# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:35:38 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C2=COc3cc(O)cc(O)c3C2=O
#
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
 GEN  GEN  5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one  ligand  30  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GEN
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
 GEN  C1   C  CR16  0  -0.434  -1.3192   0.1877  -3.4306
 GEN  C2   C  CR6   0   0.346  -0.3042   0.1623  -4.3788
 GEN  O2   O  OH1   0  -0.676  -0.5758   0.1389  -5.6946
 GEN  C3   C  CR16  0  -0.412   1.0414   0.1281  -4.0039
 GEN  C4   C  CR6   0   0.263   1.3848   0.0889  -2.6657
 GEN  O4   O  OH1   0  -0.597   2.6688   0.0560  -2.3223
 GEN  C5   C  CR66  0  -0.366   0.3725   0.1191  -1.6733
 GEN  C6   C  CR6   0   0.393   0.6983   0.0487  -0.2659
 GEN  O6   O  OC    0  -0.262   1.8694  -0.0498   0.1190
 GEN  C7   C  CR6   0  -0.151  -0.4360   0.1153   0.6475
 GEN  C8   C  CR16  0  -0.017  -1.6742   0.1865   0.1157
 GEN  O9   O  O     0  -0.273  -1.9515   0.2236  -1.1873
 GEN  C10  C  CR66  0   0.366  -0.9555   0.1843  -2.0950
 GEN  C11  C  CR6   0   0.007  -0.2647   0.0851   2.1102
 GEN  C12  C  CR16  0  -0.258  -1.0505  -0.7666   2.8893
 GEN  C13  C  CR16  0  -0.330  -0.8781  -0.8653   4.2593
 GEN  C14  C  CR6   0   0.286   0.1183  -0.1247   4.8872
 GEN  O14  O  OH1   0  -0.694   0.3165  -0.3167   6.2071
 GEN  C15  C  CR16  0  -0.251   0.8699   0.7754   4.1367
 GEN  C16  C  CR16  0  -0.260   0.6750   0.8824   2.7689
 GEN  H1   H  HCR6  0   0.271  -2.3640   0.2074  -3.7138
 GEN  H2   H  HOH1  0   0.466  -1.4792   0.4269  -5.8709
 GEN  H3   H  HCR6  0   0.245   1.8127   0.1101  -4.7633
 GEN  H4   H  HOH1  0   0.481   2.7139  -0.0192  -1.3413
 GEN  H8   H  HCR6  0   0.309  -2.5715   0.2850   0.7119
 GEN  H12  H  HCR6  0   0.260  -1.7766  -1.4150   2.4147
 GEN  H13  H  HCR6  0   0.275  -1.5037  -1.5387   4.8329
 GEN  H14  H  HOH1  0   0.457   0.9147   0.3510   6.5600
 GEN  H15  H  HCR6  0   0.280   1.6110   1.4008   4.6214
 GEN  H16  H  HCR6  0   0.277   1.3050   1.5633   2.2144

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
 GEN  C1   C2   aromatic  1.389  0.020  1.389
 GEN  C1   C10  aromatic  1.384  0.020  1.384
 GEN  C1   H1   single    0.930  0.020  1.080
 GEN  C2   O2   single    1.344  0.020  1.344
 GEN  C2   C3   aromatic  1.397  0.020  1.397
 GEN  O2   H2   single    0.850  0.020  0.980
 GEN  C3   C4   aromatic  1.382  0.020  1.382
 GEN  C3   H3   single    0.930  0.020  1.080
 GEN  C4   O4   single    1.330  0.020  1.330
 GEN  C4   C5   aromatic  1.418  0.020  1.418
 GEN  O4   H4   single    0.850  0.020  0.980
 GEN  C5   C6   aromatic  1.446  0.020  1.446
 GEN  C5   C10  aromatic  1.395  0.020  1.395
 GEN  C6   O6   double    1.237  0.020  1.237
 GEN  C6   C7   aromatic  1.458  0.020  1.458
