# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:00:50 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1CN2C(=O)Cc3ccccc23
#
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
 8P3  8P3  '2-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]benzoic acid'  ligand  33  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8P3
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
 8P3  C1    C  CR16  0  -0.265   3.9191  -1.8189  -0.7426
 8P3  C2    C  CR16  0  -0.265   2.6367  -2.1349  -1.1699
 8P3  C3    C  CR16  0  -0.306   1.5761  -1.2483  -0.9903
 8P3  C4    C  CR56  0   0.431   1.8531  -0.0410  -0.3766
 8P3  C5    C  CR56  0   0.006   3.1339   0.2893   0.0625
 8P3  C6    C  CR16  0  -0.328   4.1742  -0.5970  -0.1183
 8P3  C7    C  CH2   0  -0.611   3.0773   1.6458   0.6855
 8P3  C8    C  CR5   0   0.518   1.6197   2.0403   0.5338
 8P3  O9    O  O     0  -0.457   1.0961   3.0751   0.8882
 8P3  N10   N  NR5   0  -0.595   0.9753   1.0042  -0.0884
 8P3  C11   C  CH2   0  -0.369  -0.4146   1.0140  -0.4617
 8P3  C12   C  CR6   0   0.092  -1.2726   0.1093   0.4011
 8P3  C13   C  CR6   0  -0.097  -2.5563  -0.3079   0.0068
 8P3  C14   C  CR16  0  -0.250  -3.2941  -1.1622   0.8279
 8P3  C15   C  CR16  0  -0.255  -2.7910  -1.5945   2.0423
 8P3  C16   C  CR16  0  -0.226  -1.5299  -1.1804   2.4384
 8P3  C17   C  CR16  0  -0.281  -0.7832  -0.3451   1.6206
 8P3  C18   C  C     0   0.507  -3.1742   0.1815  -1.2521
 8P3  O19   O  O     0  -0.435  -2.8766   1.2129  -1.8067
 8P3  O20   O  OH1   0  -0.590  -4.1143  -0.6341  -1.7106
 8P3  H1    H  HCR6  0   0.255   4.7259  -2.5237  -0.8936
 8P3  H2    H  HCR6  0   0.259   2.4500  -3.0867  -1.6503
 8P3  H3    H  HCR6  0   0.267   0.5790  -1.5107  -1.3190
 8P3  H6    H  HCR6  0   0.258   5.1740  -0.3496   0.2158
 8P3  H7    H  HCH2  0   0.305   3.3504   1.6450   1.7438
 8P3  H7A   H  HCH2  0   0.305   3.7163   2.3824   0.1923
 8P3  H11   H  HCH2  0   0.297  -0.7662   2.0432  -0.3968
 8P3  H11A  H  HCH2  0   0.275  -0.4862   0.7292  -1.5117
 8P3  H14   H  HCR6  0   0.272  -4.2814  -1.4837   0.5277
 8P3  H15   H  HCR6  0   0.268  -3.3798  -2.2492   2.6701
 8P3  H16   H  HCR6  0   0.269  -1.1186  -1.5084   3.3839
 8P3  H17   H  HCR6  0   0.258   0.2032  -0.0505   1.9514
 8P3  HO20  H  HOH1  0   0.488  -4.5201  -0.2534  -2.5040

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
 8P3  C6   C1    aromatic  1.396  0.020  1.396
 8P3  C1   C2    aromatic  1.388  0.020  1.388
 8P3  C1   H1    single    0.930  0.020  1.080
 8P3  C3   C2    aromatic  1.394  0.020  1.394
 8P3  C2   H2    single    0.930  0.020  1.080
 8P3  C4   C3    aromatic  1.382  0.020  1.382
 8P3  C3   H3    single    0.930  0.020  1.080
 8P3  C5   C4    aromatic  1.394  0.020  1.394
 8P3  N10  C4    single    1.395  0.020  1.395
 8P3  C7   C5    single    1.494  0.020  1.494
 8P3  C5   C6    aromatic  1.379  0.020  1.379
 8P3  C6   H6    single    0.930  0.020  1.080
