# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 09:38:54 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-(1~{H}-indol-5-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2ccc3[nH]ccc3c2
#
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
 Q2S  Q2S  '3-(1~{H}-indol-5-yl)benzoic acid'  ligand  29  18  .  2021-08-20  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Q2S
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
 Q2S  N    N  NR15  0  -0.679  -4.7206   1.0094  -0.0664
 Q2S  O    O  OH1   0  -0.594   5.2789   0.3274   0.5367
 Q2S  C1   C  CR6   0  -0.060   3.0082  -0.1338   0.1724
 Q2S  C10  C  CR15  0  -0.024  -5.3025  -0.1350   0.4005
 Q2S  C11  C  CR15  0  -0.424  -4.3471  -1.0862   0.6141
 Q2S  C12  C  CR56  0   0.084  -3.0958  -0.4956   0.2542
 Q2S  C13  C  CR16  0  -0.408  -1.7735  -0.9476   0.2487
 Q2S  C14  C  CR16  0  -0.334   1.6836   0.2940   0.1832
 Q2S  C2   C  CR16  0  -0.279   3.3126  -1.4408  -0.2038
 Q2S  C3   C  CR16  0  -0.226   2.2862  -2.2999  -0.5634
 Q2S  C4   C  CR16  0  -0.305   0.9696  -1.8660  -0.5543
 Q2S  C5   C  CR6   0   0.114   0.6450  -0.5601  -0.1789
 Q2S  C6   C  CR6   0   0.070  -0.7579  -0.0981  -0.1650
 Q2S  C7   C  CR16  0  -0.332  -1.0708   1.2164  -0.5761
 Q2S  C8   C  CR16  0  -0.288  -2.3655   1.6903  -0.5840
 Q2S  C9   C  CR56  0   0.341  -3.3742   0.8246  -0.1654
 Q2S  O1   O  O     0  -0.439   3.8262   1.9742   0.9137
 Q2S  H5   H  HNR5  0   0.411  -5.2152   1.8553  -0.2957
 Q2S  H10  H  HOH1  0   0.488   5.9247   0.9984   0.8031
 Q2S  H6   H  HCR5  0   0.283  -6.3695  -0.1837   0.5463
 Q2S  H7   H  HCR5  0   0.249  -4.5173  -2.0859   0.9804
 Q2S  H8   H  HCR6  0   0.248  -1.5452  -1.9504   0.5897
 Q2S  H9   H  HCR6  0   0.261   1.4588   1.3046   0.4986
 Q2S  H    H  HCR6  0   0.268   4.3340  -1.7939  -0.2230
 Q2S  H1   H  HCR6  0   0.266   2.5153  -3.3136  -0.8637
 Q2S  H2   H  HCR6  0   0.262   0.1858  -2.5478  -0.8604
 Q2S  H3   H  HCR6  0   0.250  -0.2759   1.8680  -0.9171
 Q2S  H4   H  HCR6  0   0.262  -2.5873   2.6975  -0.9129
 Q2S  C    C  C     0   0.534   4.0559   0.8364   0.5788

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
 Q2S  N    C10  aromatic  1.366  0.020  1.366
 Q2S  N    C9   aromatic  1.363  0.020  1.363
 Q2S  C8   C9   aromatic  1.394  0.020  1.394
 Q2S  C8   C7   aromatic  1.379  0.020  1.379
 Q2S  O1   C    double    1.208  0.020  1.208
 Q2S  C10  C11  aromatic  1.365  0.020  1.365
 Q2S  C9   C12  aromatic  1.413  0.020  1.413
 Q2S  C7   C6   aromatic  1.412  0.020  1.412
 Q2S  C11  C12  aromatic  1.430  0.020  1.430
 Q2S  C12  C13  aromatic  1.397  0.020  1.397
 Q2S  C    O    single    1.325  0.020  1.325
 Q2S  C    C1   single    1.485  0.020  1.485
 Q2S  C14  C1   aromatic  1.392  0.020  1.392
 Q2S  C14  C5   aromatic  1.393  0.020  1.393
