# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 04:08:28 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 4-{2-[(2,3-dioxo-1-pentyl-2,3-dihydro-1H-indol-5-yl)sulfanyl]ethyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCN1C(=O)C(=O)c2cc(SCCc3ccc(cc3)C(O)=O)ccc12
#
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
 G3S  G3S  '4-{2-[(2,3-dioxo-1-pentyl-2,3-dihydro-1H-indol-5-yl)sulfanyl]ethyl}benzoic acid'  ligand  50  28  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G3S
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
 G3S  C10  C  CH2    0  -0.510  -3.4229   2.0869  -0.3213
 G3S  C13  C  CR6    0  -0.119   0.7101   1.9165   0.1347
 G3S  C15  C  CR56   0  -0.070   3.0921   1.9792  -0.0079
 G3S  C17  C  CR16   0  -0.285   2.0299  -0.0605   0.7009
 G3S  C20  C  CR5    0   0.453   5.3497   1.2229   0.1166
 G3S  C22  C  CR5    0   0.262   4.4563   2.4398  -0.2305
 G3S  C26  C  CH2    0  -0.416   5.2663  -3.4982   0.1694
 G3S  C28  C  CH3    0  -0.663   5.6327  -5.9138  -0.5107
 G3S  C04  C  CR6    0  -0.113  -6.4408  -0.9997  -0.1264
 G3S  C05  C  CR16   0  -0.274  -6.1398  -0.2215   0.9887
 G3S  C06  C  CR16   0  -0.295  -5.1797   0.7780   0.9240
 G3S  C07  C  CR6    0   0.117  -4.4935   1.0326  -0.2607
 G3S  C08  C  CR16   0  -0.294  -4.7939   0.2565  -1.3774
 G3S  C09  C  CR16   0  -0.274  -5.7524  -0.7440  -1.3100
 G3S  C11  C  CH2    0  -0.573  -2.0654   1.4798   0.0276
 G3S  C14  C  CR16   0  -0.290   1.8799   2.6205  -0.1578
 G3S  C16  C  CR56   0   0.429   3.1752   0.6503   0.4152
 G3S  C18  C  CR16   0  -0.238   0.8046   0.5908   0.5621
 G3S  C25  C  CH2    0  -0.434   4.8274  -2.1073  -0.2687
 G3S  C27  C  CH2    0  -0.419   5.1802  -4.5284  -0.9499
 G3S  N19  N  NR5    0  -0.618   4.5069   0.2285   0.4927
 G3S  O01  O  OC    -1  -0.595  -8.0793  -2.2433   1.0346
 G3S  O03  O  O      0  -0.595  -7.6831  -2.7574  -1.0964
 G3S  O21  O  O      0  -0.413   6.5544   1.1933   0.0564
 G3S  O23  O  O      0  -0.333   4.8827   3.5006  -0.6002
 G3S  S12  S  S2     0   0.048  -0.8108   2.7879  -0.0452
 G3S  H1   H  HCH2   0   0.262  -3.3802   2.5237  -1.3213
 G3S  H2   H  HCH2   0   0.262  -3.6543   2.8954   0.3757
 G3S  H3   H  HCR6   0   0.284   2.0532  -1.0917   1.0266
 G3S  H4   H  HCH2   0   0.261   4.3108  -1.4242   1.7217
 G3S  H5   H  HCH2   0   0.273   5.9480  -1.0387   1.2377
 G3S  H6   H  HCH2   0   0.217   6.2948  -3.4536   0.5431
 G3S  H7   H  HCH2   0   0.217   4.6506  -3.8271   1.0138
 G3S  H8   H  HCH3   0   0.217   6.6713  -5.9024  -0.1757
 G3S  H9   H  HCH3   0   0.217   5.0247  -6.2821   0.3178
 G3S  H10  H  HCH3   0   0.228   5.5552  -6.6361  -1.3236
 G3S  H11  H  HCR6   0   0.241  -6.6656  -0.3980   1.9179
 G3S  H12  H  HCR6   0   0.241  -4.9638   1.3735   1.8044
 G3S  H13  H  HCR6   0   0.241  -4.2745   0.4403  -2.3115
 G3S  H14  H  HCR6   0   0.241  -5.9721  -1.3340  -2.1903
 G3S  H15  H  HCH2   0   0.283  -2.0949   1.0454   1.0279
 G3S  H16  H  HCH2   0   0.285  -1.8067   0.6944  -0.6849
 G3S  H17  H  HCR6   0   0.284   1.8446   3.6486  -0.4978