 8P3  C8   C7    single    1.518  0.020  1.518
 8P3  C7   H7    single    0.970  0.020  1.090
 8P3  C7   H7A   single    0.970  0.020  1.090
 8P3  O9   C8    double    1.213  0.020  1.213
 8P3  C8   N10   single    1.370  0.020  1.370
 8P3  N10  C11   single    1.439  0.020  1.439
 8P3  C12  C11   single    1.516  0.020  1.516
 8P3  C11  H11   single    0.970  0.020  1.090
 8P3  C11  H11A  single    0.970  0.020  1.090
 8P3  C17  C12   aromatic  1.390  0.020  1.390
 8P3  C12  C13   aromatic  1.406  0.020  1.406
 8P3  C14  C13   aromatic  1.396  0.020  1.396
 8P3  C13  C18   single    1.485  0.020  1.485
 8P3  C15  C14   aromatic  1.384  0.020  1.384
 8P3  C14  H14   single    0.930  0.020  1.080
 8P3  C16  C15   aromatic  1.385  0.020  1.385
 8P3  C15  H15   single    0.930  0.020  1.080
 8P3  C16  C17   aromatic  1.387  0.020  1.387
 8P3  C16  H16   single    0.930  0.020  1.080
 8P3  C17  H17   single    0.930  0.020  1.080
 8P3  C18  O19   double    1.208  0.020  1.208
 8P3  C18  O20   single    1.326  0.020  1.326
 8P3  O20  HO20  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
 8P3  H1    C1   C6   119.77  3.000
 8P3  H1    C1   C2   119.85  3.000
 8P3  C6    C1   C2   120.38  3.000
 8P3  H2    C2   C3   119.03  3.000
 8P3  H2    C2   C1   119.75  3.000
 8P3  C3    C2   C1   121.23  3.000
 8P3  H3    C3   C4   122.09  3.000
 8P3  H3    C3   C2   120.51  3.000
 8P3  C4    C3   C2   117.40  3.000
 8P3  N10   C4   C5   109.60  3.000
 8P3  N10   C4   C3   128.32  3.000
 8P3  C5    C4   C3   122.08  3.000
 8P3  C7    C5   C6   131.85  3.000
 8P3  C6    C5   C4   119.98  3.000
 8P3  C7    C5   C4   108.17  3.000
 8P3  H6    C6   C5   120.62  3.000
 8P3  H6    C6   C1   120.45  3.000
 8P3  C5    C6   C1   118.93  3.000
 8P3  H7A   C7   H7   106.94  3.000
 8P3  H7A   C7   C8   109.96  3.000
 8P3  H7    C7   C8   109.69  3.000
 8P3  H7A   C7   C5   113.68  3.000
 8P3  H7    C7   C5   113.18  3.000
 8P3  C8    C7   C5   103.34  3.000
 8P3  N10   C8   O9   125.11  3.000
 8P3  N10   C8   C7   107.50  3.000
 8P3  O9    C8   C7   127.39  3.000
 8P3  C11   N10  C8   124.54  3.000
 8P3  C11   N10  C4   124.00  3.000
 8P3  C8    N10  C4   111.39  3.000
 8P3  H11A  C11  H11  106.43  3.000
 8P3  H11A  C11  C12  110.79  3.000
 8P3  H11   C11  C12  110.31  3.000
 8P3  H11A  C11  N10  108.14  3.000
 8P3  H11   C11  N10  107.62  3.000
 8P3  C12   C11  N10  113.26  3.000
 8P3  C17   C12  C13  118.06  3.000
 8P3  C13   C12  C11  122.28  3.000
 8P3  C17   C12  C11  119.66  3.000
 8P3  C18   C13  C14  118.71  3.000
 8P3  C18   C13  C12  121.31  3.000
 8P3  C14   C13  C12  119.95  3.000
 8P3  H14   C14  C15  118.88  3.000
 8P3  H14   C14  C13  120.10  3.000
 8P3  C15   C14  C13  121.01  3.000
 8P3  H15   C15  C16  120.71  3.000
 8P3  H15   C15  C14  120.04  3.000
 8P3  C16   C15  C14  119.24  3.000
 8P3  H16   C16  C17  119.54  3.000
 8P3  H16   C16  C15  120.35  3.000
 8P3  C17   C16  C15  120.11  3.000
 8P3  H17   C17  C16  118.35  3.000
