EPY  C4B  C3B   single    1.522  0.020  1.522
 EPY  C4B  H4B1  single    0.970  0.020  1.090
 EPY  C4B  H4B2  single    0.970  0.020  1.090
 EPY  C3B  C2B   single    1.510  0.020  1.510
 EPY  C3B  H3B1  single    0.970  0.020  1.090
 EPY  C3B  H3B2  single    0.970  0.020  1.090
 EPY  C2B  O2B   double    1.222  0.020  1.222
 EPY  C2B  N1B   single    1.351  0.020  1.351
 EPY  N1B  HNB1  single    0.860  0.020  1.020
 EPY  C1C  C3C   single    1.523  0.020  1.523
 EPY  C1C  C2C   single    1.523  0.020  1.523
 EPY  C1C  H1C1  single    0.970  0.020  1.090
 EPY  C3C  O2C   single    1.405  0.020  1.405
 EPY  C3C  H3C1  single    0.970  0.020  1.090
 EPY  C3C  H3C2  single    0.970  0.020  1.090
 EPY  O2C  HOC2  single    0.850  0.020  0.980
 EPY  C2C  O3C   single    1.422  0.020  1.422
 EPY  C2C  H2C1  single    0.970  0.020  1.090
 EPY  C2C  H2C2  single    0.970  0.020  1.090
 EPY  O3C  C4C   single    1.332  0.020  1.332
 EPY  C4C  C9C   aromatic  1.401  0.020  1.401
 EPY  C4C  C5C   aromatic  1.397  0.020  1.397
 EPY  C9C  C8C   aromatic  1.375  0.020  1.375
 EPY  C9C  H9C1  single    0.930  0.020  1.080
 EPY  C8C  C7C   aromatic  1.393  0.020  1.393
 EPY  C8C  H8C1  single    0.930  0.020  1.080
 EPY  C7C  C6C   aromatic  1.387  0.020  1.387
 EPY  C7C  N8C   single    1.444  0.020  1.444
 EPY  C6C  C5C   aromatic  1.382  0.020  1.382
 EPY  C6C  H6C1  single    0.930  0.020  1.080
 EPY  C5C  H5C1  single    0.930  0.020  1.080
 EPY  N8C  O8C   single    1.211  0.020  1.211
 EPY  N8C  O9C   double    1.211  0.020  1.211

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
 EPY  C1C   S    C1A   100.28  3.000
 EPY  H3A1  C2A  N1B   106.20  3.000
 EPY  H3A1  C2A  C1A   108.92  3.000
 EPY  N1B   C2A  C1A   111.63  3.000
 EPY  H3A1  C2A  C3A   111.35  3.000
 EPY  N1B   C2A  C3A   109.40  3.000
 EPY  C1A   C2A  C3A   109.33  3.000
 EPY  O3A   C3A  N4A   122.28  3.000
 EPY  O3A   C3A  C2A   119.53  3.000
 EPY  N4A   C3A  C2A   118.18  3.000
 EPY  HNA4  N4A  C5A   116.30  3.000
 EPY  HNA4  N4A  C3A   115.45  3.000
 EPY  C5A   N4A  C3A   128.25  3.000
 EPY  H1A2  C1A  H1A1  107.06  3.000
 EPY  H1A2  C1A  C2A   110.51  3.000
 EPY  H1A1  C1A  C2A   110.62  3.000
 EPY  H1A2  C1A  S     106.19  3.000
 EPY  H1A1  C1A  S     109.91  3.000
 EPY  C2A   C1A  S     112.33  3.000
 EPY  H5A2  C5A  H5A1  104.95  3.000
 EPY  H5A2  C5A  C6A   107.78  3.000
 EPY  H5A1  C5A  C6A   106.89  3.000
 EPY  H5A2  C5A  N4A   112.22  3.000
 EPY  H5A1  C5A  N4A   107.70  3.000
 EPY  C6A   C5A  N4A   116.55  3.000
 EPY  O7A   C6A  O6A   124.17  3.000
 EPY  O7A   C6A  C5A   122.34  3.000
 EPY  O6A   C6A  C5A   113.48  3.000
 EPY  HOA6  O6A  C6A   109.75  3.000
 EPY  C5B   C6B  O7B   124.76  3.000
 EPY  C5B   C6B  O6B   113.08  3.000
 EPY  O7B   C6B  O6B   122.15  3.000
