# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:34:40 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2,3-diphenyl-1H-indole-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc2c1[nH]c(c3ccccc3)c2c4ccccc4
#
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
 VX3  VX3  '2,3-diphenyl-1H-indole-7-carboxylic acid'  ligand  38  24  .  2022-07-22  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_VX3
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
 VX3  O2   O  O      0  -0.604  -3.5072   2.1655  -0.0636
 VX3  C16  C  CR5    0  -0.047   0.3680  -0.7240  -0.0025
 VX3  C19  C  CR16   0  -0.223   2.8874  -3.4090  -0.7829
 VX3  C3   C  C      0   0.417  -4.1027   1.0618  -0.0328
 VX3  O4   O  OC    -1  -0.584  -5.3333   0.8911  -0.0252
 VX3  C5   C  CR6    0  -0.162  -3.2263  -0.1720  -0.0055
 VX3  C6   C  CR56   0   0.304  -1.8286  -0.0830   0.0039
 VX3  N7   N  NR15   0  -0.730  -1.0319   1.0189   0.0183
 VX3  C9   C  CR5    0   0.347   0.2850   0.6533   0.0000
 VX3  C10  C  CR6    0   0.020   1.3314   1.6756  -0.0243
 VX3  C11  C  CR16   0  -0.288   2.4778   1.5123  -0.8048
 VX3  C12  C  CR16   0  -0.221   3.4568   2.4922  -0.8316
 VX3  C13  C  CR16   0  -0.246   3.3069   3.6550  -0.0863
 VX3  C14  C  CR16   0  -0.222   2.1678   3.8309   0.6865
 VX3  C15  C  CR16   0  -0.296   1.1881   2.8498   0.7178
 VX3  C17  C  CR6    0   0.015   1.5806  -1.5452   0.0483
 VX3  C18  C  CR16   0  -0.317   1.7436  -2.6247  -0.8228
 VX3  C20  C  CR16   0  -0.254   3.8958  -3.1262   0.1285
 VX3  C21  C  CR16   0  -0.212   3.7446  -2.0589   1.0035
 VX3  C22  C  CR16   0  -0.294   2.5979  -1.2820   0.9685
 VX3  C23  C  CR56   0   0.105  -0.9824  -1.2114  -0.0022
 VX3  C24  C  CR16   0  -0.373  -1.5568  -2.4860   0.0254
 VX3  C25  C  CR16   0  -0.216  -2.9331  -2.5919   0.0282
 VX3  C26  C  CR16   0  -0.316  -3.7502  -1.4534   0.0058
 VX3  H11  H  HCR6   0   0.246   2.5973   0.6188  -1.4029
 VX3  H12  H  HCR6   0   0.238   4.3364   2.3517  -1.4455
 VX3  H13  H  HCR6   0   0.238   4.0722   4.4189  -0.1098
 VX3  H14  H  HCR6   0   0.238   2.0424   4.7315   1.2727
 VX3  H15  H  HCR6   0   0.232   0.3150   2.9935   1.3425
 VX3  H18  H  HCR6   0   0.235   0.9729  -2.8402  -1.5525
 VX3  H20  H  HCR6   0   0.229   4.7914  -3.7327   0.1576
 VX3  H21  H  HCR6   0   0.227   4.5216  -1.8357   1.7232
 VX3  H22  H  HCR6   0   0.229   2.4847  -0.4611   1.6648
 VX3  H24  H  HCR6   0   0.218  -0.9364  -3.3736   0.0448
 VX3  H25  H  HCR6   0   0.215  -3.3929  -3.5715   0.0465
 VX3  H26  H  HCR6   0   0.227  -4.8257  -1.5699  -0.0008
 VX3  HN7  H  HNR5   0   0.390  -1.4238   1.9454  -0.0658
 VX3  H19  H  HCR6   0   0.234   2.9925  -4.2375  -1.4709

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
 VX3  O2   C3   deloc     1.254  0.020  1.254