 8P3  H17   C17  C12  120.03  3.000
 8P3  C16   C17  C12  121.62  3.000
 8P3  O20   C18  O19  122.74  3.000
 8P3  O20   C18  C13  112.66  3.000
 8P3  O19   C18  C13  124.60  3.000
 8P3  HO20  O20  C18  109.77  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
 8P3  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 8P3  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 8P3  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 8P3  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 8P3  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 8P3  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 8P3  CONST_07  C15   C16  C17  C12    0.00   0.0  0
 8P3  CONST_08  C15   C14  C13  C12    0.00   0.0  0
 8P3  CONST_09  C16   C17  C12  C13    0.00   0.0  0
 8P3  CONST_10  C16   C15  C14  C13    0.00   0.0  0
 8P3  CONST_11  C17   C12  C13  C14    0.00   0.0  0
 8P3  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 8P3  CONST_13  C7    C8   N10  C4     0.00   0.0  0
 8P3  CONST_14  C16   C17  C12  C11  180.00   0.0  0
 8P3  CONST_15  C14   C13  C12  C11  180.00   0.0  0
 8P3  CONST_16  C18   C13  C14  C15  180.00   0.0  0
 8P3  CONST_17  C18   C13  C12  C17  180.00   0.0  0
 8P3  CONST_18  O9    C8   N10  C4   180.00   0.0  0
 8P3  CONST_19  C11   N10  C8   C7   180.00   0.0  0
 8P3  CONST_20  H3    C3   C2   C1   180.00   0.0  0
 8P3  CONST_21  H6    C6   C1   C2   180.00   0.0  0
 8P3  CONST_22  H1    C1   C2   C3   180.00   0.0  0
 8P3  CONST_23  H2    C2   C3   C4   180.00   0.0  0
 8P3  CONST_24  H16   C16  C17  C12  180.00   0.0  0
 8P3  CONST_25  H14   C14  C13  C12  180.00   0.0  0
 8P3  CONST_26  H17   C17  C12  C13  180.00   0.0  0
 8P3  CONST_27  H15   C15  C14  C13  180.00   0.0  0
 8P3  CONST_28  C11   N10  C8   O9     0.00   0.0  0
 8P3  CONST_29  HO20  O20  C18  C13  180.00   0.0  0
 8P3  Var_01    C12   C11  N10  C4    75.23  30.0  3
 8P3  Var_02    C17   C12  C11  N10   16.61  30.0  3
 8P3  Var_03    H7    C7   C5   C4   118.13  30.0  1
 8P3  Var_04    O19   C18  C13  C12  -23.59  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
 8P3  plan-1  C11   0.020
 8P3  plan-1  C12   0.020
 8P3  plan-1  C13   0.020
 8P3  plan-1  C14   0.020
 8P3  plan-1  C15   0.020
 8P3  plan-1  C16   0.020
 8P3  plan-1  C17   0.020
 8P3  plan-1  C18   0.020
 8P3  plan-1  H14   0.020
 8P3  plan-1  H15   0.020
 8P3  plan-1  H16   0.020
 8P3  plan-1  H17   0.020
 8P3  plan-2  C1    0.020
 8P3  plan-2  C2    0.020
 8P3  plan-2  C3    0.020
 8P3  plan-2  C4    0.020
 8P3  plan-2  C5    0.020
 8P3  plan-2  C6    0.020
 8P3  plan-2  C7    0.020
 8P3  plan-2  C8    0.020
 8P3  plan-2  O9    0.020
 8P3  plan-2  N10   0.020
 8P3  plan-2  C11   0.020
 8P3  plan-2  H1    0.020
 8P3  plan-2  H2    0.020
 8P3  plan-2  H3    0.020
 8P3  plan-2  H6    0.020
 8P3  plan-3  C13   0.020
 8P3  plan-3  C18   0.020
 8P3  plan-3  O19   0.020
 8P3  plan-3  O20   0.020
 8P3  plan-3  HO20  0.020

