# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:15:52 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  28  18  .  2021-08-20  2021-08-20  
;
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  -4.7574   1.0353  -0.0852
 Q2S  O    O  OC    -1  -0.594   5.2432   0.3448   0.6279
 Q2S  C1   C  C      0  -0.079   2.9702  -0.1491   0.2231
 Q2S  C10  C  CR15   0  -0.026  -5.3487  -0.0991   0.3935
 Q2S  C11  C  CR15   0  -0.426  -4.4004  -1.0544   0.6210
 Q2S  C12  C  CR56   0   0.085  -3.1434  -0.4774   0.2576
 Q2S  C13  C  CR16   0  -0.412  -1.8236  -0.9385   0.2621
 Q2S  C14  C  C1     0  -0.365   1.6453   0.2747   0.2129
 Q2S  C2   C  C1     0  -0.309   3.2566  -1.4585  -0.1546
 Q2S  C3   C  C1     0  -0.230   2.2343  -2.3186  -0.5294
 Q2S  C4   C  C1     0  -0.325   0.9175  -1.8825  -0.5345
 Q2S  C5   C  C      0   0.110   0.6028  -0.5742  -0.1612
 Q2S  C6   C  CR6    0   0.070  -0.7988  -0.1033  -0.1584
 Q2S  C7   C  CR16   0  -0.333  -1.1035   1.2083  -0.5858
 Q2S  C8   C  CR16   0  -0.289  -2.3947   1.6921  -0.6042
 Q2S  C9   C  CR56   0   0.336  -3.4113   0.8390  -0.1788
 Q2S  O1   O  O      0  -0.593   3.7401   1.9465   0.9995
 Q2S  H5   H  HNR5   0   0.410  -5.2459   1.8801  -0.3304
 Q2S  H6   H  HCR5   0   0.281  -6.4165  -0.1394   0.5367
 Q2S  H7   H  HCR5   0   0.247  -4.5783  -2.0481   1.0001
 Q2S  H8   H  HCR6   0   0.244  -1.6027  -1.9389   0.6153
 Q2S  H9   H  H      0   0.237   1.4237   1.2869   0.5264
 Q2S  H    H  H      0   0.242   4.2825  -1.8019  -0.1556
 Q2S  H1   H  H      0   0.248   2.4634  -3.3338  -0.8285
 Q2S  H2   H  H      0   0.247   0.1315  -2.5589  -0.8485
 Q2S  H3   H  HCR6   0   0.247  -0.3018   1.8501  -0.9297
 Q2S  H4   H  HCR6   0   0.260  -2.6079   2.6974  -0.9446
 Q2S  C    C  C      0   0.397   4.0836   0.7993   0.6546

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  1.364  0.020  1.364
 Q2S  C8   C9   aromatic  1.394  0.020  1.394
 Q2S  C8   C7   aromatic  1.379  0.020  1.379
 Q2S  O1   C    deloc     1.246  0.020  1.246
 Q2S  C10  C11  aromatic  1.365  0.020  1.365
 Q2S  C9   C12  aromatic  1.412  0.020  1.412
 Q2S  C7   C6   aromatic  1.413  0.020  1.413
 Q2S  C11  C12  aromatic  1.430  0.020  1.430
 Q2S  C12  C13  aromatic  1.398  0.020  1.398
 Q2S  C    O    deloc     1.246  0.020  1.246
 Q2S  C    C1   single    1.525  0.020  1.525
 Q2S  C14  C1   aromatic  1.391  0.020  1.391
 Q2S  C14  C5   aromatic  1.396  0.020  1.396
 Q2S  C6   C13  aromatic  1.387  0.020  1.387
 Q2S  C6   C5   single    1.479  0.020  1.479
 Q2S  C1   C2   aromatic  1.393  0.020  1.393
 Q2S  C5   C4   aromatic  1.396  0.020  1.396
 Q2S  C2   C3   aromatic  1.388  0.020  1.388
 Q2S  C4   C3   aromatic  1.387  0.020  1.387
 Q2S  N    H5   single    0.860  0.020  1.020
 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   125.69  3.000
 Q2S  H5   N    C10  124.94  3.000
 Q2S  C9   N    C10  109.38  3.000
 Q2S  C2   C1   C14  118.71  3.000
 Q2S  C2   C1   C    120.75  3.000
 Q2S  C14  C1   C    120.53  3.000
 Q2S  H6   C10  C11  129.77  3.000
 Q2S  H6   C10  N    120.42  3.000
 Q2S  C11  C10  N    109.81  3.000
 Q2S  H7   C11  C12  127.32  3.000
 Q2S  H7   C11  C10  126.07  3.000
 Q2S  C12  C11  C10  106.61  3.000
 Q2S  C9   C12  C13  119.17  3.000
 Q2S  C13  C12  C11  134.09  3.000
 Q2S  C9   C12  C11  106.73  3.000
 Q2S  H8   C13  C6   120.26  3.000
 Q2S  H8   C13  C12  119.87  3.000
 Q2S  C6   C13  C12  119.85  3.000
 Q2S  H9   C14  C5   119.57  3.000
 Q2S  H9   C14  C1   118.53  3.000
 Q2S  C5   C14  C1   121.88  3.000
 Q2S  H    C2   C3   120.11  3.000
 Q2S  H    C2   C1   119.59  3.000
 Q2S  C3   C2   C1   120.30  3.000
 Q2S  H1   C3   C4   119.64  3.000
 Q2S  H1   C3   C2   119.99  3.000
 Q2S  C4   C3   C2   120.37  3.000
 Q2S  H2   C4   C5   119.92  3.000
 Q2S  H2   C4   C3   119.58  3.000
 Q2S  C5   C4   C3   120.50  3.000
 Q2S  C6   C5   C4   120.83  3.000
 Q2S  C4   C5   C14  118.24  3.000
 Q2S  C6   C5   C14  120.93  3.000
 Q2S  C7   C6   C5   119.97  3.000
 Q2S  C5   C6   C13  120.60  3.000
 Q2S  C7   C6   C13  119.43  3.000
 Q2S  H3   C7   C8   118.75  3.000
 Q2S  H3   C7   C6   119.12  3.000
 Q2S  C8   C7   C6   122.12  3.000
 Q2S  H4   C8   C9   121.38  3.000
 Q2S  H4   C8   C7   120.96  3.000
 Q2S  C9   C8   C7   117.66  3.000
 Q2S  C8   C9   C12  121.76  3.000
 Q2S  C12  C9   N    107.47  3.000
 Q2S  C8   C9   N    130.77  3.000
 Q2S  O1   C    C1   116.72  3.000
 Q2S  C1   C    O    116.53  3.000
 Q2S  O1   C    O    126.75  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
 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  Var_01    C14  C1   C    O    -179.59  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
 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  C    0.020

