# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:21:14 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(3-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)C2=CC(=O)c3c(O)cc(O)cc3O2
#
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
 O9Q  O9Q  2-(3-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one  ligand  32  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O9Q
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
 O9Q  C4   C  CR6   0   0.406  37.3688  36.6172  33.2814
 O9Q  C5   C  CR66  0  -0.351  37.5158  36.0021  32.0163
 O9Q  C6   C  CR66  0   0.417  38.3601  36.6100  31.0846
 O9Q  C7   C  CR6   0   0.532  36.8228  34.7800  31.6790
 O9Q  C8   C  CR16  0  -0.514  37.0701  34.2823  30.3515
 O9Q  C10  C  CR6   0   0.046  38.2400  34.5043  28.1459
 O9Q  C13  C  CR16  0  -0.294  38.8201  33.6802  25.5565
 O9Q  C15  C  CR16  0  -0.295  38.7040  35.4282  27.2078
 O9Q  C1   C  CR16  0  -0.470  39.0505  37.7754  31.3477
 O9Q  C2   C  CR6   0   0.399  38.8876  38.3548  32.6044
 O9Q  C3   C  CR16  0  -0.495  38.0537  37.7851  33.5694
 O9Q  C9   C  CR6   0   0.409  37.9125  34.9253  29.5129
 O9Q  O1   O  O     0  -0.467  38.5399  36.0547  29.8665
 O9Q  O2   O  O     0  -0.508  36.0653  34.2111  32.4817
 O9Q  O3   O  OH1   0  -0.628  36.5756  36.0792  34.2003
 O9Q  O4   O  OH1   0  -0.616  39.5679  39.4795  32.8431
 O9Q  C11  C  CR16  0  -0.357  38.0819  33.1694  27.7712
 O9Q  C12  C  CR6   0   0.119  38.3695  32.7401  26.4814
 O9Q  C14  C  CR16  0  -0.226  38.9854  35.0094  25.9175
 O9Q  C16  C  CH3   0  -0.721  38.2319  31.2930  26.1097
 O9Q  H1   H  HCR6  0   0.285  36.5582  33.3889  30.0254
 O9Q  H2   H  HCR6  0   0.259  39.0469  33.3687  24.5440
 O9Q  H3   H  HCR6  0   0.264  38.8299  36.4705  27.4660
 O9Q  H4   H  HCR6  0   0.288  39.7007  38.2217  30.6075
 O9Q  H5   H  HCR6  0   0.287  37.9399  38.2469  34.5436
 O9Q  H6   H  HOH1  0   0.477  36.1873  35.2577  33.8097
 O9Q  H7   H  HOH1  0   0.484  39.4108  39.7928  33.7417
 O9Q  H8   H  HCR6  0   0.257  37.7477  32.4402  28.4998
 O9Q  H9   H  HCR6  0   0.264  39.3319  35.7276  25.1860
 O9Q  H10  H  HCH3  0   0.254  39.1535  30.7484  26.3242
 O9Q  H11  H  HCH3  0   0.247  37.4324  30.8105  26.6706
 O9Q  H12  H  HCH3  0   0.248  38.0229  31.1719  25.0475

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
 O9Q  C13  C14  aromatic  1.387  0.020  1.387
 O9Q  C13  C12  aromatic  1.394  0.020  1.394
 O9Q  C14  C15  aromatic  1.385  0.020  1.385
 O9Q  C16  C12  single    1.500  0.020  1.500
 O9Q  C12  C11  aromatic  1.389  0.020  1.389
 O9Q  C15  C10  aromatic  1.396  0.020  1.396
 O9Q  C11  C10  aromatic  1.395  0.020  1.395
 O9Q  C10  C9   single    1.467  0.020  1.467
 O9Q  C9   O1   single    1.340  0.020  1.340
 O9Q  C9   C8   double    1.352  0.020  1.352
