# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:19:09 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: L-gamma-glutamyl-S-[2-(biphenyl-4-yl)-2-oxoethyl]-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSCC(=O)c1ccc(cc1)c2ccccc2)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
 48T  48T  L-gamma-glutamyl-S-[2-(biphenyl-4-yl)-2-oxoethyl]-L-cysteinylglycine  ligand  62  35  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_48T
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
 48T  N1    N  NH2   0  -0.776  -6.9983   3.0417   2.0790
 48T  CA1   C  CH1   0  -0.210  -6.4979   3.3799   0.7696
 48T  C1    C  C     0   0.522  -7.5434   4.0210  -0.1356
 48T  O11   O  OH1   0  -0.593  -6.9962   4.5916  -1.2029
 48T  CB1   C  CH2   0  -0.433  -5.9238   2.1394   0.0726
 48T  CG1   C  CH2   0  -0.576  -4.7741   1.5290   0.8603
 48T  CD1   C  C     0   0.578  -4.2383   0.2739   0.2140
 48T  OE1   O  O     0  -0.495  -4.9384  -0.5047  -0.4177
 48T  O12   O  O     0  -0.439  -8.7302   4.0110   0.0748
 48T  N2    N  NH1   0  -0.642  -2.9228   0.0489   0.3880
 48T  CA2   C  CH1   0  -0.192  -2.3060  -1.1516  -0.1046
 48T  C2    C  C     0   0.568  -2.9106  -2.3894   0.5672
 48T  O2    O  O     0  -0.482  -3.2623  -2.3846   1.7338
 48T  CB2   C  CH2   0  -0.578  -0.8094  -1.1353   0.1871
 48T  SG2   S  S2    0   0.021  -0.0397   0.2905  -0.6361
 48T  CZ4   C  CR16  0  -0.307   9.1537   1.1085  -0.7143
 48T  CE4   C  CR16  0  -0.239  10.5203   1.0380  -0.4901
 48T  CD4   C  CR16  0  -0.263  11.0059   0.5710   0.7242
 48T  CG4   C  CR16  0  -0.240  10.1140   0.1726   1.7115
 48T  CB4   C  CR16  0  -0.306   8.7474   0.2397   1.4863
 48T  CH4   C  CR6   0   0.090   8.2474   0.7098   0.2702
 48T  CH5   C  CR6   0   0.093   6.7939   0.7827   0.0298
 48T  CB5   C  CR16  0  -0.297   6.2413   1.8237  -0.7222
 48T  CG5   C  CR16  0  -0.243   4.8807   1.8907  -0.9496
 48T  CD5   C  CR6   0  -0.017   4.0238   0.9174  -0.4329
 48T  CE5   C  CR16  0  -0.273   4.5697  -0.1220   0.3196
 48T  CZ5   C  CR16  0  -0.291   5.9333  -0.1874   0.5459
 48T  O5    O  O     0  -0.383   2.1088   1.9319  -1.3570
 48T  N3    N  NH1   0  -0.644  -2.9531  -3.4749  -0.2144
 48T  CA3   C  CH2   0  -0.371  -3.4248  -4.7414   0.2707
 48T  C3    C  C     0   0.522  -3.2570  -5.8005  -0.7882
 48T  C13   C  CH2   0  -0.700   1.6645  -0.0450  -0.1392
 48T  O31   O  O     0  -0.434  -2.8012  -5.6025  -1.8852
 48T  C14   C  C     0   0.389   2.5695   1.0217  -0.7029
 48T  O32   O  OH1   0  -0.584  -3.6778  -6.9750  -0.3536
 48T  H11N  H  HNH2  0   0.356  -7.3064   3.8723   2.5677
 48T  H12N  H  HNH2  0   0.344  -7.8088   2.4394   2.0000
 48T  HA1   H  HCH1  0   0.270  -5.6909   4.1104   0.8902
 48T  HB11  H  HCH2  0   0.243  -6.7199   1.4014  -0.0552
 48T  HB12  H  HCH2  0   0.254  -5.5778   2.4075  -0.9271
 48T  H11   H  HOH1  0   0.481  -7.6850   4.9682  -1.7712
 48T  HG11  H  HCH2  0   0.256  -3.9722   2.2613   0.9859