 GEN  C7   C8   aromatic  1.349  0.020  1.349
 GEN  C7   C11  single    1.473  0.020  1.473
 GEN  C8   O9   aromatic  1.333  0.020  1.333
 GEN  C8   H8   single    0.930  0.020  1.080
 GEN  O9   C10  aromatic  1.348  0.020  1.348
 GEN  C11  C12  aromatic  1.396  0.020  1.396
 GEN  C11  C16  aromatic  1.397  0.020  1.397
 GEN  C12  C13  aromatic  1.384  0.020  1.384
 GEN  C12  H12  single    0.930  0.020  1.080
 GEN  C13  C14  aromatic  1.391  0.020  1.391
 GEN  C13  H13  single    0.930  0.020  1.080
 GEN  C14  O14  single    1.348  0.020  1.348
 GEN  C14  C15  aromatic  1.392  0.020  1.392
 GEN  O14  H14  single    0.850  0.020  0.980
 GEN  C15  C16  aromatic  1.386  0.020  1.386
 GEN  C15  H15  single    0.930  0.020  1.080
 GEN  C16  H16  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
 GEN  H1   C1   C10  120.40  3.000
 GEN  H1   C1   C2   121.79  3.000
 GEN  C10  C1   C2   117.81  3.000
 GEN  C3   C2   O2   117.19  3.000
 GEN  C3   C2   C1   121.39  3.000
 GEN  O2   C2   C1   121.40  3.000
 GEN  H2   O2   C2   111.30  3.000
 GEN  H3   C3   C4   120.12  3.000
 GEN  H3   C3   C2   119.89  3.000
 GEN  C4   C3   C2   119.98  3.000
 GEN  C5   C4   O4   120.61  3.000
 GEN  C5   C4   C3   119.98  3.000
 GEN  O4   C4   C3   119.39  3.000
 GEN  H4   O4   C4   107.66  3.000
 GEN  C10  C5   C6   120.73  3.000
 GEN  C10  C5   C4   117.97  3.000
 GEN  C6   C5   C4   121.28  3.000
 GEN  C7   C6   O6   123.05  3.000
 GEN  C7   C6   C5   115.60  3.000
 GEN  O6   C6   C5   121.34  3.000
 GEN  C11  C7   C8   119.94  3.000
 GEN  C11  C7   C6   122.06  3.000
 GEN  C8   C7   C6   118.00  3.000
 GEN  H8   C8   O9   111.33  3.000
 GEN  H8   C8   C7   123.28  3.000
 GEN  O9   C8   C7   125.28  3.000
 GEN  C10  O9   C8   120.25  3.000
 GEN  O9   C10  C5   120.08  3.000
 GEN  O9   C10  C1   117.09  3.000
 GEN  C5   C10  C1   122.82  3.000
 GEN  C16  C11  C12  117.60  3.000
 GEN  C16  C11  C7   122.32  3.000
 GEN  C12  C11  C7   120.07  3.000
 GEN  H12  C12  C13  118.33  3.000
 GEN  H12  C12  C11  119.86  3.000
 GEN  C13  C12  C11  121.71  3.000
 GEN  H13  C13  C14  120.36  3.000
 GEN  H13  C13  C12  119.76  3.000
 GEN  C14  C13  C12  119.86  3.000
 GEN  C15  C14  O14  122.71  3.000
 GEN  C15  C14  C13  119.17  3.000
 GEN  O14  C14  C13  118.12  3.000
 GEN  H14  O14  C14  110.56  3.000
 GEN  H15  C15  C16  119.54  3.000
 GEN  H15  C15  C14  120.06  3.000
 GEN  C16  C15  C14  120.41  3.000
 GEN  H16  C16  C15  118.24  3.000
 GEN  H16  C16  C11  120.64  3.000
 GEN  C15  C16  C11  121.05  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
 GEN  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 GEN  CONST_02  C4   C5   C10  C1     0.00  0.0  0
 GEN  CONST_03  C6   C5   C10  C1   180.00  0.0  0
 GEN  CONST_04  C8   O9   C10  C1   180.00  0.0  0
 GEN  CONST_05  C5   C10  C1   C2     0.00  0.0  0