 VX3  C17  C16  single    1.465  0.020  1.465
 VX3  C9   C16  aromatic  1.380  0.020  1.380
 VX3  C16  C23  aromatic  1.436  0.020  1.436
 VX3  C20  C19  aromatic  1.388  0.020  1.388
 VX3  C19  C18  aromatic  1.387  0.020  1.387
 VX3  C19  H19  single    0.930  0.020  1.080
 VX3  C5   C3   single    1.514  0.020  1.514
 VX3  C3   O4   deloc     1.242  0.020  1.242
 VX3  C6   C5   aromatic  1.401  0.020  1.401
 VX3  C5   C26  aromatic  1.384  0.020  1.384
 VX3  N7   C6   aromatic  1.360  0.020  1.360
 VX3  C23  C6   aromatic  1.410  0.020  1.410
 VX3  C9   N7   aromatic  1.367  0.020  1.367
 VX3  C10  C9   single    1.463  0.020  1.463
 VX3  C11  C10  aromatic  1.396  0.020  1.396
 VX3  C15  C10  aromatic  1.396  0.020  1.396
 VX3  C12  C11  aromatic  1.385  0.020  1.385
 VX3  C11  H11  single    0.930  0.020  1.080
 VX3  C13  C12  aromatic  1.389  0.020  1.389
 VX3  C12  H12  single    0.930  0.020  1.080
 VX3  C13  C14  aromatic  1.388  0.020  1.388
 VX3  C13  H13  single    0.930  0.020  1.080
 VX3  C14  C15  aromatic  1.387  0.020  1.387
 VX3  C14  H14  single    0.930  0.020  1.080
 VX3  C15  H15  single    0.930  0.020  1.080
 VX3  C22  C17  aromatic  1.397  0.020  1.397
 VX3  C17  C18  aromatic  1.397  0.020  1.397
 VX3  C18  H18  single    0.930  0.020  1.080
 VX3  C21  C20  aromatic  1.388  0.020  1.388
 VX3  C20  H20  single    0.930  0.020  1.080
 VX3  C21  C22  aromatic  1.386  0.020  1.386
 VX3  C21  H21  single    0.930  0.020  1.080
 VX3  C22  H22  single    0.930  0.020  1.080
 VX3  C23  C24  aromatic  1.398  0.020  1.398
 VX3  C24  C25  aromatic  1.380  0.020  1.380
 VX3  C24  H24  single    0.930  0.020  1.080
 VX3  C25  C26  aromatic  1.402  0.020  1.402
 VX3  C25  H25  single    0.930  0.020  1.080
 VX3  C26  H26  single    0.930  0.020  1.080
 VX3  N7   HN7  single    0.860  0.020  1.020

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
 VX3  C23  C16  C17  126.02  3.000
 VX3  C23  C16  C9   106.40  3.000
 VX3  C17  C16  C9   127.52  3.000
 VX3  H19  C19  C20  120.18  3.000
 VX3  H19  C19  C18  119.65  3.000
 VX3  C20  C19  C18  120.17  3.000
 VX3  C5   C3   O4   117.47  3.000
 VX3  O4   C3   O2   126.25  3.000
 VX3  C5   C3   O2   116.28  3.000
 VX3  C26  C5   C6   115.88  3.000
 VX3  C26  C5   C3   122.38  3.000
 VX3  C6   C5   C3   121.75  3.000
 VX3  C23  C6   N7   107.27  3.000
 VX3  C23  C6   C5   123.22  3.000
 VX3  N7   C6   C5   129.51  3.000
 VX3  HN7  N7   C9   128.20  3.000
 VX3  HN7  N7   C6   121.02  3.000
 VX3  C9   N7   C6   110.34  3.000
 VX3  C10  C9   N7   120.15  3.000
 VX3  C10  C9   C16  130.88  3.000
 VX3  N7   C9   C16  108.96  3.000
 VX3  C15  C10  C11  118.66  3.000
 VX3  C15  C10  C9   120.35  3.000
 VX3  C11  C10  C9   120.98  3.000
 VX3  H11  C11  C12  119.70  3.000
 VX3  H11  C11  C10  119.75  3.000
