# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:08:44 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: L-gamma-glutamyl-S-[(2-phenylethyl)carbamothioyl]-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSC(=S)NCCc1ccccc1)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
 GVX  GVX  L-gamma-glutamyl-S-[(2-phenylethyl)carbamothioyl]-L-cysteinylglycine  peptide  55  31  .  2022-07-25  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_GVX
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
 GVX  O01  O  OC    -1  -0.623  -4.9210   4.7518  -1.5576
 GVX  C02  C  C      0   0.385  -5.7144   4.3637  -0.6741
 GVX  O03  O  O      0  -0.606  -6.9388   4.5917  -0.6249
 GVX  C04  C  CH1    0  -0.216  -5.0960   3.4978   0.4538
 GVX  N05  N  NH2    0  -0.786  -5.9563   3.2476   1.5991
 GVX  C06  C  CH2    0  -0.421  -4.6151   2.1723  -0.1398
 GVX  C07  C  CH2    0  -0.565  -3.8464   1.3199   0.8634
 GVX  C08  C  C      0   0.569  -3.3505   0.0331   0.2531
 GVX  O09  O  O      0  -0.499  -4.0515  -0.6869  -0.4448
 GVX  N10  N  NH1    0  -0.639  -2.0658  -0.2798   0.5133
 GVX  C11  C  CH1    0  -0.199  -1.4853  -1.5049   0.0388
 GVX  C12  C  C      0   0.554  -2.1529  -2.7280   0.6857
 GVX  O13  O  O      0  -0.496  -2.5610  -2.6936   1.8370
 GVX  N14  N  NH1    0  -0.626  -2.1831  -3.8062  -0.0926
 GVX  C15  C  CH2    0  -0.411  -2.6670  -5.0973   0.3239
 GVX  C16  C  C      0   0.400  -2.5304  -6.1259  -0.8179
 GVX  O17  O  OC    -1  -0.608  -2.8997  -7.2789  -0.5394
 GVX  O18  O  O      0  -0.599  -2.0709  -5.7127  -1.9000
 GVX  C19  C  CH2    0  -0.580  -0.0002  -1.5515   0.3872
 GVX  S20  S  S2     0   0.058   0.8270  -0.1631  -0.4318
 GVX  C21  C  C      0   0.087   2.4911  -0.3061   0.1355
 GVX  S22  S  S1     0  -0.311   3.0380  -1.5209   1.1224
 GVX  N23  N  NH1    0  -0.571   3.2562   0.6741  -0.3235
 GVX  C24  C  CH2    0  -0.227   4.6715   0.7996  -0.0313
 GVX  C25  C  CH2    0  -0.567   5.2140   2.1039  -0.6050
 GVX  C26  C  C      0   0.122   6.6821   2.2355  -0.3097
 GVX  C27  C  C1     0  -0.302   7.6277   1.6566  -1.1533
 GVX  C28  C  C1     0  -0.239   8.9832   1.7398  -0.8653
 GVX  C29  C  C1     0  -0.270   9.4130   2.4043   0.2762
 GVX  C30  C  C1     0  -0.240   8.4789   2.9856   1.1236
 GVX  C31  C  C1     0  -0.305   7.1238   2.9001   0.8314
 GVX  H2   H  HCH1   0   0.212  -4.2110   4.0320   0.8212
 GVX  H3   H  HNH2   0   0.336  -6.1734   4.1325   2.0415
 GVX  H4   H  HNH2   0   0.323  -6.8497   2.9135   1.2545
 GVX  H6   H  HCH2   0   0.220  -5.4752   1.6097  -0.5162
 GVX  H7   H  HCH2   0   0.231  -3.9807   2.3869  -1.0014
 GVX  H8   H  HCH2   0   0.241  -3.0131   1.8941   1.2768
 GVX  H9   H  HCH2   0   0.267  -4.4955   1.0707   1.7068
 GVX  H10  H  HNH1   0   0.405  -1.5489   0.2832   1.1699
 GVX  H11  H  HCH1   0   0.289  -1.6019  -1.5672  -1.0479
 GVX  H12  H  HNH1   0   0.390  -1.8612  -3.7659  -1.0502
 GVX  H13  H  HCH2   0   0.244  -2.1125  -5.4553   1.1963
 GVX  H14  H  HCH2   0   0.244  -3.7171  -5.0392   0.6261
 GVX  H16  H  HCH2   0   0.300   0.1519  -1.4778   1.4641
