# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 04:34:17 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: L-gamma-glutamyl-S-octyl-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCSC[C@H](NC(=O)CC[C@H](N)C(O)=O)C(=O)NCC(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
 GTY  GTY  L-gamma-glutamyl-S-octyl-L-cysteinylglycine  ligand  59  28  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GTY
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
 GTY  N1    N  NH2    0  -0.786  -5.3562   3.5928   1.5220
 GTY  CA1   C  CH1    0  -0.215  -4.4840   3.7844   0.3740
 GTY  C1    C  C      0   0.385  -5.0762   4.6324  -0.7806
 GTY  O11   O  O      0  -0.607  -6.2997   4.8702  -0.7551
 GTY  O12   O  OC    -1  -0.623  -4.2673   4.9946  -1.6606
 GTY  CB1   C  CH2    0  -0.422  -4.0439   2.4277  -0.1805
 GTY  CG1   C  CH2    0  -0.564  -3.3135   1.5765   0.8524
 GTY  CD1   C  C      0   0.565  -2.8947   0.2400   0.2933
 GTY  OE1   O  O      0  -0.503  -3.6509  -0.4743  -0.3521
 GTY  N2    N  NH1    0  -0.638  -1.6245  -0.1274   0.5398
 GTY  CA2   C  CH1    0  -0.186  -1.1060  -1.3874   0.0830
 GTY  C2    C  C      0   0.553  -1.8355  -2.5608   0.7503
 GTY  O2    O  O      0  -0.501  -2.2343  -2.4931   1.9040
 GTY  CB2   C  CH2    0  -0.573   0.3772  -1.4978   0.4213
 GTY  SG2   S  S2     0  -0.028   1.3023  -0.1438  -0.3589
 GTY  C1S   C  CH2    0  -0.543   2.9785  -0.5658   0.1977
 GTY  C2S   C  CH2    0  -0.422   3.9472   0.5352  -0.2068
 GTY  C3S   C  CH2    0  -0.411   5.3823   0.2130   0.1947
 GTY  C4S   C  CH2    0  -0.412   6.3549   1.3300  -0.1632
 GTY  C5S   C  CH2    0  -0.412   7.7958   1.0206   0.2221
 GTY  C6S   C  CH2    0  -0.406   8.7608   2.1505  -0.1150
 GTY  C7S   C  CH2    0  -0.419  10.2039   1.8486   0.2693
 GTY  C8S   C  CH3    0  -0.661  11.1553   2.9904  -0.0612
 GTY  N3    N  NH1    0  -0.628  -1.9257  -3.6499  -0.0099
 GTY  CA3   C  CH2    0  -0.411  -2.4689  -4.9080   0.4323
 GTY  C3    C  C      0   0.399  -2.3837  -5.9660  -0.6872
 GTY  O31   O  OC    -1  -0.609  -2.8026  -7.0954  -0.3824
 GTY  O32   O  O      0  -0.599  -1.9127  -5.5974  -1.7805
 GTY  HN11  H  HNH2   0   0.336  -5.5368   4.4946   1.9466
 GTY  HN12  H  HNH2   0   0.323  -6.2618   3.2910   1.1793
 GTY  HA1   H  HCH1   0   0.211  -3.5844   4.3016   0.7296
 GTY  HB11  H  HCH2   0   0.231  -3.3959   2.5954  -1.0424
 GTY  HB12  H  HCH2   0   0.219  -4.9205   1.8847  -0.5474
 GTY  HG11  H  HCH2   0   0.266  -3.9726   1.3994   1.7058
 GTY  HG12  H  HCH2   0   0.240  -2.4489   2.1224   1.2391
 GTY  HN2   H  HNH1   0   0.401  -1.0379   0.4652   1.1054
 GTY  HA2   H  HCH1   0   0.277  -1.2245  -1.4601  -1.0034
 GTY  HB21  H  HCH2   0   0.292   0.7587  -2.4532   0.0586
 GTY  HB22  H  HCH2   0   0.280   0.5235  -1.4625   1.5038
 GTY  H1S1  H  HCH2   0   0.260   3.2738  -1.5209  -0.2420
 GTY  H1S2  H  HCH2   0   0.261   2.9696  -0.6850   1.2834
 GTY  H2S1  H  HCH2   0   0.228   3.6391   1.4762   0.2580
 GTY  H2S2  H  HCH2   0   0.228   3.8983   0.6902  -1.2889
 GTY  H3S1  H  HCH2   0   0.215   5.6982  -0.7162  -0.2910