 O9Q  O1   C6   single    1.351  0.020  1.351
 O9Q  C8   C7   single    1.439  0.020  1.439
 O9Q  C6   C1   aromatic  1.380  0.020  1.380
 O9Q  C6   C5   aromatic  1.397  0.020  1.397
 O9Q  C1   C2   aromatic  1.393  0.020  1.393
 O9Q  C7   C5   single    1.445  0.020  1.445
 O9Q  C7   O2   double    1.242  0.020  1.242
 O9Q  C5   C4   aromatic  1.414  0.020  1.414
 O9Q  C2   O4   single    1.336  0.020  1.336
 O9Q  C2   C3   aromatic  1.397  0.020  1.397
 O9Q  C4   C3   aromatic  1.384  0.020  1.384
 O9Q  C4   O3   single    1.328  0.020  1.328
 O9Q  C8   H1   single    0.930  0.020  1.080
 O9Q  C13  H2   single    0.930  0.020  1.080
 O9Q  C15  H3   single    0.930  0.020  1.080
 O9Q  C1   H4   single    0.930  0.020  1.080
 O9Q  C3   H5   single    0.930  0.020  1.080
 O9Q  O3   H6   single    0.850  0.020  0.980
 O9Q  O4   H7   single    0.850  0.020  0.980
 O9Q  C11  H8   single    0.930  0.020  1.080
 O9Q  C14  H9   single    0.930  0.020  1.080
 O9Q  C16  H10  single    0.970  0.020  1.090
 O9Q  C16  H11  single    0.970  0.020  1.090
 O9Q  C16  H12  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
 O9Q  O3   C4   C3   119.57  3.000
 O9Q  O3   C4   C5   120.32  3.000
 O9Q  C3   C4   C5   120.11  3.000
 O9Q  C7   C5   C6   120.16  3.000
 O9Q  C7   C5   C4   121.79  3.000
 O9Q  C6   C5   C4   118.05  3.000
 O9Q  O1   C6   C1   116.91  3.000
 O9Q  C1   C6   C5   122.88  3.000
 O9Q  O1   C6   C5   120.21  3.000
 O9Q  O2   C7   C8   122.86  3.000
 O9Q  O2   C7   C5   121.95  3.000
 O9Q  C8   C7   C5   115.18  3.000
 O9Q  H1   C8   C9   120.10  3.000
 O9Q  H1   C8   C7   118.90  3.000
 O9Q  C9   C8   C7   120.99  3.000
 O9Q  C11  C10  C9   119.95  3.000
 O9Q  C9   C10  C15  120.69  3.000
 O9Q  C11  C10  C15  119.36  3.000
 O9Q  H2   C13  C14  119.59  3.000
 O9Q  H2   C13  C12  119.60  3.000
 O9Q  C14  C13  C12  120.80  3.000
 O9Q  H3   C15  C14  119.35  3.000
 O9Q  H3   C15  C10  121.08  3.000
 O9Q  C14  C15  C10  119.56  3.000
 O9Q  H4   C1   C2   121.06  3.000
 O9Q  H4   C1   C6   121.25  3.000
 O9Q  C2   C1   C6   117.69  3.000
 O9Q  O4   C2   C3   121.60  3.000
 O9Q  C3   C2   C1   121.55  3.000
 O9Q  O4   C2   C1   116.85  3.000
 O9Q  H5   C3   C2   120.65  3.000
 O9Q  H5   C3   C4   119.63  3.000
 O9Q  C2   C3   C4   119.72  3.000
 O9Q  O1   C9   C10  112.54  3.000
 O9Q  O1   C9   C8   121.96  3.000
 O9Q  C10  C9   C8   125.50  3.000
 O9Q  C9   O1   C6   121.49  3.000
 O9Q  H6   O3   C4   107.32  3.000
 O9Q  H7   O4   C2   110.92  3.000
 O9Q  H8   C11  C12  118.69  3.000
 O9Q  H8   C11  C10  119.88  3.000
 O9Q  C12  C11  C10  121.42  3.000
 O9Q  C16  C12  C11  120.60  3.000
 O9Q  C11  C12  C13  118.33  3.000
 O9Q  C16  C12  C13  121.05  3.000
 O9Q  H9   C14  C15  119.60  3.000