 GVX  H17  H  HCH2   0   0.311   0.4386  -2.4857   0.0410
 GVX  H18  H  HNH1   0   0.420   2.8481   1.3771  -0.9252
 GVX  H19  H  HCH2   0   0.255   4.8182   0.7702   1.0504
 GVX  H20  H  HCH2   0   0.254   5.2090  -0.0554  -0.4500
 GVX  H21  H  HCH2   0   0.264   5.0475   2.1267  -1.6852
 GVX  H22  H  HCH2   0   0.265   4.6665   2.9460  -0.1749
 GVX  H23  H  H      0   0.250   7.3005   1.1412  -2.0492
 GVX  H24  H  H      0   0.255   9.7041   1.2881  -1.5349
 GVX  H25  H  H      0   0.255  10.4692   2.4717   0.5028
 GVX  H26  H  H      0   0.255   8.8051   3.5079   2.0138
 GVX  H27  H  H      0   0.249   6.4026   3.3620   1.4959

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
 GVX  O18  C16  deloc     1.246  0.020  1.246
 GVX  C15  C16  single    1.543  0.020  1.543
 GVX  C15  N14  single    1.440  0.020  1.440
 GVX  C16  O17  deloc     1.242  0.020  1.242
 GVX  O13  C12  double    1.222  0.020  1.222
 GVX  N14  C12  single    1.330  0.020  1.330
 GVX  C12  C11  single    1.536  0.020  1.536
 GVX  C19  C11  single    1.526  0.020  1.526
 GVX  C19  S20  single    1.812  0.020  1.812
 GVX  C11  N10  single    1.436  0.020  1.436
 GVX  N10  C08  single    1.348  0.020  1.348
 GVX  C29  C28  aromatic  1.389  0.020  1.389
 GVX  C29  C30  aromatic  1.389  0.020  1.389
 GVX  C28  C27  aromatic  1.388  0.020  1.388
 GVX  S20  C21  single    1.764  0.020  1.764
 GVX  C08  C07  single    1.508  0.020  1.508
 GVX  C08  O09  double    1.223  0.020  1.223
 GVX  C07  C06  single    1.524  0.020  1.524
 GVX  C30  C31  aromatic  1.389  0.020  1.389
 GVX  O03  C02  deloc     1.246  0.020  1.246
 GVX  C27  C26  aromatic  1.393  0.020  1.393
 GVX  N23  C21  single    1.325  0.020  1.325
 GVX  N23  C24  single    1.451  0.020  1.451
 GVX  C21  S22  double    1.658  0.020  1.658
 GVX  C31  C26  aromatic  1.392  0.020  1.392
 GVX  C26  C25  single    1.503  0.020  1.503
 GVX  C02  C04  single    1.551  0.020  1.551
 GVX  C02  O01  deloc     1.249  0.020  1.249
 GVX  C04  C06  single    1.530  0.020  1.530
 GVX  C04  N05  single    1.454  0.020  1.454
 GVX  C24  C25  single    1.525  0.020  1.525
 GVX  C04  H2   single    0.970  0.020  1.090
 GVX  N05  H3   single    0.890  0.020  1.040
 GVX  N05  H4   single    0.890  0.020  1.040
 GVX  C06  H6   single    0.970  0.020  1.090
 GVX  C06  H7   single    0.970  0.020  1.090
 GVX  C07  H8   single    0.970  0.020  1.090
 GVX  C07  H9   single    0.970  0.020  1.090
 GVX  N10  H10  single    0.860  0.020  1.020
 GVX  C11  H11  single    0.970  0.020  1.090
 GVX  N14  H12  single    0.860  0.020  1.020
 GVX  C15  H13  single    0.970  0.020  1.090
 GVX  C15  H14  single    0.970  0.020  1.090
 GVX  C19  H16  single    0.970  0.020  1.090
 GVX  C19  H17  single    0.970  0.020  1.090
 GVX  N23  H18  single    0.860  0.020  1.020
 GVX  C24  H19  single    0.970  0.020  1.090
 GVX  C24  H20  single    0.970  0.020  1.090
 GVX  C25  H21  single    0.970  0.020  1.090
 GVX  C25  H22  single    0.970  0.020  1.090
 GVX  C27  H23  single    0.930  0.020  1.080
 GVX  C28  H24  single    0.930  0.020  1.080
