# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:38:17 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: 5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-4H-1-benzopyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1O)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
 J8D  J8D  5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-4H-1-benzopyran-4-one  ligand  34  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J8D
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
 J8D  C01  C  CH3   0  -0.436  -6.5326   0.5587   0.1502
 J8D  O6   O  O2    0  -0.479  -5.5659  -0.4392  -0.1271
 J8D  C13  C  CR6   0   0.307  -4.2658  -0.1091  -0.0901
 J8D  C12  C  CR6   0   0.307  -3.3794  -1.1578  -0.3990
 J8D  C11  C  CR16  0  -0.375  -2.0185  -0.9302  -0.3929
 J8D  O5   O  OH1   0  -0.628  -3.8329  -2.3870  -0.7068
 J8D  C14  C  CR16  0  -0.361  -3.7596   1.1441   0.2223
 J8D  C15  C  CR16  0  -0.319  -2.3905   1.3658   0.2228
 J8D  C10  C  CR6   0   0.015  -1.5074   0.3380  -0.0900
 J8D  C9   C  CR6   0   0.412  -0.0653   0.5813  -0.1076
 J8D  O4   O  O     0  -0.469   0.6516  -0.5471  -0.0085
 J8D  C6   C  CR66  0   0.422   2.0013  -0.5302  -0.0264
 J8D  C1   C  CR16  0  -0.514   2.6432  -1.7509   0.0652
 J8D  C2   C  CR6   0   0.398   4.0359  -1.7534   0.0588
 J8D  O1   O  OH1   0  -0.616   4.7381  -2.8868   0.1488
 J8D  C3   C  CR16  0  -0.455   4.7680  -0.5674  -0.0399
 J8D  C4   C  CR6   0   0.403   4.1041   0.6419  -0.1319
 J8D  O2   O  OH1   0  -0.630   4.8019   1.7685  -0.2285
 J8D  C5   C  CR66  0  -0.353   2.6889   0.6790  -0.1248
 J8D  C7   C  CR6   0   0.533   1.9579   1.9222  -0.2246
 J8D  O3   O  O     0  -0.511   2.5367   3.0176  -0.3178
 J8D  C8   C  CR16  0  -0.520   0.5268   1.7930  -0.2230
 J8D  H1   H  HCH3  0   0.267  -7.5040   0.0849   0.0396
 J8D  H2   H  HCH3  0   0.237  -6.4365   0.9390   1.1695
 J8D  H3   H  HCH3  0   0.237  -6.4598   1.3929  -0.5509
 J8D  H4   H  HCR6  0   0.272  -1.3635  -1.7544  -0.6433
 J8D  H5   H  HOH1  0   0.475  -4.7971  -2.4084  -0.6742
 J8D  H6   H  HCR6  0   0.293  -4.4208   1.9616   0.4750
 J8D  H7   H  HCR6  0   0.266  -2.0278   2.3475   0.4938
 J8D  H8   H  HCR6  0   0.295   2.0726  -2.6681   0.1446
 J8D  H9   H  HOH1  0   0.484   4.1538  -3.6519   0.2084
 J8D  H10  H  HCR6  0   0.280   5.8502  -0.5968  -0.0446
 J8D  H11  H  HOH1  0   0.476   4.1526   2.5126  -0.2833
 J8D  H12  H  HCR6  0   0.283  -0.0778   2.6814  -0.3340

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
 J8D  O2   C4   single    1.329  0.020  1.329
 J8D  O3   C7   double    1.242  0.020  1.242
 J8D  C4   C3   aromatic  1.383  0.020  1.383
 J8D  C4   C5   aromatic  1.416  0.020  1.416
 J8D  C3   C2   aromatic  1.397  0.020  1.397
 J8D  C7   C5   single    1.446  0.020  1.446
 J8D  C7   C8   single    1.437  0.020  1.437
 J8D  C5   C6   aromatic  1.394  0.020  1.394
 J8D  C2   O1   single    1.336  0.020  1.336