 48T  HG12  H  HCH2  0   0.282  -5.1117   1.2688   1.8671
 48T  H2    H  HNH1  0   0.406  -2.3812   0.6788   0.9587
 48T  HA2   H  HCH1  0   0.286  -2.4522  -1.2226  -1.1876
 48T  HB21  H  HCH2  0   0.286  -0.6322  -1.0836   1.2639
 48T  HB22  H  HCH2  0   0.297  -0.3607  -2.0567  -0.1865
 48T  H3    H  HNH1  0   0.408  -2.7054  -3.4030  -1.1896
 48T  H131  H  HCH2  0   0.310   1.7455  -0.0613   0.9512
 48T  H132  H  HCH2  0   0.308   1.9783  -1.0287  -0.4983
 48T  HG4   H  HCR6  0   0.261  10.4825  -0.1875   2.6631
 48T  HD4   H  HCR6  0   0.261  12.0723   0.5178   0.9004
 48T  HE4   H  HCR6  0   0.260  11.2069   1.3425  -1.2694
 48T  HZ4   H  HCR6  0   0.258   8.7922   1.4567  -1.6736
 48T  HZ5   H  HCR6  0   0.265   6.3319  -1.0185   1.1130
 48T  HB5   H  HCR6  0   0.263   6.8780   2.6039  -1.1191
 48T  HE5   H  HCR6  0   0.268   3.9437  -0.9005   0.7354
 48T  HG5   H  HCR6  0   0.267   4.4791   2.7125  -1.5272
 48T  HA31  H  HCH2  0   0.294  -2.8743  -5.0507   1.1637
 48T  HA32  H  HCH2  0   0.292  -4.4804  -4.6971   0.5570
 48T  H32   H  HOH1  0   0.490  -3.5624  -7.6513  -1.0384
 48T  HB4   H  HCR6  0   0.258   8.0651  -0.0566   2.2733

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
 48T  N1   CA1   single    1.442  0.020  1.442
 48T  CA1  C1    single    1.524  0.020  1.524
 48T  CA1  CB1   single    1.534  0.020  1.534
 48T  C1   O11   single    1.328  0.020  1.328
 48T  C1   O12   double    1.205  0.020  1.205
 48T  CB1  CG1   single    1.521  0.020  1.521
 48T  CG1  CD1   single    1.510  0.020  1.510
 48T  CD1  OE1   double    1.223  0.020  1.223
 48T  CD1  N2    single    1.346  0.020  1.346
 48T  N2   CA2   single    1.437  0.020  1.437
 48T  CA2  C2    single    1.533  0.020  1.533
 48T  CA2  CB2   single    1.525  0.020  1.525
 48T  C2   O2    double    1.219  0.020  1.219
 48T  C2   N3    single    1.338  0.020  1.338
 48T  CB2  SG2   single    1.817  0.020  1.817
 48T  SG2  C13   single    1.807  0.020  1.807
 48T  CB4  CG4   aromatic  1.387  0.020  1.387
 48T  CB4  CH4   aromatic  1.396  0.020  1.396
 48T  CG4  CD4   aromatic  1.389  0.020  1.389
 48T  CD4  CE4   aromatic  1.389  0.020  1.389
 48T  CE4  CZ4   aromatic  1.387  0.020  1.387
 48T  CZ4  CH4   aromatic  1.396  0.020  1.396
 48T  CH4  CH5   single    1.475  0.020  1.475
 48T  CH5  CZ5   aromatic  1.396  0.020  1.396
 48T  CH5  CB5   aromatic  1.398  0.020  1.398
 48T  CZ5  CE5   aromatic  1.384  0.020  1.384
 48T  CE5  CD5   aromatic  1.394  0.020  1.394
 48T  CD5  CG5   aromatic  1.396  0.020  1.396
 48T  CD5  C14   single    1.483  0.020  1.483
 48T  CG5  CB5   aromatic  1.381  0.020  1.381
 48T  O5   C14   double    1.212  0.020  1.212
 48T  N3   CA3   single    1.436  0.020  1.436
 48T  CA3  C3    single    1.507  0.020  1.507
 48T  C3   O31   double    1.204  0.020  1.204
 48T  C3   O32   single    1.321  0.020  1.321
 48T  C13  C14   single    1.508  0.020  1.508
 48T  N1   H11N  single    0.890  0.020  1.040
 48T  N1   H12N  single    0.890  0.020  1.040
