# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:07:33 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 7,8-dihydroxy-4-phenyl-2H-chromen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2c(OC(=O)C=C2c3ccccc3)c1O
#
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
 KOM  KOM  7,8-dihydroxy-4-phenyl-2H-chromen-2-one  ligand  29  19  .  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_KOM
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
 KOM  O15   O  O     0  -0.433   0.9333  -3.6624  -0.1128
 KOM  C13   C  CR6   0   0.567   0.6825  -2.4832  -0.1060
 KOM  O14   O  O     0  -0.481   1.7342  -1.6228  -0.1710
 KOM  C4    C  CR66  0   0.308   1.5870  -0.2772  -0.1384
 KOM  C5    C  CR6   0   0.183   2.7634   0.4594  -0.1589
 KOM  O9    O  OH1   0  -0.631   3.9938  -0.0872  -0.2243
 KOM  C6    C  CR6   0   0.306   2.6812   1.8515  -0.1034
 KOM  O10   O  OH1   0  -0.619   3.7814   2.6161  -0.1193
 KOM  C1    C  CR16  0  -0.346   1.4343   2.4708  -0.0181
 KOM  C12   C  CR16  0  -0.559  -0.6308  -1.8889  -0.0549
 KOM  C11   C  CR6   0   0.247  -0.8191  -0.5487  -0.0536
 KOM  C3    C  CR66  0  -0.028   0.3290   0.3269  -0.0741
 KOM  C2    C  CR16  0  -0.358   0.2775   1.7223  -0.0002
 KOM  C18   C  CR6   0   0.027  -2.1902  -0.0023  -0.0268
 KOM  C24   C  CR16  0  -0.283  -3.0713  -0.3838   0.9833
 KOM  C23   C  CR16  0  -0.241  -4.3721   0.0992   0.9978
 KOM  C22   C  CR16  0  -0.255  -4.8079   0.9583  -0.0017
 KOM  C21   C  CR16  0  -0.242  -3.9368   1.3358  -1.0157
 KOM  C20   C  CR16  0  -0.289  -2.6328   0.8640  -1.0266
 KOM  HO9   H  HOH1  0   0.487   3.9580  -1.0509  -0.2304
 KOM  HO10  H  HOH1  0   0.481   4.5799   2.0758  -0.1689
 KOM  H1    H  HCR6  0   0.279   1.3872   3.5502   0.0393
 KOM  H12   H  HCR6  0   0.286  -1.4675  -2.5737  -0.0506
 KOM  H2    H  HCR6  0   0.274  -0.6746   2.2264   0.0829
 KOM  H24   H  HCR6  0   0.262  -2.7352  -1.0488   1.7691
 KOM  H23   H  HCR6  0   0.263  -5.0453  -0.1982   1.7910
 KOM  H22   H  HCR6  0   0.263  -5.8234   1.3320   0.0088
 KOM  H21   H  HCR6  0   0.264  -4.2730   1.9970  -1.8034
 KOM  H20   H  HCR6  0   0.270  -1.9644   1.1563  -1.8267

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
 KOM  O15  C13   double    1.206  0.020  1.206
 KOM  C13  O14   single    1.360  0.020  1.360
 KOM  C13  C12   single    1.442  0.020  1.442
 KOM  O14  C4    single    1.354  0.020  1.354
 KOM  C4   C5    aromatic  1.388  0.020  1.388
 KOM  C4   C3    aromatic  1.397  0.020  1.397
 KOM  C5   O9    single    1.348  0.020  1.348
 KOM  C5   C6    aromatic  1.396  0.020  1.396
 KOM  C6   O10   single    1.340  0.020  1.340
 KOM  C6   C1    aromatic  1.395  0.020  1.395
 KOM  C1   C2    aromatic  1.378  0.020  1.378
 KOM  C12  C11   double    1.353  0.020  1.353
 KOM  C11  C3    single    1.444  0.020  1.444
 KOM  C11  C18   single    1.476  0.020  1.476
 KOM  C3   C2    aromatic  1.398  0.020  1.398
 KOM  C18  C24   aromatic  1.394  0.020  1.394
 KOM  C18  C20   aromatic  1.395  0.020  1.395
 KOM  C24  C23   aromatic  1.388  0.020  1.388
 KOM  C23  C22   aromatic  1.388  0.020  1.388
 KOM  C22  C21   aromatic  1.389  0.020  1.389
 KOM  C21  C20   aromatic  1.387  0.020  1.387
 KOM  O9   HO9   single    0.850  0.020  0.980
 KOM  O10  HO10  single    0.850  0.020  0.980
 KOM  C1   H1    single    0.930  0.020  1.080
 KOM  C12  H12   single    0.930  0.020  1.080
 KOM  C2   H2    single    0.930  0.020  1.080
 KOM  C24  H24   single    0.930  0.020  1.080
 KOM  C23  H23   single    0.930  0.020  1.080
 KOM  C22  H22   single    0.930  0.020  1.080
 KOM  C21  H21   single    0.930  0.020  1.080
 KOM  C20  H20   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
 KOM  C12   C13  O14  116.42  3.000
 KOM  C12   C13  O15  126.34  3.000
 KOM  O14   C13  O15  117.23  3.000
 KOM  C4    O14  C13  122.91  3.000
 KOM  C3    C4   C5   122.30  3.000
 KOM  C3    C4   O14  121.92  3.000
 KOM  C5    C4   O14  115.78  3.000
 KOM  C6    C5   O9   117.40  3.000