 GTY  H3S2  H  HCH2   0   0.214   5.4266   0.0250   1.2727
 GTY  H4S1  H  HCH2   0   0.209   6.0374   2.2552   0.3303
 GTY  H4S2  H  HCH2   0   0.209   6.3006   1.5272  -1.2395
 GTY  H5S1  H  HCH2   0   0.207   8.1195   0.1035  -0.2827
 GTY  H5S2  H  HCH2   0   0.207   7.8476   0.8088   1.2959
 GTY  H6S1  H  HCH2   0   0.206   8.4353   3.0666   0.3909
 GTY  H6S2  H  HCH2   0   0.206   8.7086   2.3646  -1.1884
 GTY  H7S1  H  HCH2   0   0.210  10.5322   0.9383  -0.2420
 GTY  H7S2  H  HCH2   0   0.210  10.2547   1.6287   1.3403
 GTY  H8S1  H  HCH3   0   0.225  12.1786   2.7607   0.2381
 GTY  H8S2  H  HCH3   0   0.215  11.1630   3.2000  -1.1325
 GTY  H8S3  H  HCH3   0   0.215  10.8593   3.9089   0.4496
 GTY  HN3   H  HNH1   0   0.387  -1.6086  -3.6417  -0.9696
 GTY  HA31  H  HCH2   0   0.242  -1.9306  -5.2738   1.3118
 GTY  HA32  H  HCH2   0   0.243  -3.5150  -4.7961   0.7342

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
 GTY  N1   CA1   single  1.454  0.020  1.454
 GTY  N1   HN11  single  0.890  0.020  1.040
 GTY  N1   HN12  single  0.890  0.020  1.040
 GTY  CA1  C1    single  1.550  0.020  1.550
 GTY  CA1  CB1   single  1.530  0.020  1.530
 GTY  CA1  HA1   single  0.970  0.020  1.090
 GTY  C1   O11   deloc   1.247  0.020  1.247
 GTY  C1   O12   deloc   1.249  0.020  1.249
 GTY  CB1  CG1   single  1.525  0.020  1.525
 GTY  CB1  HB11  single  0.970  0.020  1.090
 GTY  CB1  HB12  single  0.970  0.020  1.090
 GTY  CG1  CD1   single  1.508  0.020  1.508
 GTY  CG1  HG11  single  0.970  0.020  1.090
 GTY  CG1  HG12  single  0.970  0.020  1.090
 GTY  CD1  OE1   double  1.224  0.020  1.224
 GTY  CD1  N2    single  1.345  0.020  1.345
 GTY  N2   CA2   single  1.437  0.020  1.437
 GTY  N2   HN2   single  0.860  0.020  1.020
 GTY  CA2  C2    single  1.534  0.020  1.534
 GTY  CA2  CB2   single  1.525  0.020  1.525
 GTY  CA2  HA2   single  0.970  0.020  1.090
 GTY  C2   O2    double  1.223  0.020  1.223
 GTY  C2   N3    single  1.331  0.020  1.331
 GTY  CB2  SG2   single  1.816  0.020  1.816
 GTY  CB2  HB21  single  0.970  0.020  1.090
 GTY  CB2  HB22  single  0.970  0.020  1.090
 GTY  SG2  C1S   single  1.816  0.020  1.816
 GTY  C1S  C2S   single  1.521  0.020  1.521
 GTY  C1S  H1S1  single  0.970  0.020  1.090
 GTY  C1S  H1S2  single  0.970  0.020  1.090
 GTY  C2S  C3S   single  1.525  0.020  1.525
 GTY  C2S  H2S1  single  0.970  0.020  1.090
 GTY  C2S  H2S2  single  0.970  0.020  1.090
 GTY  C3S  C4S   single  1.524  0.020  1.524
 GTY  C3S  H3S1  single  0.970  0.020  1.090
 GTY  C3S  H3S2  single  0.970  0.020  1.090
 GTY  C4S  C5S   single  1.523  0.020  1.523
 GTY  C4S  H4S1  single  0.970  0.020  1.090
 GTY  C4S  H4S2  single  0.970  0.020  1.090
 GTY  C5S  C6S   single  1.524  0.020  1.524
 GTY  C5S  H5S1  single  0.970  0.020  1.090
 GTY  C5S  H5S2  single  0.970  0.020  1.090
 GTY  C6S  C7S   single  1.524  0.020  1.524
 GTY  C6S  H6S1  single  0.970  0.020  1.090
 GTY  C6S  H6S2  single  0.970  0.020  1.090
 GTY  C7S  C8S   single  1.523  0.020  1.523
 GTY  C7S  H7S1  single  0.970  0.020  1.090
 GTY  C7S  H7S2  single  0.970  0.020  1.090