 G3S  H18  H  HCR6   0   0.286  -0.0897   0.0311   0.7980
 G3S  H19  H  HCH2   0   0.231   3.8007  -2.1465  -0.6451
 G3S  H20  H  HCH2   0   0.235   5.4516  -1.7646  -1.0990
 G3S  H21  H  HCH2   0   0.214   4.1505  -4.5782  -1.3165
 G3S  H22  H  HCH2   0   0.215   5.7872  -4.1941  -1.7968
 G3S  C24  C  CH2    0  -0.322   4.9224  -1.1051   0.8746
 G3S  C02  C  C      0   0.394  -7.4947  -2.0970  -0.0563

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
 G3S  O03  C02  deloc     1.246  0.020  1.246
 G3S  C02  O01  deloc     1.246  0.020  1.246
 G3S  C02  C04  single    1.523  0.020  1.523
 G3S  C05  C06  aromatic  1.387  0.020  1.387
 G3S  C05  C04  aromatic  1.393  0.020  1.393
 G3S  C06  C07  aromatic  1.393  0.020  1.393
 G3S  C04  C09  aromatic  1.393  0.020  1.393
 G3S  C11  S12  single    1.814  0.020  1.814
 G3S  C11  C10  single    1.527  0.020  1.527
 G3S  S12  C13  single    1.762  0.020  1.762
 G3S  C07  C08  aromatic  1.393  0.020  1.393
 G3S  C07  C10  single    1.504  0.020  1.504
 G3S  C09  C08  aromatic  1.387  0.020  1.387
 G3S  C13  C18  aromatic  1.396  0.020  1.396
 G3S  C13  C14  aromatic  1.396  0.020  1.396
 G3S  C18  C17  aromatic  1.395  0.020  1.395
 G3S  C14  C15  aromatic  1.380  0.020  1.380
 G3S  C17  C16  aromatic  1.378  0.020  1.378
 G3S  C15  C16  aromatic  1.397  0.020  1.397
 G3S  C15  C22  single    1.457  0.020  1.457
 G3S  C16  N19  single    1.399  0.020  1.399
 G3S  C28  C27  single    1.522  0.020  1.522
 G3S  C22  O23  double    1.202  0.020  1.202
 G3S  C22  C20  single    1.549  0.020  1.549
 G3S  C25  C24  single    1.523  0.020  1.523
 G3S  C25  C26  single    1.523  0.020  1.523
 G3S  N19  C20  single    1.357  0.020  1.357
 G3S  N19  C24  single    1.448  0.020  1.448
 G3S  C27  C26  single    1.524  0.020  1.524
 G3S  C20  O21  double    1.207  0.020  1.207
 G3S  C10  H1   single    0.970  0.020  1.090
 G3S  C10  H2   single    0.970  0.020  1.090
 G3S  C17  H3   single    0.930  0.020  1.080
 G3S  C24  H4   single    0.970  0.020  1.090
 G3S  C24  H5   single    0.970  0.020  1.090
 G3S  C26  H6   single    0.970  0.020  1.090
 G3S  C26  H7   single    0.970  0.020  1.090
 G3S  C28  H8   single    0.970  0.020  1.090
 G3S  C28  H9   single    0.970  0.020  1.090
 G3S  C28  H10  single    0.970  0.020  1.090
 G3S  C05  H11  single    0.930  0.020  1.080
 G3S  C06  H12  single    0.930  0.020  1.080
 G3S  C08  H13  single    0.930  0.020  1.080
 G3S  C09  H14  single    0.930  0.020  1.080
 G3S  C11  H15  single    0.970  0.020  1.090
 G3S  C11  H16  single    0.970  0.020  1.090
 G3S  C14  H17  single    0.930  0.020  1.080
 G3S  C18  H18  single    0.930  0.020  1.080
 G3S  C25  H19  single    0.970  0.020  1.090
 G3S  C25  H20  single    0.970  0.020  1.090
 G3S  C27  H21  single    0.970  0.020  1.090
 G3S  C27  H22  single    0.970  0.020  1.090

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
 G3S  H2   C10  H1   107.25  3.000
 G3S  H2   C10  C11  109.68  3.000
 G3S  H1   C10  C11  109.47  3.000