 48T  CA1  HA1   single    0.970  0.020  1.090
 48T  CB1  HB11  single    0.970  0.020  1.090
 48T  CB1  HB12  single    0.970  0.020  1.090
 48T  O11  H11   single    0.850  0.020  0.980
 48T  CG1  HG11  single    0.970  0.020  1.090
 48T  CG1  HG12  single    0.970  0.020  1.090
 48T  N2   H2    single    0.860  0.020  1.020
 48T  CA2  HA2   single    0.970  0.020  1.090
 48T  CB2  HB21  single    0.970  0.020  1.090
 48T  CB2  HB22  single    0.970  0.020  1.090
 48T  N3   H3    single    0.860  0.020  1.020
 48T  C13  H131  single    0.970  0.020  1.090
 48T  C13  H132  single    0.970  0.020  1.090
 48T  CB4  HB4   single    0.930  0.020  1.080
 48T  CG4  HG4   single    0.930  0.020  1.080
 48T  CD4  HD4   single    0.930  0.020  1.080
 48T  CE4  HE4   single    0.930  0.020  1.080
 48T  CZ4  HZ4   single    0.930  0.020  1.080
 48T  CZ5  HZ5   single    0.930  0.020  1.080
 48T  CB5  HB5   single    0.930  0.020  1.080
 48T  CE5  HE5   single    0.930  0.020  1.080
 48T  CG5  HG5   single    0.930  0.020  1.080
 48T  CA3  HA31  single    0.970  0.020  1.090
 48T  CA3  HA32  single    0.970  0.020  1.090
 48T  O32  H32   single    0.850  0.020  0.980

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
 48T  H12N  N1   H11N  106.39  3.000
 48T  H12N  N1   CA1   110.27  3.000
 48T  H11N  N1   CA1   110.59  3.000
 48T  HA1   CA1  CB1   108.27  3.000
 48T  HA1   CA1  C1    106.87  3.000
 48T  CB1   CA1  C1    109.08  3.000
 48T  HA1   CA1  N1    108.19  3.000
 48T  CB1   CA1  N1    110.65  3.000
 48T  C1    CA1  N1    113.57  3.000
 48T  O12   C1   O11   123.33  3.000
 48T  O12   C1   CA1   124.62  3.000
 48T  O11   C1   CA1   112.05  3.000
 48T  H11   O11  C1    110.20  3.000
 48T  HB12  CB1  HB11  106.84  3.000
 48T  HB12  CB1  CG1   109.47  3.000
 48T  HB11  CB1  CG1   109.88  3.000
 48T  HB12  CB1  CA1   109.64  3.000
 48T  HB11  CB1  CA1   109.05  3.000
 48T  CG1   CB1  CA1   111.84  3.000
 48T  HG12  CG1  HG11  106.27  3.000
 48T  HG12  CG1  CD1   107.81  3.000
 48T  HG11  CG1  CD1   110.23  3.000
 48T  HG12  CG1  CB1   109.81  3.000
 48T  HG11  CG1  CB1   110.18  3.000
 48T  CD1   CG1  CB1   112.34  3.000
 48T  N2    CD1  OE1   121.33  3.000
 48T  N2    CD1  CG1   115.49  3.000
 48T  OE1   CD1  CG1   123.17  3.000
 48T  H2    N2   CA2   119.05  3.000
 48T  H2    N2   CD1   119.60  3.000
 48T  CA2   N2   CD1   120.99  3.000
 48T  HA2   CA2  CB2   108.71  3.000
 48T  HA2   CA2  C2    109.17  3.000
 48T  CB2   CA2  C2    108.18  3.000
 48T  HA2   CA2  N2    109.63  3.000
 48T  CB2   CA2  N2    110.29  3.000
 48T  C2    CA2  N2    110.81  3.000
 48T  N3    C2   O2    123.59  3.000
 48T  N3    C2   CA2   114.30  3.000
 48T  O2    C2   CA2   122.03  3.000
 48T  HB22  CB2  HB21  108.11  3.000
 48T  HB22  CB2  SG2   109.47  3.000
 48T  HB21  CB2  SG2   109.91  3.000
 48T  HB22  CB2  CA2   109.22  3.000
 48T  HB21  CB2  CA2   110.38  3.000
 48T  SG2   CB2  CA2   109.72  3.000
 48T  C13   SG2  CB2    97.43  3.000