 O9Q  H9   C14  C13  119.88  3.000
 O9Q  C15  C14  C13  120.52  3.000
 O9Q  H12  C16  H11  108.18  3.000
 O9Q  H12  C16  H10  107.35  3.000
 O9Q  H11  C16  H10  107.31  3.000
 O9Q  H12  C16  C12  111.50  3.000
 O9Q  H11  C16  C12  111.52  3.000
 O9Q  H10  C16  C12  110.79  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
 O9Q  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 O9Q  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 O9Q  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 O9Q  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 O9Q  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 O9Q  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 O9Q  CONST_07  C13  C14  C15  C10    0.00   0.0  0
 O9Q  CONST_08  C13  C12  C11  C10    0.00   0.0  0
 O9Q  CONST_09  C12  C13  C14  C15    0.00   0.0  0
 O9Q  CONST_10  C12  C11  C10  C15    0.00   0.0  0
 O9Q  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 O9Q  CONST_12  C14  C15  C10  C11    0.00   0.0  0
 O9Q  CONST_13  C14  C15  C10  C9   180.00   0.0  0
 O9Q  CONST_14  C12  C11  C10  C9   180.00   0.0  0
 O9Q  CONST_15  O4   C2   C3   C4   180.00   0.0  0
 O9Q  CONST_16  O4   C2   C1   C6   180.00   0.0  0
 O9Q  CONST_17  O3   C4   C5   C6   180.00   0.0  0
 O9Q  CONST_18  O3   C4   C5   C7     0.00   0.0  0
 O9Q  CONST_19  C16  C12  C11  C10  180.00   0.0  0
 O9Q  CONST_20  O3   C4   C3   C2   180.00   0.0  0
 O9Q  CONST_21  C16  C12  C13  C14  180.00   0.0  0
 O9Q  CONST_22  H4   C1   C6   C5   180.00   0.0  0
 O9Q  CONST_23  H5   C3   C4   C5   180.00   0.0  0
 O9Q  CONST_24  H9   C14  C15  C10  180.00   0.0  0
 O9Q  CONST_25  H3   C15  C14  C13  180.00   0.0  0
 O9Q  CONST_26  H8   C11  C12  C13  180.00   0.0  0
 O9Q  CONST_27  H2   C13  C14  C15  180.00   0.0  0
 O9Q  Var_01    C8   C7   C5   C4   179.69  30.0  1
 O9Q  Var_02    C9   C8   C7   C5     0.98  30.0  1
 O9Q  Var_03    C10  C9   O1   C6   179.47  30.0  1
 O9Q  Var_04    C15  C10  C9   C8   156.64  30.0  2
 O9Q  Var_05    H10  C16  C12  C13   90.77  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
 O9Q  plan-1  C10  0.020
 O9Q  plan-1  C13  0.020
 O9Q  plan-1  C15  0.020
 O9Q  plan-1  C9   0.020
 O9Q  plan-1  C11  0.020
 O9Q  plan-1  C12  0.020
 O9Q  plan-1  C14  0.020
 O9Q  plan-1  C16  0.020
 O9Q  plan-1  H2   0.020
 O9Q  plan-1  H3   0.020
 O9Q  plan-1  H8   0.020
 O9Q  plan-1  H9   0.020
 O9Q  plan-2  C4   0.020
 O9Q  plan-2  C5   0.020
 O9Q  plan-2  C6   0.020
 O9Q  plan-2  C7   0.020
 O9Q  plan-2  C1   0.020
 O9Q  plan-2  C2   0.020
 O9Q  plan-2  C3   0.020
 O9Q  plan-2  O1   0.020
 O9Q  plan-2  O3   0.020
 O9Q  plan-2  O4   0.020
 O9Q  plan-2  H4   0.020
 O9Q  plan-2  H5   0.020
 O9Q  plan-3  C5   0.020
 O9Q  plan-3  C7   0.020
 O9Q  plan-3  C8   0.020
 O9Q  plan-3  O2   0.020