 GEN  CONST_06  O9   C10  C1   C2   180.00  0.0  0
 GEN  CONST_07  C5   C4   C3   C2     0.00  0.0  0
 GEN  CONST_08  C10  C1   C2   C3     0.00  0.0  0
 GEN  CONST_09  C6   C5   C4   C3   180.00  0.0  0
 GEN  CONST_10  C10  C5   C4   C3     0.00  0.0  0
 GEN  CONST_11  C7   C6   C5   C4   180.00  0.0  0
 GEN  CONST_12  O9   C10  C5   C4   180.00  0.0  0
 GEN  CONST_13  C8   C7   C6   C5     0.00  0.0  0
 GEN  CONST_14  C11  C7   C6   C5   180.00  0.0  0
 GEN  CONST_15  C8   O9   C10  C5     0.00  0.0  0
 GEN  CONST_16  O9   C10  C5   C6     0.00  0.0  0
 GEN  CONST_17  O9   C8   C7   C6     0.00  0.0  0
 GEN  CONST_20  C10  C5   C6   C7     0.00  0.0  0
 GEN  CONST_21  C10  O9   C8   C7     0.00  0.0  0
 GEN  CONST_22  C13  C12  C11  C7   180.00  0.0  0
 GEN  CONST_23  C15  C16  C11  C7   180.00  0.0  0
 GEN  CONST_26  C11  C7   C8   O9   180.00  0.0  0
 GEN  CONST_27  C14  C13  C12  C11    0.00  0.0  0
 GEN  CONST_28  C14  C15  C16  C11    0.00  0.0  0
 GEN  CONST_29  C15  C16  C11  C12    0.00  0.0  0
 GEN  CONST_30  C15  C14  C13  C12    0.00  0.0  0
 GEN  CONST_31  C16  C11  C12  C13    0.00  0.0  0
 GEN  CONST_32  C16  C15  C14  C13    0.00  0.0  0
 GEN  CONST_33  O4   C4   C3   C2   180.00  0.0  0
 GEN  CONST_34  C10  C1   C2   O2   180.00  0.0  0
 GEN  CONST_35  C4   C3   C2   O2   180.00  0.0  0
 GEN  CONST_36  O6   C6   C5   C4     0.00  0.0  0
 GEN  CONST_37  C6   C5   C4   O4     0.00  0.0  0
 GEN  CONST_38  C10  C5   C4   O4   180.00  0.0  0
 GEN  CONST_39  C10  C5   C6   O6   180.00  0.0  0
 GEN  CONST_40  C8   C7   C6   O6   180.00  0.0  0
 GEN  CONST_41  C11  C7   C6   O6     0.00  0.0  0
 GEN  CONST_42  O14  C14  C13  C12  180.00  0.0  0
 GEN  CONST_43  C16  C15  C14  O14  180.00  0.0  0
 GEN  CONST_44  H3   C3   C2   C1   180.00  0.0  0
 GEN  CONST_45  H1   C1   C2   C3   180.00  0.0  0
 GEN  CONST_46  H8   C8   C7   C6   180.00  0.0  0
 GEN  CONST_47  H12  C12  C11  C7     0.00  0.0  0
 GEN  CONST_48  H16  C16  C11  C7     0.00  0.0  0
 GEN  CONST_49  H13  C13  C12  C11  180.00  0.0  0
 GEN  CONST_50  H15  C15  C16  C11  180.00  0.0  0

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
 GEN  plan-1  C7   0.020
 GEN  plan-1  C11  0.020
 GEN  plan-1  C12  0.020
 GEN  plan-1  C13  0.020
 GEN  plan-1  C14  0.020
 GEN  plan-1  O14  0.020
 GEN  plan-1  C15  0.020
 GEN  plan-1  C16  0.020
 GEN  plan-1  H12  0.020
 GEN  plan-1  H13  0.020
 GEN  plan-1  H15  0.020
 GEN  plan-1  H16  0.020
 GEN  plan-2  C1   0.020
 GEN  plan-2  C2   0.020
 GEN  plan-2  O2   0.020
 GEN  plan-2  C3   0.020
 GEN  plan-2  C4   0.020
 GEN  plan-2  O4   0.020
 GEN  plan-2  C5   0.020
 GEN  plan-2  C6   0.020
 GEN  plan-2  O9   0.020
 GEN  plan-2  C10  0.020
 GEN  plan-2  H1   0.020
 GEN  plan-2  H3   0.020
 GEN  plan-3  C5   0.020
 GEN  plan-3  C6   0.020
 GEN  plan-3  O6   0.020
 GEN  plan-3  C7   0.020