 GVX  C29  H25  single    0.930  0.020  1.080
 GVX  C30  H26  single    0.930  0.020  1.080
 GVX  C31  H27  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
 GVX  C04  C02  O03  117.72  3.000
 GVX  C04  C02  O01  115.76  3.000
 GVX  O03  C02  O01  126.51  3.000
 GVX  H2   C04  C06  107.36  3.000
 GVX  H2   C04  N05  107.29  3.000
 GVX  C06  C04  N05  110.03  3.000
 GVX  H2   C04  C02  107.06  3.000
 GVX  N05  C04  C02  115.66  3.000
 GVX  C06  C04  C02  109.09  3.000
 GVX  H4   N05  H3   104.33  3.000
 GVX  H4   N05  C04  108.08  3.000
 GVX  H3   N05  C04  108.69  3.000
 GVX  H7   C06  H6   106.64  3.000
 GVX  H7   C06  C07  109.66  3.000
 GVX  H6   C06  C07  109.58  3.000
 GVX  H7   C06  C04  108.58  3.000
 GVX  H6   C06  C04  109.38  3.000
 GVX  C07  C06  C04  112.81  3.000
 GVX  H9   C07  H8   106.30  3.000
 GVX  H9   C07  C08  108.24  3.000
 GVX  H8   C07  C08  110.52  3.000
 GVX  H9   C07  C06  109.62  3.000
 GVX  H8   C07  C06  109.85  3.000
 GVX  C08  C07  C06  112.13  3.000
 GVX  N10  C08  O09  121.32  3.000
 GVX  O09  C08  C07  122.99  3.000
 GVX  N10  C08  C07  115.69  3.000
 GVX  H10  N10  C11  118.98  3.000
 GVX  H10  N10  C08  119.02  3.000
 GVX  C11  N10  C08  121.30  3.000
 GVX  H11  C11  C19  109.17  3.000
 GVX  H11  C11  C12  109.05  3.000
 GVX  C19  C11  C12  107.60  3.000
 GVX  H11  C11  N10  109.48  3.000
 GVX  C19  C11  N10  110.12  3.000
 GVX  C12  C11  N10  111.37  3.000
 GVX  N14  C12  O13  124.51  3.000
 GVX  N14  C12  C11  114.13  3.000
 GVX  O13  C12  C11  121.30  3.000
 GVX  H12  N14  C15  114.62  3.000
 GVX  H12  N14  C12  120.97  3.000
 GVX  C15  N14  C12  124.41  3.000
 GVX  H14  C15  H13  106.47  3.000
 GVX  H14  C15  C16  108.95  3.000
 GVX  H13  C15  C16  109.10  3.000
 GVX  H14  C15  N14  110.77  3.000
 GVX  H13  C15  N14  110.71  3.000
 GVX  C16  C15  N14  110.73  3.000
 GVX  O18  C16  O17  127.74  3.000
 GVX  O17  C16  C15  115.25  3.000
 GVX  O18  C16  C15  117.02  3.000
 GVX  H17  C19  H16  108.42  3.000
 GVX  H17  C19  S20  109.26  3.000
 GVX  H16  C19  S20  109.33  3.000
 GVX  H17  C19  C11  110.24  3.000
 GVX  H16  C19  C11  111.05  3.000
 GVX  S20  C19  C11  108.52  3.000
 GVX  C21  S20  C19  102.90  3.000
 GVX  N23  C21  S22  123.89  3.000
 GVX  S22  C21  S20  124.19  3.000
 GVX  N23  C21  S20  111.92  3.000
 GVX  H18  N23  C24  116.96  3.000
 GVX  H18  N23  C21  119.15  3.000
 GVX  C24  N23  C21  123.88  3.000
 GVX  H20  C24  H19  106.99  3.000
 GVX  H20  C24  C25  110.48  3.000
 GVX  H19  C24  C25  110.36  3.000
 GVX  H20  C24  N23  109.56  3.000
 GVX  H19  C24  N23  109.17  3.000
 GVX  C25  C24  N23  110.21  3.000
 GVX  H22  C25  H21  107.25  3.000
 GVX  H22  C25  C26  110.15  3.000
 GVX  H21  C25  C26  109.94  3.000
 GVX  H22  C25  C24  109.44  3.000
 GVX  H21  C25  C24  109.60  3.000
 GVX  C26  C25  C24  110.40  3.000
 GVX  C31  C26  C27  118.63  3.000
 GVX  C31  C26  C25  120.84  3.000
 GVX  C27  C26  C25  120.50  3.000
 GVX  H23  C27  C28  119.64  3.000
 GVX  H23  C27  C26  119.54  3.000
 GVX  C28  C27  C26  120.81  3.000