 EPY  H5B1  C5B  C4B   108.83  3.000
 EPY  H5B1  C5B  N5B   107.59  3.000
 EPY  C4B   C5B  N5B   113.73  3.000
 EPY  H5B1  C5B  C6B   105.52  3.000
 EPY  C4B   C5B  C6B   113.42  3.000
 EPY  N5B   C5B  C6B   107.30  3.000
 EPY  HN52  N5B  HN51  107.40  3.000
 EPY  HN52  N5B  C5B   111.36  3.000
 EPY  HN51  N5B  C5B   111.61  3.000
 EPY  H4B2  C4B  H4B1  106.56  3.000
 EPY  H4B2  C4B  C3B   110.48  3.000
 EPY  H4B1  C4B  C3B   108.74  3.000
 EPY  H4B2  C4B  C5B   109.73  3.000
 EPY  H4B1  C4B  C5B   106.58  3.000
 EPY  C3B   C4B  C5B   114.38  3.000
 EPY  H3B2  C3B  H3B1  106.14  3.000
 EPY  H3B2  C3B  C2B   110.29  3.000
 EPY  H3B1  C3B  C2B   106.85  3.000
 EPY  H3B2  C3B  C4B   110.14  3.000
 EPY  H3B1  C3B  C4B   110.65  3.000
 EPY  C2B   C3B  C4B   112.52  3.000
 EPY  HNB1  N1B  C2B   118.87  3.000
 EPY  HNB1  N1B  C2A   117.53  3.000
 EPY  C2B   N1B  C2A   122.68  3.000
 EPY  H1C1  C1C  C2C   109.03  3.000
 EPY  H1C1  C1C  C3C   108.66  3.000
 EPY  C2C   C1C  C3C   114.12  3.000
 EPY  H1C1  C1C  S     108.32  3.000
 EPY  C2C   C1C  S     110.06  3.000
 EPY  C3C   C1C  S     106.48  3.000
 EPY  H3C2  C3C  H3C1  107.32  3.000
 EPY  H3C2  C3C  O2C   111.45  3.000
 EPY  H3C1  C3C  O2C   112.15  3.000
 EPY  H3C2  C3C  C1C   108.88  3.000
 EPY  H3C1  C3C  C1C   108.01  3.000
 EPY  O2C   C3C  C1C   108.93  3.000
 EPY  HOC2  O2C  C3C   107.79  3.000
 EPY  H2C2  C2C  H2C1  107.65  3.000
 EPY  H2C2  C2C  O3C   109.19  3.000
 EPY  H2C1  C2C  O3C   111.27  3.000
 EPY  H2C2  C2C  C1C   110.72  3.000
 EPY  H2C1  C2C  C1C   110.14  3.000
 EPY  O3C   C2C  C1C   107.88  3.000
 EPY  C4C   O3C  C2C   119.80  3.000
 EPY  C5C   C4C  C9C   119.67  3.000
 EPY  C5C   C4C  O3C   124.43  3.000
 EPY  C9C   C4C  O3C   115.89  3.000
 EPY  H9C1  C9C  C8C   120.19  3.000
 EPY  H9C1  C9C  C4C   119.41  3.000
 EPY  C8C   C9C  C4C   120.40  3.000
 EPY  H8C1  C8C  C7C   121.13  3.000
 EPY  H8C1  C8C  C9C   119.48  3.000
 EPY  C7C   C8C  C9C   119.39  3.000
 EPY  N8C   C7C  C6C   119.60  3.000
 EPY  N8C   C7C  C8C   119.56  3.000
 EPY  C6C   C7C  C8C   120.84  3.000
 EPY  H6C1  C6C  C5C   119.04  3.000
 EPY  H6C1  C6C  C7C   121.14  3.000
 EPY  C5C   C6C  C7C   119.82  3.000
 EPY  H5C1  C5C  C6C   118.58  3.000
 EPY  H5C1  C5C  C4C   121.55  3.000
 EPY  C6C   C5C  C4C   119.87  3.000
 EPY  O9C   N8C  O8C   123.49  3.000
 EPY  O9C   N8C  C7C   118.32  3.000
 EPY  O8C   N8C  C7C   118.19  3.000
 EPY  N1B   C2B  O2B   122.85  3.000
 EPY  N1B   C2B  C3B   114.52  3.000
 EPY  O2B   C2B  C3B   122.62  3.000
 EPY  HOB6  O6B  C6B   103.66  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
 EPY  CONST_01  C7C   C8C  C9C  C4C    0.00   0.0  0
 EPY  CONST_02  C7C   C6C  C5C  C4C    0.00   0.0  0
 EPY  CONST_03  C6C   C5C  C4C  C9C    0.00   0.0  0