 48T  HZ4   CZ4  CH4   119.99  3.000
 48T  HZ4   CZ4  CE4   119.25  3.000
 48T  CH4   CZ4  CE4   120.74  3.000
 48T  HE4   CE4  CD4   120.16  3.000
 48T  HE4   CE4  CZ4   119.64  3.000
 48T  CD4   CE4  CZ4   120.20  3.000
 48T  HD4   CD4  CG4   120.20  3.000
 48T  HD4   CD4  CE4   120.23  3.000
 48T  CG4   CD4  CE4   119.57  3.000
 48T  HG4   CG4  CB4   119.64  3.000
 48T  HG4   CG4  CD4   120.13  3.000
 48T  CB4   CG4  CD4   120.24  3.000
 48T  HB4   CB4  CH4   119.97  3.000
 48T  HB4   CB4  CG4   119.31  3.000
 48T  CH4   CB4  CG4   120.70  3.000
 48T  CH5   CH4  CB4   120.75  3.000
 48T  CH5   CH4  CZ4   120.70  3.000
 48T  CB4   CH4  CZ4   118.54  3.000
 48T  CZ5   CH5  CB5   118.21  3.000
 48T  CB5   CH5  CH4   120.92  3.000
 48T  CZ5   CH5  CH4   120.86  3.000
 48T  HB5   CB5  CG5   118.95  3.000
 48T  HB5   CB5  CH5   120.10  3.000
 48T  CG5   CB5  CH5   120.94  3.000
 48T  HG5   CG5  CD5   119.97  3.000
 48T  HG5   CG5  CB5   119.37  3.000
 48T  CD5   CG5  CB5   120.66  3.000
 48T  C14   CD5  CE5   122.32  3.000
 48T  C14   CD5  CG5   119.05  3.000
 48T  CE5   CD5  CG5   118.63  3.000
 48T  HE5   CE5  CZ5   118.24  3.000
 48T  HE5   CE5  CD5   121.14  3.000
 48T  CZ5   CE5  CD5   120.61  3.000
 48T  HZ5   CZ5  CE5   119.01  3.000
 48T  HZ5   CZ5  CH5   120.03  3.000
 48T  CE5   CZ5  CH5   120.95  3.000
 48T  H3    N3   CA3   118.04  3.000
 48T  H3    N3   C2    119.94  3.000
 48T  CA3   N3   C2    121.91  3.000
 48T  HA32  CA3  HA31  106.46  3.000
 48T  HA32  CA3  C3    108.63  3.000
 48T  HA31  CA3  C3    108.60  3.000
 48T  HA32  CA3  N3    111.68  3.000
 48T  HA31  CA3  N3    111.10  3.000
 48T  C3    CA3  N3    110.24  3.000
 48T  O32   C3   O31   124.50  3.000
 48T  O32   C3   CA3   110.99  3.000
 48T  O31   C3   CA3   124.52  3.000
 48T  H132  C13  H131  107.03  3.000
 48T  H132  C13  C14   109.97  3.000
 48T  H131  C13  C14   109.80  3.000
 48T  H132  C13  SG2   110.34  3.000
 48T  H131  C13  SG2   110.29  3.000
 48T  C14   C13  SG2   109.39  3.000
 48T  C13   C14  O5    120.32  3.000
 48T  C13   C14  CD5   118.08  3.000
 48T  O5    C14  CD5   121.60  3.000
 48T  H32   O32  C3    110.48  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
 48T  CONST_01  CG4   CD4  CE4  CZ4     0.00   0.0  0
 48T  CONST_02  CG4   CB4  CH4  CZ4     0.00   0.0  0
 48T  CONST_05  CB4   CG4  CD4  CE4     0.00   0.0  0
 48T  CONST_06  CB4   CH4  CZ4  CE4     0.00   0.0  0
 48T  CONST_07  CH5   CH4  CZ4  CE4   180.00   0.0  0
 48T  CONST_08  CH4   CB4  CG4  CD4     0.00   0.0  0
 48T  CONST_09  CH4   CZ4  CE4  CD4     0.00   0.0  0
 48T  CONST_10  CH5   CH4  CB4  CG4   180.00   0.0  0
 48T  CONST_13  CE5   CZ5  CH5  CH4   180.00   0.0  0
 48T  CONST_14  CG5   CB5  CH5  CH4   180.00   0.0  0
 48T  CONST_15  CD5   CE5  CZ5  CH5     0.00   0.0  0
 48T  CONST_16  CD5   CG5  CB5  CH5     0.00   0.0  0
 48T  CONST_17  CE5   CZ5  CH5  CB5     0.00   0.0  0
 48T  CONST_18  CE5   CD5  CG5  CB5     0.00   0.0  0
 48T  CONST_19  CZ5   CE5  CD5  CG5     0.00   0.0  0
