# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 23:49:46 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(4-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)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
 O9T  O9T  2-(4-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_O9T
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
 O9T  C4   C  CR6   0   0.405  37.5387  36.6894  33.5460
 O9T  C5   C  CR66  0  -0.352  37.6010  36.0371  32.2930
 O9T  C6   C  CR66  0   0.418  38.4376  36.5757  31.3130
 O9T  C7   C  CR6   0   0.533  36.8280  34.8482  32.0148
 O9T  C8   C  CR16  0  -0.516  36.9914  34.3068  30.6924
 O9T  C10  C  CR6   0   0.007  38.0755  34.4157  28.4365
 O9T  C13  C  CR6   0   0.098  38.5208  33.5075  25.8092
 O9T  C15  C  CR16  0  -0.289  37.8000  33.0938  28.0813
 O9T  C1   C  CR16  0  -0.469  39.2001  37.7079  31.5180
 O9T  C2   C  CR6   0   0.400  39.1197  38.3253  32.7645
 O9T  C3   C  CR16  0  -0.496  38.2974  37.8239  33.7761
 O9T  C9   C  CR6   0   0.411  37.8313  34.8833  29.8028
 O9T  O1   O  O     0  -0.468  38.5342  35.9840  30.1027
 O9T  O2   O  OH1   0  -0.617  39.8659  39.4183  32.9484
 O9T  O3   O  OH1   0  -0.628  36.7546  36.2189  34.5090
 O9T  O4   O  O     0  -0.509  36.0724  34.3441  32.8619
 O9T  C11  C  CR16  0  -0.259  38.5816  35.2775  27.4610
 O9T  C12  C  CR16  0  -0.281  38.7922  34.8260  26.1694
 O9T  C14  C  CR16  0  -0.278  38.0194  32.6518  26.7893
 O9T  C16  C  CH3   0  -0.722  38.7903  33.0170  24.4195
 O9T  H1   H  HCR6  0   0.284  36.4191  33.4357  30.4097
 O9T  H2   H  HCR6  0   0.263  37.4279  32.3940  28.8184
 O9T  H3   H  HCR6  0   0.287  39.8407  38.1008  30.7400
 O9T  H4   H  HCR6  0   0.287  38.2503  38.3136  34.7416
 O9T  H5   H  HOH1  0   0.484  39.7499  39.7672  33.8400
 O9T  H6   H  HOH1  0   0.477  36.3048  35.4125  34.1539
 O9T  H7   H  HCR6  0   0.264  38.7995  36.3106  27.6934
 O9T  H8   H  HCR6  0   0.257  39.1734  35.5162  25.4266
 O9T  H9   H  HCR6  0   0.259  37.8012  31.6204  26.5406
 O9T  H10  H  HCH3  0   0.256  39.8142  32.6460  24.3359
 O9T  H11  H  HCH3  0   0.249  38.1264  32.1976  24.1465
 O9T  H12  H  HCH3  0   0.249  38.6728  33.8120  23.6842

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
 O9T  C16  C13  single    1.498  0.020  1.498
 O9T  C13  C12  aromatic  1.393  0.020  1.393
 O9T  C13  C14  aromatic  1.394  0.020  1.394
 O9T  C12  C11  aromatic  1.384  0.020  1.384
 O9T  C14  C15  aromatic  1.383  0.020  1.383
 O9T  C11  C10  aromatic  1.397  0.020  1.397
 O9T  C15  C10  aromatic  1.396  0.020  1.396
 O9T  C10  C9   single    1.465  0.020  1.465
 O9T  C9   O1   single    1.340  0.020  1.340
 O9T  C9   C8   double    1.352  0.020  1.352
 O9T  O1   C6   single    1.351  0.020  1.351
 O9T  C8   C7   single    1.438  0.020  1.438
 O9T  C6   C1   aromatic  1.380  0.020  1.380
 O9T  C6   C5   aromatic  1.397  0.020  1.397
 O9T  C1   C2   aromatic  1.393  0.020  1.393
 O9T  C7   C5   single    1.445  0.020  1.445
 O9T  C7   O4   double    1.242  0.020  1.242
 O9T  C5   C4   aromatic  1.414  0.020  1.414
 O9T  C2   O2   single    1.336  0.020  1.336
 O9T  C2   C3   aromatic  1.397  0.020  1.397
 O9T  C4   C3   aromatic  1.384  0.020  1.384
 O9T  C4   O3   single    1.328  0.020  1.328
 O9T  C8   H1   single    0.930  0.020  1.080
 O9T  C15  H2   single    0.930  0.020  1.080
 O9T  C1   H3   single    0.930  0.020  1.080
 O9T  C3   H4   single    0.930  0.020  1.080
 O9T  O2   H5   single    0.850  0.020  0.980
 O9T  O3   H6   single    0.850  0.020  0.980
 O9T  C11  H7   single    0.930  0.020  1.080
 O9T  C12  H8   single    0.930  0.020  1.080
 O9T  C14  H9   single    0.930  0.020  1.080
 O9T  C16  H10  single    0.970  0.020  1.090
 O9T  C16  H11  single    0.970  0.020  1.090
 O9T  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
 O9T  O3   C4   C3   119.57  3.000
 O9T  O3   C4   C5   120.35  3.000
 O9T  C3   C4   C5   120.08  3.000
 O9T  C7   C5   C6   120.17  3.000
 O9T  C7   C5   C4   121.77  3.000
 O9T  C6   C5   C4   118.06  3.000
 O9T  O1   C6   C1   116.93  3.000
 O9T  C1   C6   C5   122.89  3.000