 J8D  C2   C1   aromatic  1.393  0.020  1.393
 J8D  C8   C9   double    1.354  0.020  1.354
 J8D  C6   C1   aromatic  1.382  0.020  1.382
 J8D  C6   O4   single    1.350  0.020  1.350
 J8D  C9   O4   single    1.341  0.020  1.341
 J8D  C9   C10  single    1.463  0.020  1.463
 J8D  C10  C15  aromatic  1.391  0.020  1.391
 J8D  C10  C11  aromatic  1.400  0.020  1.400
 J8D  C15  C14  aromatic  1.387  0.020  1.387
 J8D  C11  C12  aromatic  1.380  0.020  1.380
 J8D  C14  C13  aromatic  1.387  0.020  1.387
 J8D  C12  C13  aromatic  1.407  0.020  1.407
 J8D  C12  O5   single    1.346  0.020  1.346
 J8D  C13  O6   single    1.342  0.020  1.342
 J8D  O6   C01  single    1.417  0.020  1.417
 J8D  C01  H1   single    0.970  0.020  1.090
 J8D  C01  H2   single    0.970  0.020  1.090
 J8D  C01  H3   single    0.970  0.020  1.090
 J8D  C11  H4   single    0.930  0.020  1.080
 J8D  O5   H5   single    0.850  0.020  0.980
 J8D  C14  H6   single    0.930  0.020  1.080
 J8D  C15  H7   single    0.930  0.020  1.080
 J8D  C1   H8   single    0.930  0.020  1.080
 J8D  O1   H9   single    0.850  0.020  0.980
 J8D  C3   H10  single    0.930  0.020  1.080
 J8D  O2   H11  single    0.850  0.020  0.980
 J8D  C8   H12  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
 J8D  H3   C01  H2   109.10  3.000
 J8D  H3   C01  H1   109.11  3.000
 J8D  H2   C01  H1   109.00  3.000
 J8D  H3   C01  O6   111.52  3.000
 J8D  H2   C01  O6   111.59  3.000
 J8D  H1   C01  O6   106.44  3.000
 J8D  C13  O6   C01  118.84  3.000
 J8D  C14  C13  C12  119.52  3.000
 J8D  C12  C13  O6   114.89  3.000
 J8D  C14  C13  O6   125.60  3.000
 J8D  O5   C12  C11  118.95  3.000
 J8D  O5   C12  C13  121.23  3.000
 J8D  C11  C12  C13  119.82  3.000
 J8D  H4   C11  C10  121.26  3.000
 J8D  H4   C11  C12  118.06  3.000
 J8D  C10  C11  C12  120.68  3.000
 J8D  H5   O5   C12  110.44  3.000
 J8D  H6   C14  C15  118.85  3.000
 J8D  H6   C14  C13  120.83  3.000
 J8D  C15  C14  C13  120.32  3.000
 J8D  H7   C15  C10  120.96  3.000
 J8D  H7   C15  C14  118.45  3.000
 J8D  C10  C15  C14  120.57  3.000
 J8D  C9   C10  C15  120.39  3.000
 J8D  C15  C10  C11  119.09  3.000
 J8D  C9   C10  C11  120.52  3.000
 J8D  C8   C9   O4   121.73  3.000
 J8D  O4   C9   C10  112.73  3.000
 J8D  C8   C9   C10  125.54  3.000
 J8D  C6   O4   C9   121.55  3.000
 J8D  C5   C6   C1   122.78  3.000
 J8D  C1   C6   O4   116.90  3.000
 J8D  C5   C6   O4   120.32  3.000
 J8D  H8   C1   C2   121.71  3.000
 J8D  H8   C1   C6   120.53  3.000
 J8D  C2   C1   C6   117.75  3.000
 J8D  C3   C2   O1   116.71  3.000
 J8D  O1   C2   C1   121.78  3.000
 J8D  C3   C2   C1   121.52  3.000
 J8D  H9   O1   C2   111.02  3.000
 J8D  H10  C3   C4   120.23  3.000
 J8D  H10  C3   C2   120.06  3.000
 J8D  C4   C3   C2   119.71  3.000
 J8D  C5   C4   O2   120.20  3.000
 J8D  C5   C4   C3   120.17  3.000
 J8D  O2   C4   C3   119.62  3.000
 J8D  H11  O2   C4   107.29  3.000
 J8D  C7   C5   C4   121.85  3.000