 GTY  C8S  H8S1  single  0.970  0.020  1.090
 GTY  C8S  H8S2  single  0.970  0.020  1.090
 GTY  C8S  H8S3  single  0.970  0.020  1.090
 GTY  N3   CA3   single  1.440  0.020  1.440
 GTY  N3   HN3   single  0.860  0.020  1.020
 GTY  CA3  C3    single  1.543  0.020  1.543
 GTY  CA3  HA31  single  0.970  0.020  1.090
 GTY  CA3  HA32  single  0.970  0.020  1.090
 GTY  C3   O31   deloc   1.243  0.020  1.243
 GTY  C3   O32   deloc   1.246  0.020  1.246

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
 GTY  HN12  N1   HN11  104.32  3.000
 GTY  HN12  N1   CA1   107.94  3.000
 GTY  HN11  N1   CA1   108.69  3.000
 GTY  HA1   CA1  CB1   107.44  3.000
 GTY  HA1   CA1  C1    107.27  3.000
 GTY  CB1   CA1  C1    108.96  3.000
 GTY  HA1   CA1  N1    107.34  3.000
 GTY  CB1   CA1  N1    109.98  3.000
 GTY  C1    CA1  N1    115.52  3.000
 GTY  O12   C1   O11   126.49  3.000
 GTY  O12   C1   CA1   115.85  3.000
 GTY  O11   C1   CA1   117.65  3.000
 GTY  HB12  CB1  HB11  106.68  3.000
 GTY  HB12  CB1  CG1   109.50  3.000
 GTY  HB11  CB1  CG1   109.66  3.000
 GTY  HB12  CB1  CA1   109.33  3.000
 GTY  HB11  CB1  CA1   108.71  3.000
 GTY  CG1   CB1  CA1   112.78  3.000
 GTY  HG12  CG1  HG11  106.36  3.000
 GTY  HG12  CG1  CD1   110.74  3.000
 GTY  HG11  CG1  CD1   108.26  3.000
 GTY  HG12  CG1  CB1   109.85  3.000
 GTY  HG11  CG1  CB1   109.30  3.000
 GTY  CD1   CG1  CB1   112.13  3.000
 GTY  N2    CD1  OE1   121.37  3.000
 GTY  N2    CD1  CG1   115.87  3.000
 GTY  OE1   CD1  CG1   122.76  3.000
 GTY  HN2   N2   CA2   118.95  3.000
 GTY  HN2   N2   CD1   119.48  3.000
 GTY  CA2   N2   CD1   121.46  3.000
 GTY  HA2   CA2  CB2   108.68  3.000
 GTY  HA2   CA2  C2    109.23  3.000
 GTY  CB2   CA2  C2    108.09  3.000
 GTY  HA2   CA2  N2    109.54  3.000
 GTY  CB2   CA2  N2    110.11  3.000
 GTY  C2    CA2  N2    111.15  3.000
 GTY  N3    C2   O2    124.20  3.000
 GTY  N3    C2   CA2   114.17  3.000
 GTY  O2    C2   CA2   121.54  3.000
 GTY  HB22  CB2  HB21  108.11  3.000
 GTY  HB22  CB2  SG2   109.47  3.000
 GTY  HB21  CB2  SG2   109.40  3.000
 GTY  HB22  CB2  CA2   110.33  3.000
 GTY  HB21  CB2  CA2   109.25  3.000
 GTY  SG2   CB2  CA2   110.25  3.000
 GTY  C1S   SG2  CB2    99.51  3.000
 GTY  H1S2  C1S  H1S1  107.88  3.000
 GTY  H1S2  C1S  C2S   110.39  3.000
 GTY  H1S1  C1S  C2S   110.72  3.000
 GTY  H1S2  C1S  SG2   108.82  3.000
 GTY  H1S1  C1S  SG2   109.23  3.000
 GTY  C2S   C1S  SG2   109.76  3.000
 GTY  H2S2  C2S  H2S1  106.60  3.000
 GTY  H2S2  C2S  C3S   109.41  3.000
 GTY  H2S1  C2S  C3S   109.58  3.000
 GTY  H2S2  C2S  C1S   109.69  3.000
 GTY  H2S1  C2S  C1S   109.29  3.000
 GTY  C3S   C2S  C1S   112.11  3.000
 GTY  H3S2  C3S  H3S1  106.22  3.000
 GTY  H3S2  C3S  C4S   109.34  3.000
 GTY  H3S1  C3S  C4S   109.49  3.000
 GTY  H3S2  C3S  C2S   109.48  3.000
 GTY  H3S1  C3S  C2S   109.52  3.000
 GTY  C4S   C3S  C2S   112.59  3.000
 GTY  H4S2  C4S  H4S1  106.03  3.000
 GTY  H4S2  C4S  C5S   109.39  3.000
 GTY  H4S1  C4S  C5S   109.37  3.000
 GTY  H4S2  C4S  C3S   109.34  3.000
 GTY  H4S1  C4S  C3S   109.16  3.000