 GVX  H24  C28  C29  120.12  3.000
 GVX  H24  C28  C27  119.79  3.000
 GVX  C29  C28  C27  120.08  3.000
 GVX  H25  C29  C30  120.17  3.000
 GVX  H25  C29  C28  120.25  3.000
 GVX  C30  C29  C28  119.58  3.000
 GVX  H26  C30  C31  119.78  3.000
 GVX  H26  C30  C29  120.07  3.000
 GVX  C31  C30  C29  120.14  3.000
 GVX  H27  C31  C30  119.60  3.000
 GVX  H27  C31  C26  119.65  3.000
 GVX  C30  C31  C26  120.75  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
 GVX  CONST_01  C29  C28  C27  C26     0.00   0.0  0
 GVX  CONST_02  C29  C30  C31  C26     0.00   0.0  0
 GVX  CONST_03  C30  C29  C28  C27     0.00   0.0  0
 GVX  CONST_04  C30  C31  C26  C27     0.00   0.0  0
 GVX  CONST_05  C31  C30  C29  C28     0.00   0.0  0
 GVX  CONST_06  C31  C26  C27  C28     0.00   0.0  0
 GVX  CONST_07  C28  C27  C26  C25   180.00   0.0  0
 GVX  CONST_08  C30  C31  C26  C25   180.00   0.0  0
 GVX  CONST_09  H24  C28  C27  C26   180.00   0.0  0
 GVX  CONST_10  H26  C30  C31  C26   180.00   0.0  0
 GVX  CONST_11  H25  C29  C28  C27   180.00   0.0  0
 GVX  CONST_12  H27  C31  C26  C27   180.00   0.0  0
 GVX  CONST_13  H23  C27  C28  C29   180.00   0.0  0
 GVX  CONST_14  C11  N10  C08  C07   180.00   0.0  0
 GVX  CONST_15  C11  N10  C08  O09     0.00   0.0  0
 GVX  CONST_16  C15  N14  C12  C11   180.00   0.0  0
 GVX  CONST_17  C15  N14  C12  O13     0.00   0.0  0
 GVX  CONST_18  H10  N10  C08  C07     0.00   0.0  0
 GVX  CONST_19  H12  N14  C12  C11     0.00   0.0  0
 GVX  Var_01    C27  C26  C25  C24    85.53  30.0  2
 GVX  Var_02    C26  C25  C24  N23  -179.75  30.0  3
 GVX  Var_03    C08  C07  C06  C04  -178.58  30.0  1
 GVX  Var_04    N10  C08  C07  C06   133.47  30.0  2
 GVX  Var_05    C16  C15  N14  C12  -178.80  30.0  2
 GVX  Var_06    O18  C16  C15  N14    -1.49  30.0  3
 GVX  Var_07    N23  C21  S20  C19  -177.49  30.0  3
 GVX  Var_08    C24  N23  C21  S20  -179.23  30.0  1
 GVX  Var_09    C25  C24  N23  C21  -174.69  30.0  3
 GVX  Var_10    H16  C19  S20  C21    55.74  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
 GVX  chir_01  C04  C02  C06  N05  positiv
 GVX  chir_02  C11  N10  C12  C19  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
 GVX  plan-1  C25  0.020
 GVX  plan-1  C26  0.020
 GVX  plan-1  C27  0.020
 GVX  plan-1  C28  0.020
 GVX  plan-1  C29  0.020
 GVX  plan-1  C30  0.020
 GVX  plan-1  C31  0.020
 GVX  plan-1  H23  0.020
 GVX  plan-1  H24  0.020
 GVX  plan-1  H25  0.020
 GVX  plan-1  H26  0.020
 GVX  plan-1  H27  0.020
 GVX  plan-2  S20  0.020
 GVX  plan-2  C21  0.020
 GVX  plan-2  S22  0.020
 GVX  plan-2  N23  0.020
 GVX  plan-3  C07  0.020
 GVX  plan-3  C08  0.020
 GVX  plan-3  O09  0.020
 GVX  plan-3  N10  0.020
 GVX  plan-3  C11  0.020
 GVX  plan-3  H10  0.020
 GVX  plan-4  C11  0.020
 GVX  plan-4  C12  0.020
 GVX  plan-4  O13  0.020
 GVX  plan-4  N14  0.020
 GVX  plan-4  C15  0.020
 GVX  plan-4  H12  0.020
 GVX  plan-5  O01  0.020
 GVX  plan-5  C02  0.020
 GVX  plan-5  O03  0.020
 GVX  plan-5  C04  0.020
 GVX  plan-6  C15  0.020
 GVX  plan-6  C16  0.020
 GVX  plan-6  O17  0.020
 GVX  plan-6  O18  0.020