 48T  CONST_20  CZ5   CH5  CB5  CG5     0.00   0.0  0
 48T  CONST_21  C14   CD5  CG5  CB5   180.00   0.0  0
 48T  CONST_22  C14   CD5  CE5  CZ5   180.00   0.0  0
 48T  CONST_23  HD4   CD4  CE4  CZ4   180.00   0.0  0
 48T  CONST_24  HB4   CB4  CH4  CZ4   180.00   0.0  0
 48T  CONST_25  HG4   CG4  CD4  CE4   180.00   0.0  0
 48T  CONST_26  HZ4   CZ4  CE4  CD4   180.00   0.0  0
 48T  CONST_27  HE4   CE4  CD4  CG4   180.00   0.0  0
 48T  CONST_28  HZ5   CZ5  CH5  CH4     0.00   0.0  0
 48T  CONST_29  HB5   CB5  CH5  CH4     0.00   0.0  0
 48T  CONST_30  HE5   CE5  CZ5  CH5   180.00   0.0  0
 48T  CONST_31  HG5   CG5  CB5  CH5   180.00   0.0  0
 48T  CONST_32  CA2   N2   CD1  CG1   180.00   0.0  0
 48T  CONST_33  CA2   N2   CD1  OE1     0.00   0.0  0
 48T  CONST_34  CA3   N3   C2   CA2   180.00   0.0  0
 48T  CONST_35  CA3   N3   C2   O2      0.00   0.0  0
 48T  CONST_36  H2    N2   CD1  CG1     0.00   0.0  0
 48T  CONST_37  H3    N3   C2   CA2     0.00   0.0  0
 48T  CONST_38  H11   O11  C1   CA1   180.00   0.0  0
 48T  CONST_39  H32   O32  C3   CA3   180.00   0.0  0
 48T  Var_01    O5    C14  CD5  CG5    -0.19  30.0  2
 48T  Var_02    CD5   C14  C13  SG2  -178.80  30.0  3
 48T  Var_03    CD1   CG1  CB1  CA1   177.60  30.0  3
 48T  Var_04    OE1   CD1  CG1  CB1   -32.56  30.0  3
 48T  Var_05    C3    CA3  N3   C2   -175.49  30.0  3
 48T  Var_06    C14   C13  SG2  CB2   179.98  30.0  3
 48T  Var_07    O31   C3   CA3  N3     -0.52  30.0  3
 48T  Var_08    HB21  CB2  SG2  C13    60.49  30.0  1

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
 48T  chir_01  CA1  N1  C1  CB1  positiv
 48T  chir_02  CA2  N2  C2  CB2  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
 48T  plan-1  CZ4  0.020
 48T  plan-1  CE4  0.020
 48T  plan-1  CD4  0.020
 48T  plan-1  CG4  0.020
 48T  plan-1  CB4  0.020
 48T  plan-1  CH4  0.020
 48T  plan-1  CH5  0.020
 48T  plan-1  HG4  0.020
 48T  plan-1  HD4  0.020
 48T  plan-1  HE4  0.020
 48T  plan-1  HZ4  0.020
 48T  plan-1  HB4  0.020
 48T  plan-2  CH4  0.020
 48T  plan-2  CH5  0.020
 48T  plan-2  CB5  0.020
 48T  plan-2  CG5  0.020
 48T  plan-2  CD5  0.020
 48T  plan-2  CE5  0.020
 48T  plan-2  CZ5  0.020
 48T  plan-2  C14  0.020
 48T  plan-2  HZ5  0.020
 48T  plan-2  HB5  0.020
 48T  plan-2  HE5  0.020
 48T  plan-2  HG5  0.020
 48T  plan-3  CG1  0.020
 48T  plan-3  CD1  0.020
 48T  plan-3  OE1  0.020
 48T  plan-3  N2   0.020
 48T  plan-3  CA2  0.020
 48T  plan-3  H2   0.020
 48T  plan-4  CA2  0.020
 48T  plan-4  C2   0.020
 48T  plan-4  O2   0.020
 48T  plan-4  N3   0.020
 48T  plan-4  CA3  0.020
 48T  plan-4  H3   0.020
 48T  plan-5  CD5  0.020
 48T  plan-5  O5   0.020
 48T  plan-5  C13  0.020
 48T  plan-5  C14  0.020
 48T  plan-6  CA1  0.020
 48T  plan-6  C1   0.020
 48T  plan-6  O11  0.020
 48T  plan-6  O12  0.020
 48T  plan-6  H11  0.020
 48T  plan-7  CA3  0.020
 48T  plan-7  C3   0.020
 48T  plan-7  O31  0.020
 48T  plan-7  O32  0.020
 48T  plan-7  H32  0.020