 O9T  O1   C6   C5   120.18  3.000
 O9T  O4   C7   C8   122.92  3.000
 O9T  O4   C7   C5   121.87  3.000
 O9T  C8   C7   C5   115.21  3.000
 O9T  H1   C8   C9   120.05  3.000
 O9T  H1   C8   C7   118.95  3.000
 O9T  C9   C8   C7   120.99  3.000
 O9T  C11  C10  C9   120.99  3.000
 O9T  C9   C10  C15  120.44  3.000
 O9T  C11  C10  C15  118.56  3.000
 O9T  C16  C13  C14  121.05  3.000
 O9T  C14  C13  C12  117.97  3.000
 O9T  C16  C13  C12  120.97  3.000
 O9T  H2   C15  C14  118.95  3.000
 O9T  H2   C15  C10  120.44  3.000
 O9T  C14  C15  C10  120.59  3.000
 O9T  H3   C1   C2   121.11  3.000
 O9T  H3   C1   C6   121.22  3.000
 O9T  C2   C1   C6   117.68  3.000
 O9T  O2   C2   C3   121.52  3.000
 O9T  C3   C2   C1   121.52  3.000
 O9T  O2   C2   C1   116.96  3.000
 O9T  H4   C3   C2   120.57  3.000
 O9T  H4   C3   C4   119.65  3.000
 O9T  C2   C3   C4   119.77  3.000
 O9T  O1   C9   C10  112.56  3.000
 O9T  O1   C9   C8   121.91  3.000
 O9T  C10  C9   C8   125.53  3.000
 O9T  C9   O1   C6   121.53  3.000
 O9T  H5   O2   C2   110.86  3.000
 O9T  H6   O3   C4   107.27  3.000
 O9T  H7   C11  C12  118.79  3.000
 O9T  H7   C11  C10  120.84  3.000
 O9T  C12  C11  C10  120.36  3.000
 O9T  H8   C12  C11  119.04  3.000
 O9T  H8   C12  C13  119.61  3.000
 O9T  C11  C12  C13  121.34  3.000
 O9T  H9   C14  C15  119.14  3.000
 O9T  H9   C14  C13  119.70  3.000
 O9T  C15  C14  C13  121.16  3.000
 O9T  H12  C16  H11  108.31  3.000
 O9T  H12  C16  H10  107.29  3.000
 O9T  H11  C16  H10  107.26  3.000
 O9T  H12  C16  C13  111.58  3.000
 O9T  H11  C16  C13  111.66  3.000
 O9T  H10  C16  C13  110.54  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
 O9T  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 O9T  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 O9T  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 O9T  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 O9T  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 O9T  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 O9T  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 O9T  CONST_08  C13  C14  C15  C10    0.00   0.0  0
 O9T  CONST_09  C12  C13  C14  C15    0.00   0.0  0
 O9T  CONST_10  C12  C11  C10  C15    0.00   0.0  0
 O9T  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 O9T  CONST_12  C14  C15  C10  C11    0.00   0.0  0
 O9T  CONST_13  C12  C11  C10  C9   180.00   0.0  0
 O9T  CONST_14  C14  C15  C10  C9   180.00   0.0  0
 O9T  CONST_15  O2   C2   C3   C4   180.00   0.0  0
 O9T  CONST_16  O2   C2   C1   C6   180.00   0.0  0
 O9T  CONST_17  O3   C4   C5   C6   180.00   0.0  0
 O9T  CONST_18  O3   C4   C5   C7     0.00   0.0  0
 O9T  CONST_19  C16  C13  C14  C15  180.00   0.0  0
 O9T  CONST_20  O3   C4   C3   C2   180.00   0.0  0
 O9T  CONST_21  C16  C13  C12  C11  180.00   0.0  0
 O9T  CONST_22  H3   C1   C6   C5   180.00   0.0  0
 O9T  CONST_23  H4   C3   C4   C5   180.00   0.0  0
 O9T  CONST_24  H8   C12  C11  C10  180.00   0.0  0
 O9T  CONST_25  H9   C14  C15  C10  180.00   0.0  0
 O9T  CONST_26  H7   C11  C12  C13  180.00   0.0  0
 O9T  CONST_27  H2   C15  C14  C13  180.00   0.0  0
 O9T  Var_01    C8   C7   C5   C4   179.57  30.0  1
 O9T  Var_02    C9   C8   C7   C5     0.88  30.0  1
 O9T  Var_03    C10  C9   O1   C6   179.44  30.0  1
 O9T  Var_04    C11  C10  C9   C8   158.31  30.0  3
 O9T  Var_05    H10  C16  C13  C12   88.43  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
 O9T  plan-1  C10  0.020
 O9T  plan-1  C13  0.020
 O9T  plan-1  C15  0.020
 O9T  plan-1  C9   0.020
 O9T  plan-1  C11  0.020
 O9T  plan-1  C12  0.020
 O9T  plan-1  C14  0.020
 O9T  plan-1  C16  0.020
 O9T  plan-1  H2   0.020
 O9T  plan-1  H7   0.020
 O9T  plan-1  H8   0.020
 O9T  plan-1  H9   0.020
 O9T  plan-2  C4   0.020
 O9T  plan-2  C5   0.020
 O9T  plan-2  C6   0.020
 O9T  plan-2  C7   0.020
 O9T  plan-2  C1   0.020
 O9T  plan-2  C2   0.020
 O9T  plan-2  C3   0.020
 O9T  plan-2  O1   0.020
 O9T  plan-2  O2   0.020
 O9T  plan-2  O3   0.020
 O9T  plan-2  H3   0.020
 O9T  plan-2  H4   0.020
 O9T  plan-3  C5   0.020
 O9T  plan-3  C7   0.020
 O9T  plan-3  C8   0.020
 O9T  plan-3  O4   0.020