 J8D  C7   C5   C6   120.08  3.000
 J8D  C4   C5   C6   118.07  3.000
 J8D  C8   C7   O3   122.91  3.000
 J8D  C8   C7   C5   115.23  3.000
 J8D  O3   C7   C5   121.86  3.000
 J8D  H12  C8   C7   118.90  3.000
 J8D  H12  C8   C9   120.01  3.000
 J8D  C7   C8   C9   121.08  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
 J8D  CONST_01  C10  C15  C14  C13    0.00   0.0  0
 J8D  CONST_02  C10  C11  C12  C13    0.00   0.0  0
 J8D  CONST_03  C15  C10  C11  C12    0.00   0.0  0
 J8D  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 J8D  CONST_05  C14  C15  C10  C11    0.00   0.0  0
 J8D  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 J8D  CONST_07  C3   C4   C5   C6     0.00   0.0  0
 J8D  CONST_08  C3   C2   C1   C6     0.00   0.0  0
 J8D  CONST_09  C4   C3   C2   C1     0.00   0.0  0
 J8D  CONST_10  C4   C5   C6   C1     0.00   0.0  0
 J8D  CONST_11  C5   C4   C3   C2     0.00   0.0  0
 J8D  CONST_12  C5   C6   C1   C2     0.00   0.0  0
 J8D  CONST_13  C9   C10  C11  C12  180.00   0.0  0
 J8D  CONST_14  C9   C10  C15  C14  180.00   0.0  0
 J8D  CONST_15  C15  C14  C13  O6   180.00   0.0  0
 J8D  CONST_16  C11  C12  C13  O6   180.00   0.0  0
 J8D  CONST_17  C10  C11  C12  O5   180.00   0.0  0
 J8D  CONST_18  C14  C13  C12  O5   180.00   0.0  0
 J8D  CONST_19  O2   C4   C5   C6   180.00   0.0  0
 J8D  CONST_20  O1   C2   C1   C6   180.00   0.0  0
 J8D  CONST_21  O2   C4   C3   C2   180.00   0.0  0
 J8D  CONST_22  C4   C3   C2   O1   180.00   0.0  0
 J8D  CONST_23  C7   C5   C4   O2     0.00   0.0  0
 J8D  CONST_24  H7   C15  C14  C13  180.00   0.0  0
 J8D  CONST_25  H4   C11  C12  C13  180.00   0.0  0
 J8D  CONST_26  H6   C14  C13  C12  180.00   0.0  0
 J8D  CONST_27  H8   C1   C6   O4     0.00   0.0  0
 J8D  CONST_28  H10  C3   C2   C1   180.00   0.0  0
 J8D  Var_01    C8   C9   C10  C11  159.52  30.0  3
 J8D  Var_02    C7   C8   C9   C10  179.77  30.0  1
 J8D  Var_03    C5   C7   C8   C9     1.27  30.0  1
 J8D  Var_04    C5   C6   O4   C9     1.20  30.0  1
 J8D  Var_05    C8   C7   C5   C6    -0.45  30.0  1
 J8D  Var_06    C14  C13  O6   C01    1.10  30.0  2
 J8D  Var_07    H1   C01  O6   C13  178.54  30.0  3

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
 J8D  plan-1  O6   0.020
 J8D  plan-1  C13  0.020
 J8D  plan-1  C12  0.020
 J8D  plan-1  C11  0.020
 J8D  plan-1  O5   0.020
 J8D  plan-1  C14  0.020
 J8D  plan-1  C15  0.020
 J8D  plan-1  C10  0.020
 J8D  plan-1  C9   0.020
 J8D  plan-1  H4   0.020
 J8D  plan-1  H6   0.020
 J8D  plan-1  H7   0.020
 J8D  plan-2  O4   0.020
 J8D  plan-2  C6   0.020
 J8D  plan-2  C1   0.020
 J8D  plan-2  C2   0.020
 J8D  plan-2  O1   0.020
 J8D  plan-2  C3   0.020
 J8D  plan-2  C4   0.020
 J8D  plan-2  O2   0.020
 J8D  plan-2  C5   0.020
 J8D  plan-2  C7   0.020
 J8D  plan-2  H8   0.020
 J8D  plan-2  H10  0.020
 J8D  plan-3  C5   0.020
 J8D  plan-3  C7   0.020
 J8D  plan-3  O3   0.020
 J8D  plan-3  C8   0.020