 Q2S  C6   C13  aromatic  1.387  0.020  1.387
 Q2S  C6   C5   single    1.477  0.020  1.477
 Q2S  C1   C2   aromatic  1.394  0.020  1.394
 Q2S  C5   C4   aromatic  1.397  0.020  1.397
 Q2S  C2   C3   aromatic  1.386  0.020  1.386
 Q2S  C4   C3   aromatic  1.386  0.020  1.386
 Q2S  N    H5   single    0.860  0.020  1.020
 Q2S  O    H10  single    0.850  0.020  0.980
 Q2S  C10  H6   single    0.930  0.020  1.080
 Q2S  C11  H7   single    0.930  0.020  1.080
 Q2S  C13  H8   single    0.930  0.020  1.080
 Q2S  C14  H9   single    0.930  0.020  1.080
 Q2S  C2   H    single    0.930  0.020  1.080
 Q2S  C3   H1   single    0.930  0.020  1.080
 Q2S  C4   H2   single    0.930  0.020  1.080
 Q2S  C7   H3   single    0.930  0.020  1.080
 Q2S  C8   H4   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
 Q2S  H5   N    C9   125.67  3.000
 Q2S  H5   N    C10  124.94  3.000
 Q2S  C9   N    C10  109.40  3.000
 Q2S  H10  O    C    109.90  3.000
 Q2S  C2   C1   C14  119.88  3.000
 Q2S  C2   C1   C    122.18  3.000
 Q2S  C14  C1   C    117.94  3.000
 Q2S  H6   C10  C11  129.80  3.000
 Q2S  H6   C10  N    120.38  3.000
 Q2S  C11  C10  N    109.82  3.000
 Q2S  H7   C11  C12  127.35  3.000
 Q2S  H7   C11  C10  126.07  3.000
 Q2S  C12  C11  C10  106.58  3.000
 Q2S  C9   C12  C13  119.18  3.000
 Q2S  C13  C12  C11  134.07  3.000
 Q2S  C9   C12  C11  106.75  3.000
 Q2S  H8   C13  C6   120.42  3.000
 Q2S  H8   C13  C12  119.83  3.000
 Q2S  C6   C13  C12  119.73  3.000
 Q2S  H9   C14  C5   119.57  3.000
 Q2S  H9   C14  C1   119.14  3.000
 Q2S  C5   C14  C1   121.28  3.000
 Q2S  H    C2   C3   119.52  3.000
 Q2S  H    C2   C1   121.17  3.000
 Q2S  C3   C2   C1   119.31  3.000
 Q2S  H1   C3   C4   119.76  3.000
 Q2S  H1   C3   C2   119.74  3.000
 Q2S  C4   C3   C2   120.50  3.000
 Q2S  H2   C4   C5   119.75  3.000
 Q2S  H2   C4   C3   119.23  3.000
 Q2S  C5   C4   C3   121.00  3.000
 Q2S  C6   C5   C4   121.04  3.000
 Q2S  C4   C5   C14  118.02  3.000
 Q2S  C6   C5   C14  120.94  3.000
 Q2S  C7   C6   C5   119.92  3.000
 Q2S  C5   C6   C13  120.44  3.000
 Q2S  C7   C6   C13  119.64  3.000
 Q2S  H3   C7   C8   118.73  3.000
 Q2S  H3   C7   C6   119.28  3.000
 Q2S  C8   C7   C6   121.98  3.000
 Q2S  H4   C8   C9   121.39  3.000
 Q2S  H4   C8   C7   120.93  3.000
 Q2S  C9   C8   C7   117.67  3.000
 Q2S  C8   C9   C12  121.80  3.000
 Q2S  C12  C9   N    107.45  3.000
 Q2S  C8   C9   N    130.75  3.000
 Q2S  O1   C    C1   123.86  3.000
 Q2S  C1   C    O    113.05  3.000
 Q2S  O1   C    O    123.09  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
 Q2S  CONST_01  C12  C11  C10  N      0.00   0.0  0
 Q2S  CONST_02  C7   C8   C9   N    180.00   0.0  0
 Q2S  CONST_03  C11  C12  C9   N      0.00   0.0  0
 Q2S  CONST_04  C13  C12  C9   N    180.00   0.0  0