 G3S  H2   C10  C07  110.03  3.000
 G3S  H1   C10  C07  110.19  3.000
 G3S  C11  C10  C07  110.17  3.000
 G3S  S12  C13  C18  124.01  3.000
 G3S  C18  C13  C14  119.09  3.000
 G3S  S12  C13  C14  116.89  3.000
 G3S  C16  C15  C14  121.83  3.000
 G3S  C16  C15  C22  106.93  3.000
 G3S  C14  C15  C22  131.24  3.000
 G3S  H3   C17  C18  119.61  3.000
 G3S  H3   C17  C16  122.44  3.000
 G3S  C18  C17  C16  117.95  3.000
 G3S  O21  C20  N19  128.03  3.000
 G3S  O21  C20  C22  125.73  3.000
 G3S  N19  C20  C22  106.24  3.000
 G3S  O23  C22  C20  123.91  3.000
 G3S  C20  C22  C15  104.92  3.000
 G3S  O23  C22  C15  131.17  3.000
 G3S  H7   C26  H6   106.08  3.000
 G3S  H7   C26  C27  109.36  3.000
 G3S  H6   C26  C27  109.34  3.000
 G3S  H7   C26  C25  109.51  3.000
 G3S  H6   C26  C25  109.37  3.000
 G3S  C27  C26  C25  112.95  3.000
 G3S  H10  C28  H9   107.62  3.000
 G3S  H10  C28  H8   107.66  3.000
 G3S  H9   C28  H8   107.50  3.000
 G3S  H10  C28  C27  111.51  3.000
 G3S  H9   C28  C27  111.13  3.000
 G3S  H8   C28  C27  111.22  3.000
 G3S  C09  C04  C05  118.09  3.000
 G3S  C09  C04  C02  120.88  3.000
 G3S  C05  C04  C02  121.02  3.000
 G3S  H11  C05  C06  119.59  3.000
 G3S  H11  C05  C04  119.43  3.000
 G3S  C06  C05  C04  120.99  3.000
 G3S  H12  C06  C07  119.48  3.000
 G3S  H12  C06  C05  119.70  3.000
 G3S  C07  C06  C05  120.82  3.000
 G3S  C08  C07  C06  118.29  3.000
 G3S  C08  C07  C10  120.80  3.000
 G3S  C06  C07  C10  120.88  3.000
 G3S  H13  C08  C09  119.67  3.000
 G3S  H13  C08  C07  119.53  3.000
 G3S  C09  C08  C07  120.80  3.000
 G3S  H14  C09  C08  119.60  3.000
 G3S  H14  C09  C04  119.39  3.000
 G3S  C08  C09  C04  121.01  3.000
 G3S  H16  C11  H15  108.57  3.000
 G3S  H16  C11  S12  109.20  3.000
 G3S  H15  C11  S12  110.04  3.000
 G3S  H16  C11  C10  110.33  3.000
 G3S  H15  C11  C10  110.09  3.000
 G3S  S12  C11  C10  108.59  3.000
 G3S  H17  C14  C15  120.26  3.000
 G3S  H17  C14  C13  121.12  3.000
 G3S  C15  C14  C13  118.62  3.000
 G3S  N19  C16  C17  128.62  3.000
 G3S  N19  C16  C15  111.11  3.000
 G3S  C17  C16  C15  120.27  3.000
 G3S  H18  C18  C17  117.60  3.000
 G3S  H18  C18  C13  120.16  3.000
 G3S  C17  C18  C13  122.24  3.000
 G3S  H20  C25  H19  106.59  3.000
 G3S  H20  C25  C26  109.88  3.000
 G3S  H19  C25  C26  109.67  3.000
 G3S  H20  C25  C24  109.15  3.000
 G3S  H19  C25  C24  109.89  3.000
 G3S  C26  C25  C24  111.53  3.000
 G3S  H22  C27  H21  106.06  3.000
 G3S  H22  C27  C28  109.66  3.000
 G3S  H21  C27  C28  109.57  3.000
 G3S  H22  C27  C26  109.31  3.000
 G3S  H21  C27  C26  109.28  3.000
 G3S  C28  C27  C26  112.75  3.000
 G3S  C16  N19  C24  124.43  3.000
 G3S  C24  N19  C20  124.74  3.000
 G3S  C16  N19  C20  110.79  3.000
 G3S  C11  S12  C13  103.66  3.000
 G3S  H5   C24  H4   106.63  3.000
 G3S  H5   C24  N19  107.56  3.000
 G3S  H4   C24  N19  108.23  3.000
 G3S  H5   C24  C25  110.41  3.000
 G3S  H4   C24  C25  110.79  3.000
 G3S  N19  C24  C25  112.96  3.000
 G3S  O03  C02  O01  126.69  3.000
 G3S  O01  C02  C04  116.70  3.000