 KOM  C6    C5   C4   118.61  3.000
 KOM  O9    C5   C4   123.99  3.000
 KOM  HO9   O9   C5   111.82  3.000
 KOM  C1    C6   O10  118.78  3.000
 KOM  C1    C6   C5   119.87  3.000
 KOM  O10   C6   C5   121.36  3.000
 KOM  HO10  O10  C6   111.12  3.000
 KOM  H1    C1   C2   120.31  3.000
 KOM  H1    C1   C6   119.02  3.000
 KOM  C2    C1   C6   120.67  3.000
 KOM  H12   C12  C11  121.30  3.000
 KOM  H12   C12  C13  116.34  3.000
 KOM  C11   C12  C13  122.32  3.000
 KOM  C18   C11  C3   120.95  3.000
 KOM  C18   C11  C12  119.72  3.000
 KOM  C3    C11  C12  119.33  3.000
 KOM  C2    C3   C11  125.11  3.000
 KOM  C2    C3   C4   117.85  3.000
 KOM  C11   C3   C4   117.02  3.000
 KOM  H2    C2   C3   120.14  3.000
 KOM  H2    C2   C1   119.16  3.000
 KOM  C3    C2   C1   120.70  3.000
 KOM  C20   C18  C24  119.26  3.000
 KOM  C20   C18  C11  120.77  3.000
 KOM  C24   C18  C11  119.94  3.000
 KOM  H24   C24  C23  119.81  3.000
 KOM  H24   C24  C18  119.85  3.000
 KOM  C23   C24  C18  120.33  3.000
 KOM  H23   C23  C22  120.17  3.000
 KOM  H23   C23  C24  119.68  3.000
 KOM  C22   C23  C24  120.15  3.000
 KOM  H22   C22  C21  120.12  3.000
 KOM  H22   C22  C23  120.09  3.000
 KOM  C21   C22  C23  119.79  3.000
 KOM  H21   C21  C20  119.64  3.000
 KOM  H21   C21  C22  120.17  3.000
 KOM  C20   C21  C22  120.20  3.000
 KOM  H20   C20  C21  119.63  3.000
 KOM  H20   C20  C18  120.09  3.000
 KOM  C21   C20  C18  120.27  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
 KOM  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 KOM  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 KOM  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 KOM  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 KOM  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 KOM  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 KOM  CONST_07  C22  C23  C24  C18    0.00   0.0  0
 KOM  CONST_08  C22  C21  C20  C18    0.00   0.0  0
 KOM  CONST_09  C21  C20  C18  C24    0.00   0.0  0
 KOM  CONST_10  C21  C22  C23  C24    0.00   0.0  0
 KOM  CONST_11  C20  C18  C24  C23    0.00   0.0  0
 KOM  CONST_12  C20  C21  C22  C23    0.00   0.0  0
 KOM  CONST_13  C23  C24  C18  C11  180.00   0.0  0
 KOM  CONST_14  C21  C20  C18  C11  180.00   0.0  0
 KOM  CONST_15  O9   C5   C4   O14    0.00   0.0  0
 KOM  CONST_16  O10  C6   C5   C4   180.00   0.0  0
 KOM  CONST_17  C3   C4   C5   O9   180.00   0.0  0
 KOM  CONST_18  C1   C6   C5   O9   180.00   0.0  0
 KOM  CONST_19  C2   C1   C6   O10  180.00   0.0  0
 KOM  CONST_20  H2   C2   C3   C4   180.00   0.0  0
 KOM  CONST_21  H1   C1   C6   C5   180.00   0.0  0
 KOM  CONST_22  H24  C24  C18  C11    0.00   0.0  0
 KOM  CONST_23  H20  C20  C18  C11    0.00   0.0  0
 KOM  CONST_24  H23  C23  C24  C18  180.00   0.0  0
 KOM  CONST_25  H21  C21  C20  C18  180.00   0.0  0
 KOM  CONST_26  H22  C22  C23  C24  180.00   0.0  0
 KOM  Var_01    C5   C4   O14  C13  177.45  30.0  1
 KOM  Var_02    C3   C11  C12  C13   -1.40  30.0  1
 KOM  Var_03    C11  C12  C13  O14   -0.83  30.0  1
 KOM  Var_04    C12  C13  O14  C4     2.52  30.0  1
 KOM  Var_05    C12  C11  C3   C4     2.03  30.0  1
 KOM  Var_06    C24  C18  C11  C12   55.16  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
 KOM  plan-1  C11  0.020
 KOM  plan-1  C18  0.020
 KOM  plan-1  C24  0.020
 KOM  plan-1  C23  0.020
 KOM  plan-1  C22  0.020
 KOM  plan-1  C21  0.020
 KOM  plan-1  C20  0.020
 KOM  plan-1  H24  0.020
 KOM  plan-1  H23  0.020
 KOM  plan-1  H22  0.020
 KOM  plan-1  H21  0.020
 KOM  plan-1  H20  0.020
 KOM  plan-2  O14  0.020
 KOM  plan-2  C4   0.020
 KOM  plan-2  C5   0.020
 KOM  plan-2  O9   0.020
 KOM  plan-2  C6   0.020
 KOM  plan-2  O10  0.020
 KOM  plan-2  C1   0.020
 KOM  plan-2  C11  0.020
 KOM  plan-2  C3   0.020
 KOM  plan-2  C2   0.020
 KOM  plan-2  H1   0.020
 KOM  plan-2  H2   0.020
 KOM  plan-3  O15  0.020
 KOM  plan-3  C13  0.020
 KOM  plan-3  O14  0.020
 KOM  plan-3  C12  0.020