 Q2S  CONST_05  C6   C5   C14  C1   180.00   0.0  0
 Q2S  CONST_06  C4   C5   C14  C1     0.00   0.0  0
 Q2S  CONST_07  C4   C3   C2   C1     0.00   0.0  0
 Q2S  CONST_08  C8   C9   N    C10  180.00   0.0  0
 Q2S  CONST_09  C12  C9   N    C10    0.00   0.0  0
 Q2S  CONST_10  C9   C12  C11  C10    0.00   0.0  0
 Q2S  CONST_11  C13  C12  C11  C10  180.00   0.0  0
 Q2S  CONST_12  C9   N    C10  C11    0.00   0.0  0
 Q2S  CONST_13  C8   C9   C12  C11  180.00   0.0  0
 Q2S  CONST_14  C6   C13  C12  C11  180.00   0.0  0
 Q2S  CONST_15  C7   C8   C9   C12    0.00   0.0  0
 Q2S  CONST_16  C7   C6   C13  C12    0.00   0.0  0
 Q2S  CONST_17  C5   C6   C13  C12  180.00   0.0  0
 Q2S  CONST_18  C8   C9   C12  C13    0.00   0.0  0
 Q2S  CONST_19  C8   C7   C6   C13    0.00   0.0  0
 Q2S  CONST_22  C3   C2   C1   C14    0.00   0.0  0
 Q2S  CONST_24  C3   C4   C5   C14    0.00   0.0  0
 Q2S  CONST_25  C5   C14  C1   C2     0.00   0.0  0
 Q2S  CONST_26  C5   C4   C3   C2     0.00   0.0  0
 Q2S  CONST_27  C6   C5   C4   C3   180.00   0.0  0
 Q2S  CONST_29  C8   C7   C6   C5   180.00   0.0  0
 Q2S  CONST_30  C9   C8   C7   C6     0.00   0.0  0
 Q2S  CONST_31  C9   C12  C13  C6     0.00   0.0  0
 Q2S  CONST_32  C5   C14  C1   C    180.00   0.0  0
 Q2S  CONST_33  C3   C2   C1   C    180.00   0.0  0
 Q2S  CONST_34  H7   C11  C10  N    180.00   0.0  0
 Q2S  CONST_35  H4   C8   C9   N      0.00   0.0  0
 Q2S  CONST_36  H1   C3   C2   C1   180.00   0.0  0
 Q2S  CONST_37  H5   N    C10  C11  180.00   0.0  0
 Q2S  CONST_38  H8   C13  C12  C11    0.00   0.0  0
 Q2S  CONST_39  H6   C10  C11  C12  180.00   0.0  0
 Q2S  CONST_40  H3   C7   C6   C13  180.00   0.0  0
 Q2S  CONST_41  H    C2   C1   C14  180.00   0.0  0
 Q2S  CONST_42  H2   C4   C5   C14  180.00   0.0  0
 Q2S  CONST_43  H9   C14  C1   C2   180.00   0.0  0
 Q2S  CONST_44  H10  O    C    C1   180.00   0.0  0
 Q2S  Var_01    C14  C1   C    O    179.82  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
 Q2S  plan-1  C1   0.020
 Q2S  plan-1  C14  0.020
 Q2S  plan-1  C2   0.020
 Q2S  plan-1  C3   0.020
 Q2S  plan-1  C4   0.020
 Q2S  plan-1  C5   0.020
 Q2S  plan-1  C6   0.020
 Q2S  plan-1  H9   0.020
 Q2S  plan-1  H    0.020
 Q2S  plan-1  H1   0.020
 Q2S  plan-1  H2   0.020
 Q2S  plan-1  C    0.020
 Q2S  plan-2  N    0.020
 Q2S  plan-2  C10  0.020
 Q2S  plan-2  C11  0.020
 Q2S  plan-2  C12  0.020
 Q2S  plan-2  C13  0.020
 Q2S  plan-2  C5   0.020
 Q2S  plan-2  C6   0.020
 Q2S  plan-2  C7   0.020
 Q2S  plan-2  C8   0.020
 Q2S  plan-2  C9   0.020
 Q2S  plan-2  H5   0.020
 Q2S  plan-2  H6   0.020
 Q2S  plan-2  H7   0.020
 Q2S  plan-2  H8   0.020
 Q2S  plan-2  H3   0.020
 Q2S  plan-2  H4   0.020
 Q2S  plan-3  O    0.020
 Q2S  plan-3  C1   0.020
 Q2S  plan-3  O1   0.020
 Q2S  plan-3  H10  0.020
 Q2S  plan-3  C    0.020