 EPY  CONST_04  C6C   C7C  C8C  C9C    0.00   0.0  0
 EPY  CONST_05  C5C   C4C  C9C  C8C    0.00   0.0  0
 EPY  CONST_06  C5C   C6C  C7C  C8C    0.00   0.0  0
 EPY  CONST_07  C8C   C9C  C4C  O3C  180.00   0.0  0
 EPY  CONST_08  C6C   C5C  C4C  O3C  180.00   0.0  0
 EPY  CONST_09  N8C   C7C  C8C  C9C  180.00   0.0  0
 EPY  CONST_10  N8C   C7C  C6C  C5C  180.00   0.0  0
 EPY  CONST_11  H8C1  C8C  C9C  C4C  180.00   0.0  0
 EPY  CONST_12  H6C1  C6C  C5C  C4C  180.00   0.0  0
 EPY  CONST_13  H5C1  C5C  C4C  C9C  180.00   0.0  0
 EPY  CONST_14  H9C1  C9C  C8C  C7C  180.00   0.0  0
 EPY  CONST_15  O8C   N8C  C7C  C8C    0.00   0.0  0
 EPY  CONST_16  O9C   N8C  C7C  C8C  180.00   0.0  0
 EPY  CONST_17  O8C   N8C  C7C  C6C  180.00   0.0  0
 EPY  CONST_18  O9C   N8C  C7C  C6C    0.00   0.0  0
 EPY  CONST_19  C5A   N4A  C3A  C2A    0.00   0.0  0
 EPY  CONST_20  C3B   C2B  N1B  C2A  180.00   0.0  0
 EPY  CONST_21  O2B   C2B  N1B  C2A    0.00   0.0  0
 EPY  CONST_22  O3A   C3A  N4A  C5A  180.00   0.0  0
 EPY  CONST_23  HNA4  N4A  C3A  C2A  180.00   0.0  0
 EPY  CONST_24  HNB1  N1B  C2B  C3B    0.00   0.0  0
 EPY  CONST_25  HOA6  O6A  C6A  C5A  180.00   0.0  0
 EPY  CONST_26  HOB6  O6B  C6B  O7B  180.00   0.0  0
 EPY  Var_01    C9C   C4C  O3C  C2C  176.67  30.0  2
 EPY  Var_02    H2C1  C2C  O3C  C4C   55.38  30.0  2
 EPY  Var_03    C6A   C5A  N4A  C3A   79.06  30.0  3
 EPY  Var_04    O6A   C6A  C5A  N4A   -5.08  30.0  3
 EPY  Var_05    C2B   C3B  C4B  C5B  177.45  30.0  3
 EPY  Var_06    O2B   C2B  C3B  C4B   32.73  30.0  3
 EPY  Var_07    H1A1  C1A  S    C1C   51.87  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
 EPY  chir_01  C2A  C3A  C1A  N1B  positiv
 EPY  chir_02  C5B  N5B  C6B  C4B  positiv
 EPY  chir_03  C1C  S    C3C  C2C  negativ

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
 EPY  plan-1  O3C   0.020
 EPY  plan-1  C4C   0.020
 EPY  plan-1  C9C   0.020
 EPY  plan-1  C8C   0.020
 EPY  plan-1  C7C   0.020
 EPY  plan-1  C6C   0.020
 EPY  plan-1  C5C   0.020
 EPY  plan-1  N8C   0.020
 EPY  plan-1  H9C1  0.020
 EPY  plan-1  H8C1  0.020
 EPY  plan-1  H6C1  0.020
 EPY  plan-1  H5C1  0.020
 EPY  plan-2  C2A   0.020
 EPY  plan-2  C3A   0.020
 EPY  plan-2  N4A   0.020
 EPY  plan-2  C5A   0.020
 EPY  plan-2  O3A   0.020
 EPY  plan-2  HNA4  0.020
 EPY  plan-3  C2A   0.020
 EPY  plan-3  C3B   0.020
 EPY  plan-3  O2B   0.020
 EPY  plan-3  N1B   0.020
 EPY  plan-3  HNB1  0.020
 EPY  plan-3  C2B   0.020
 EPY  plan-4  C7C   0.020
 EPY  plan-4  N8C   0.020
 EPY  plan-4  O8C   0.020
 EPY  plan-4  O9C   0.020
 EPY  plan-5  C5A   0.020
 EPY  plan-5  C6A   0.020
 EPY  plan-5  O6A   0.020
 EPY  plan-5  O7A   0.020
 EPY  plan-5  HOA6  0.020
 EPY  plan-6  C6B   0.020
 EPY  plan-6  O7B   0.020
 EPY  plan-6  C5B   0.020
 EPY  plan-6  HOB6  0.020
 EPY  plan-6  O6B   0.020