 G3S  O03  C02  C04  116.61  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
 G3S  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 G3S  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 G3S  CONST_03  C18  C13  C14  C15     0.00   0.0  0
 G3S  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 G3S  CONST_05  C14  C13  C18  C17     0.00   0.0  0
 G3S  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 G3S  CONST_07  C07  C06  C05  C04     0.00   0.0  0
 G3S  CONST_08  C07  C08  C09  C04     0.00   0.0  0
 G3S  CONST_09  C08  C07  C06  C05     0.00   0.0  0
 G3S  CONST_10  C08  C09  C04  C05     0.00   0.0  0
 G3S  CONST_11  C09  C04  C05  C06     0.00   0.0  0
 G3S  CONST_12  C09  C08  C07  C06     0.00   0.0  0
 G3S  CONST_13  C16  N19  C20  C22     0.00   0.0  0
 G3S  CONST_14  C05  C06  C07  C10   180.00   0.0  0
 G3S  CONST_15  C09  C08  C07  C10   180.00   0.0  0
 G3S  CONST_16  S12  C13  C14  C15   180.00   0.0  0
 G3S  CONST_17  S12  C13  C18  C17   180.00   0.0  0
 G3S  CONST_18  C06  C05  C04  C02   180.00   0.0  0
 G3S  CONST_19  C08  C09  C04  C02   180.00   0.0  0
 G3S  CONST_20  C24  N19  C20  C22   180.00   0.0  0
 G3S  CONST_21  O21  C20  N19  C16   180.00   0.0  0
 G3S  CONST_22  H3   C17  C18  C13   180.00   0.0  0
 G3S  CONST_23  H17  C14  C15  C22     0.00   0.0  0
 G3S  CONST_24  H12  C06  C05  C04   180.00   0.0  0
 G3S  CONST_25  H13  C08  C09  C04   180.00   0.0  0
 G3S  CONST_26  H14  C09  C04  C05   180.00   0.0  0
 G3S  CONST_27  H11  C05  C06  C07   180.00   0.0  0
 G3S  CONST_28  H18  C18  C13  C14   180.00   0.0  0
 G3S  CONST_29  O21  C20  N19  C24     0.00   0.0  0
 G3S  Var_01    C25  C24  N19  C20   -96.88  30.0  3
 G3S  Var_02    O03  C02  C04  C05  -178.87  30.0  3
 G3S  Var_03    C11  C10  C07  C06    89.57  30.0  2
 G3S  Var_04    C18  C13  S12  C11   -13.77  30.0  2
 G3S  Var_05    N19  C24  C25  C26  -179.78  30.0  3
 G3S  Var_06    S12  C11  C10  C07  -179.55  30.0  1
 G3S  Var_07    H15  C11  S12  C13    67.59  30.0  1
 G3S  Var_08    C27  C26  C25  C24   179.84  30.0  3
 G3S  Var_09    C25  C26  C27  C28   179.44  30.0  3
 G3S  Var_10    H8   C28  C27  C26   -60.27  30.0  3

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
 G3S  plan-1  C10  0.020
 G3S  plan-1  C04  0.020
 G3S  plan-1  C05  0.020
 G3S  plan-1  C06  0.020
 G3S  plan-1  C07  0.020
 G3S  plan-1  C08  0.020
 G3S  plan-1  C09  0.020
 G3S  plan-1  H11  0.020
 G3S  plan-1  H12  0.020
 G3S  plan-1  H13  0.020
 G3S  plan-1  H14  0.020
 G3S  plan-1  C02  0.020
 G3S  plan-2  C13  0.020
 G3S  plan-2  C15  0.020
 G3S  plan-2  C17  0.020
 G3S  plan-2  C20  0.020
 G3S  plan-2  C22  0.020
 G3S  plan-2  C14  0.020
 G3S  plan-2  C16  0.020
 G3S  plan-2  C18  0.020
 G3S  plan-2  N19  0.020
 G3S  plan-2  O21  0.020
 G3S  plan-2  O23  0.020
 G3S  plan-2  S12  0.020
 G3S  plan-2  H3   0.020
 G3S  plan-2  H17  0.020
 G3S  plan-2  H18  0.020
 G3S  plan-2  C24  0.020
 G3S  plan-3  C04  0.020
 G3S  plan-3  O01  0.020
 G3S  plan-3  O03  0.020
 G3S  plan-3  C02  0.020