 GTY  C5S   C4S  C3S   113.29  3.000
 GTY  H5S2  C5S  H5S1  106.01  3.000
 GTY  H5S2  C5S  C6S   109.28  3.000
 GTY  H5S1  C5S  C6S   109.37  3.000
 GTY  H5S2  C5S  C4S   109.39  3.000
 GTY  H5S1  C5S  C4S   109.44  3.000
 GTY  C6S   C5S  C4S   113.11  3.000
 GTY  H6S2  C6S  H6S1  105.94  3.000
 GTY  H6S2  C6S  C7S   109.32  3.000
 GTY  H6S1  C6S  C7S   109.30  3.000
 GTY  H6S2  C6S  C5S   109.36  3.000
 GTY  H6S1  C6S  C5S   109.25  3.000
 GTY  C7S   C6S  C5S   113.40  3.000
 GTY  H7S2  C7S  H7S1  106.03  3.000
 GTY  H7S2  C7S  C8S   109.52  3.000
 GTY  H7S1  C7S  C8S   109.56  3.000
 GTY  H7S2  C7S  C6S   109.30  3.000
 GTY  H7S1  C7S  C6S   109.33  3.000
 GTY  C8S   C7S  C6S   112.86  3.000
 GTY  H8S3  C8S  H8S2  107.44  3.000
 GTY  H8S3  C8S  H8S1  107.64  3.000
 GTY  H8S2  C8S  H8S1  107.65  3.000
 GTY  H8S3  C8S  C7S   111.09  3.000
 GTY  H8S2  C8S  C7S   111.19  3.000
 GTY  H8S1  C8S  C7S   111.64  3.000
 GTY  HN3   N3   CA3   114.65  3.000
 GTY  HN3   N3   C2    120.95  3.000
 GTY  CA3   N3   C2    124.40  3.000
 GTY  HA32  CA3  HA31  106.42  3.000
 GTY  HA32  CA3  C3    108.85  3.000
 GTY  HA31  CA3  C3    109.08  3.000
 GTY  HA32  CA3  N3    110.85  3.000
 GTY  HA31  CA3  N3    110.70  3.000
 GTY  C3    CA3  N3    110.82  3.000
 GTY  O32   C3   O31   127.70  3.000
 GTY  O32   C3   CA3   117.04  3.000
 GTY  O31   C3   CA3   115.26  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
 GTY  CONST_01  CA2   N2   CD1  CG1   180.00   0.0  0
 GTY  CONST_02  CA2   N2   CD1  OE1     0.00   0.0  0
 GTY  CONST_03  CA3   N3   C2   CA2   180.00   0.0  0
 GTY  CONST_04  CA3   N3   C2   O2      0.00   0.0  0
 GTY  CONST_05  HN2   N2   CD1  CG1     0.00   0.0  0
 GTY  CONST_06  HN3   N3   C2   CA2     0.00   0.0  0
 GTY  Var_01    CD1   CG1  CB1  CA1   179.62  30.0  3
 GTY  Var_02    OE1   CD1  CG1  CB1   -47.02  30.0  3
 GTY  Var_03    C3    CA3  N3   C2   -178.34  30.0  3
 GTY  Var_04    C2S   C1S  SG2  CB2  -173.59  30.0  3
 GTY  Var_05    C3S   C2S  C1S  SG2  -178.10  30.0  3
 GTY  Var_06    C4S   C3S  C2S  C1S  -178.06  30.0  3
 GTY  Var_07    C5S   C4S  C3S  C2S  -179.59  30.0  3
 GTY  Var_08    C6S   C5S  C4S  C3S  -178.97  30.0  3
 GTY  Var_09    C7S   C6S  C5S  C4S   179.93  30.0  3
 GTY  Var_10    C8S   C7S  C6S  C5S  -179.48  30.0  3
 GTY  Var_11    O31   C3   CA3  N3    178.38  30.0  3
 GTY  Var_12    HB21  CB2  SG2  C1S   -58.99  30.0  1
 GTY  Var_13    H8S1  C8S  C7S  C6S   178.98  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
 GTY  chir_01  CA1  N1  C1  CB1  positiv
 GTY  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
 GTY  plan-1  CG1  0.020
 GTY  plan-1  CD1  0.020
 GTY  plan-1  OE1  0.020
 GTY  plan-1  N2   0.020
 GTY  plan-1  CA2  0.020
 GTY  plan-1  HN2  0.020
 GTY  plan-2  CA2  0.020
 GTY  plan-2  C2   0.020
 GTY  plan-2  O2   0.020
 GTY  plan-2  N3   0.020
 GTY  plan-2  CA3  0.020
 GTY  plan-2  HN3  0.020
 GTY  plan-3  CA1  0.020
 GTY  plan-3  C1   0.020
 GTY  plan-3  O11  0.020
 GTY  plan-3  O12  0.020
 GTY  plan-4  CA3  0.020
 GTY  plan-4  C3   0.020
 GTY  plan-4  O31  0.020
 GTY  plan-4  O32  0.020