 VX3  C12  C11  C10  120.55  3.000
 VX3  H12  C12  C13  120.06  3.000
 VX3  H12  C12  C11  119.58  3.000
 VX3  C13  C12  C11  120.36  3.000
 VX3  H13  C13  C14  120.22  3.000
 VX3  H13  C13  C12  120.21  3.000
 VX3  C14  C13  C12  119.56  3.000
 VX3  H14  C14  C15  119.65  3.000
 VX3  H14  C14  C13  120.16  3.000
 VX3  C15  C14  C13  120.19  3.000
 VX3  H15  C15  C14  119.25  3.000
 VX3  H15  C15  C10  120.05  3.000
 VX3  C14  C15  C10  120.68  3.000
 VX3  C22  C17  C18  118.13  3.000
 VX3  C18  C17  C16  120.54  3.000
 VX3  C22  C17  C16  121.33  3.000
 VX3  H18  C18  C17  119.40  3.000
 VX3  H18  C18  C19  119.58  3.000
 VX3  C17  C18  C19  121.01  3.000
 VX3  H20  C20  C21  120.27  3.000
 VX3  H20  C20  C19  120.31  3.000
 VX3  C21  C20  C19  119.42  3.000
 VX3  H21  C21  C22  119.69  3.000
 VX3  H21  C21  C20  119.96  3.000
 VX3  C22  C21  C20  120.35  3.000
 VX3  H22  C22  C21  119.70  3.000
 VX3  H22  C22  C17  119.38  3.000
 VX3  C21  C22  C17  120.92  3.000
 VX3  C24  C23  C6   118.86  3.000
 VX3  C24  C23  C16  134.09  3.000
 VX3  C6   C23  C16  107.02  3.000
 VX3  H24  C24  C25  120.54  3.000
 VX3  H24  C24  C23  120.80  3.000
 VX3  C25  C24  C23  118.66  3.000
 VX3  H25  C25  C26  119.20  3.000
 VX3  H25  C25  C24  119.55  3.000
 VX3  C26  C25  C24  121.26  3.000
 VX3  H26  C26  C25  119.49  3.000
 VX3  H26  C26  C5   118.42  3.000
 VX3  C25  C26  C5   122.10  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
 VX3  CONST_01  C21  C22  C17  C16  180.00   0.0  0
 VX3  CONST_02  C19  C18  C17  C16  180.00   0.0  0
 VX3  CONST_03  C6   N7   C9   C16    0.00   0.0  0
 VX3  CONST_06  C5   C6   C23  C16  180.00   0.0  0
 VX3  CONST_07  N7   C6   C23  C16    0.00   0.0  0
 VX3  CONST_08  C25  C24  C23  C16  180.00   0.0  0
 VX3  CONST_09  C22  C21  C20  C19    0.00   0.0  0
 VX3  CONST_10  C22  C17  C18  C19    0.00   0.0  0
 VX3  CONST_11  C9   N7   C6   C5   180.00   0.0  0
 VX3  CONST_12  C24  C23  C6   C5     0.00   0.0  0
 VX3  CONST_13  C24  C25  C26  C5     0.00   0.0  0
 VX3  CONST_14  C25  C26  C5   C6     0.00   0.0  0
 VX3  CONST_15  C10  C9   N7   C6   180.00   0.0  0
 VX3  CONST_16  C17  C16  C23  C6   180.00   0.0  0
 VX3  CONST_17  C9   C16  C23  C6     0.00   0.0  0
 VX3  CONST_18  C25  C24  C23  C6     0.00   0.0  0
 VX3  CONST_19  C26  C5   C6   N7   180.00   0.0  0
 VX3  CONST_20  C24  C23  C6   N7   180.00   0.0  0
 VX3  CONST_21  C17  C16  C9   N7   180.00   0.0  0
 VX3  CONST_22  C23  C16  C9   N7     0.00   0.0  0
 VX3  CONST_27  C24  C23  C16  C9   180.00   0.0  0
 VX3  CONST_28  C23  C6   N7   C9     0.00   0.0  0
 VX3  CONST_29  C12  C11  C10  C9   180.00   0.0  0
 VX3  CONST_30  C14  C15  C10  C9   180.00   0.0  0
 VX3  CONST_31  C17  C16  C9   C10    0.00   0.0  0
 VX3  CONST_32  C23  C16  C9   C10  180.00   0.0  0
 VX3  CONST_33  C13  C12  C11  C10    0.00   0.0  0
 VX3  CONST_34  C13  C14  C15  C10    0.00   0.0  0
 VX3  CONST_35  C14  C15  C10  C11    0.00   0.0  0
 VX3  CONST_36  C14  C13  C12  C11    0.00   0.0  0
 VX3  CONST_37  C15  C10  C11  C12    0.00   0.0  0
 VX3  CONST_38  C15  C14  C13  C12    0.00   0.0  0
 VX3  CONST_39  C24  C23  C16  C17    0.00   0.0  0
 VX3  CONST_40  C20  C21  C22  C17    0.00   0.0  0
 VX3  CONST_41  C20  C19  C18  C17    0.00   0.0  0
 VX3  CONST_42  C21  C20  C19  C18    0.00   0.0  0
 VX3  CONST_44  C21  C22  C17  C18    0.00   0.0  0
 VX3  CONST_46  C26  C5   C6   C23    0.00   0.0  0
 VX3  CONST_47  C26  C25  C24  C23    0.00   0.0  0
 VX3  CONST_48  N7   C6   C5   C3     0.00   0.0  0
 VX3  CONST_49  C23  C6   C5   C3   180.00   0.0  0
 VX3  CONST_50  C25  C26  C5   C3   180.00   0.0  0
 VX3  CONST_51  H22  C22  C17  C16    0.00   0.0  0
 VX3  CONST_52  H18  C18  C17  C16    0.00   0.0  0
 VX3  CONST_53  HN7  N7   C9   C16  180.00   0.0  0
 VX3  CONST_54  H24  C24  C23  C16    0.00   0.0  0
 VX3  CONST_55  H21  C21  C20  C19  180.00   0.0  0
 VX3  CONST_56  H25  C25  C26  C5   180.00   0.0  0
 VX3  CONST_57  H26  C26  C5   C6   180.00   0.0  0
 VX3  CONST_58  H11  C11  C10  C9     0.00   0.0  0
 VX3  CONST_59  H15  C15  C10  C9     0.00   0.0  0
 VX3  CONST_60  H12  C12  C11  C10  180.00   0.0  0
 VX3  CONST_61  H14  C14  C15  C10  180.00   0.0  0
 VX3  CONST_62  H13  C13  C12  C11  180.00   0.0  0
 VX3  CONST_63  H19  C19  C18  C17  180.00   0.0  0
 VX3  CONST_64  H20  C20  C19  C18  180.00   0.0  0
 VX3  Var_01    C6   C5   C3   O2     0.88  30.0  2

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
 VX3  plan-1  C9   0.020
 VX3  plan-1  C10  0.020
 VX3  plan-1  C11  0.020
 VX3  plan-1  C12  0.020
 VX3  plan-1  C13  0.020
 VX3  plan-1  C14  0.020
 VX3  plan-1  C15  0.020
 VX3  plan-1  H11  0.020
 VX3  plan-1  H12  0.020
 VX3  plan-1  H13  0.020
 VX3  plan-1  H14  0.020
 VX3  plan-1  H15  0.020
 VX3  plan-2  C16  0.020
 VX3  plan-2  C19  0.020
 VX3  plan-2  C17  0.020
 VX3  plan-2  C18  0.020
 VX3  plan-2  C20  0.020
 VX3  plan-2  C21  0.020
 VX3  plan-2  C22  0.020
 VX3  plan-2  H18  0.020
 VX3  plan-2  H20  0.020
 VX3  plan-2  H21  0.020
 VX3  plan-2  H22  0.020
 VX3  plan-2  H19  0.020
 VX3  plan-3  C16  0.020
 VX3  plan-3  C3   0.020
 VX3  plan-3  C5   0.020
 VX3  plan-3  C6   0.020
 VX3  plan-3  N7   0.020
 VX3  plan-3  C9   0.020
 VX3  plan-3  C10  0.020
 VX3  plan-3  C17  0.020
 VX3  plan-3  C23  0.020
 VX3  plan-3  C24  0.020
 VX3  plan-3  C25  0.020
 VX3  plan-3  C26  0.020
 VX3  plan-3  H24  0.020
 VX3  plan-3  H25  0.020
 VX3  plan-3  H26  0.020
 VX3  plan-3  HN7  0.020
 VX3  plan-4  O2   0.020
 VX3  plan-4  C3   0.020
 VX3  plan-4  O4   0.020
 VX3  plan-4  C5   0.020

