# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 09:54:19 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3,5,7-trihydroxy-2-(4-hydroxy-3-methoxyphenyl)-4H-1-benzopyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)C2=C(O)C(=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
 IRH  IRH  3,5,7-trihydroxy-2-(4-hydroxy-3-methoxyphenyl)-4H-1-benzopyran-4-one  ligand  35  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IRH
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
 IRH  C01  C  CH3   0  -0.436  -3.5621   2.8898  -1.2231
 IRH  O25  O  O2    0  -0.488  -4.2910   1.8223  -0.6494
 IRH  C16  C  CR6   0   0.324  -3.6186   0.7379  -0.2128
 IRH  C15  C  CR16  0  -0.421  -2.2490   0.5715  -0.2650
 IRH  C17  C  CR6   0   0.286  -4.4321  -0.2740   0.3301
 IRH  O24  O  OH1   0  -0.620  -5.7649  -0.1348   0.4016
 IRH  C18  C  CR16  0  -0.327  -3.8418  -1.4317   0.8054
 IRH  C19  C  CR16  0  -0.308  -2.4666  -1.6033   0.7465
 IRH  C14  C  CR6   0   0.039  -1.6540  -0.6089   0.2098
 IRH  C11  C  CR6   0   0.226  -0.2003  -0.7499   0.1535
 IRH  O12  O  O     0  -0.467   0.4373   0.4402   0.2360
 IRH  C4   C  CR66  0   0.415   1.7709   0.5546   0.1826
 IRH  C5   C  CR16  0  -0.515   2.3041   1.8297   0.2677
 IRH  C6   C  CR6   0   0.400   3.6882   1.9581   0.2325
 IRH  O29  O  OH1   0  -0.615   4.2878   3.1491   0.3160
 IRH  C1   C  CR16  0  -0.457   4.5264   0.8437   0.1065
 IRH  C2   C  CR6   0   0.403   3.9771  -0.4186   0.0177
 IRH  O30  O  OH1   0  -0.625   4.7783  -1.4735  -0.0969
 IRH  C3   C  CR66  0  -0.328   2.5693  -0.5839   0.0563
 IRH  C9   C  CR6   0   0.422   1.9544  -1.8737  -0.0352
 IRH  O13  O  O     0  -0.511   2.5886  -2.9357  -0.1638
 IRH  C10  C  CR6   0   0.181   0.5081  -1.8986   0.0109
 IRH  O27  O  OH1   0  -0.627  -0.0909  -3.0942  -0.1130
 IRH  H1   H  HCH3  0   0.234  -3.0169   2.5732  -2.1159
 IRH  H2   H  HCH3  0   0.266  -4.2907   3.6455  -1.5042
 IRH  H3   H  HCH3  0   0.234  -2.8562   3.3256  -0.5115
 IRH  H4   H  HCR6  0   0.289  -1.6334   1.3532  -0.6887
 IRH  H5   H  HOH1  0   0.476  -6.0339   0.7185   0.0392
 IRH  H6   H  HCR6  0   0.273  -4.4654  -2.2050   1.2359
 IRH  H7   H  HCR6  0   0.262  -2.0440  -2.5101   1.1505
 IRH  H8   H  HCR6  0   0.295   1.6554   2.6908   0.3688
 IRH  H9   H  HOH1  0   0.484   3.6419   3.8517   0.4557
 IRH  H10  H  HCR6  0   0.282   5.6009   0.9732   0.0831
 IRH  H11  H  HOH1  0   0.480   4.2210  -2.2815  -0.1457
 IRH  H12  H  HOH1  0   0.475   0.6018  -3.7594  -0.2435

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
 IRH  O30  C2   single    1.330  0.020  1.330
 IRH  C2   C1   aromatic  1.380  0.020  1.380
 IRH  C2   C3   aromatic  1.418  0.020  1.418
 IRH  C1   C6   aromatic  1.400  0.020  1.400
 IRH  O13  C9   double    1.244  0.020  1.244
 IRH  C3   C9   single    1.432  0.020  1.432
 IRH  C3   C4   aromatic  1.396  0.020  1.396
 IRH  C9   C10  single    1.447  0.020  1.447
 IRH  C6   O29  single    1.336  0.020  1.336
 IRH  C6   C5   aromatic  1.390  0.020  1.390
 IRH  C4   C5   aromatic  1.385  0.020  1.385
 IRH  C4   O12  single    1.340  0.020  1.340
 IRH  O27  C10  single    1.343  0.020  1.343
 IRH  C10  C11  double    1.357  0.020  1.357
 IRH  O12  C11  single    1.353  0.020  1.353
 IRH  C11  C14  single    1.462  0.020  1.462
 IRH  C14  C15  aromatic  1.405  0.020  1.405
 IRH  C14  C19  aromatic  1.392  0.020  1.392
 IRH  C15  C16  aromatic  1.381  0.020  1.381
 IRH  C19  C18  aromatic  1.387  0.020  1.387
 IRH  C16  O25  single    1.349  0.020  1.349
 IRH  C16  C17  aromatic  1.407  0.020  1.407
 IRH  O25  C01  single    1.414  0.020  1.414
 IRH  C18  C17  aromatic  1.384  0.020  1.384
 IRH  C17  O24  single    1.342  0.020  1.342
 IRH  C01  H1   single    0.970  0.020  1.090
 IRH  C01  H2   single    0.970  0.020  1.090
 IRH  C01  H3   single    0.970  0.020  1.090
 IRH  C15  H4   single    0.930  0.020  1.080
 IRH  O24  H5   single    0.850  0.020  0.980
 IRH  C18  H6   single    0.930  0.020  1.080
 IRH  C19  H7   single    0.930  0.020  1.080
 IRH  C5   H8   single    0.930  0.020  1.080
 IRH  O29  H9   single    0.850  0.020  0.980
 IRH  C1   H10  single    0.930  0.020  1.080
 IRH  O30  H11  single    0.850  0.020  0.980
 IRH  O27  H12  single    0.850  0.020  0.980

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
 IRH  H3   C01  H2   108.91  3.000
 IRH  H3   C01  H1   108.97  3.000
 IRH  H2   C01  H1   108.94  3.000
 IRH  H3   C01  O25  111.70  3.000
 IRH  H2   C01  O25  106.52  3.000
 IRH  H1   C01  O25  111.70  3.000
 IRH  C16  O25  C01  118.77  3.000
 IRH  C17  C16  C15  120.09  3.000
 IRH  C17  C16  O25  114.51  3.000
 IRH  C15  C16  O25  125.40  3.000
 IRH  H4   C15  C14  119.92  3.000
 IRH  H4   C15  C16  119.50  3.000
 IRH  C14  C15  C16  120.58  3.000
 IRH  C18  C17  O24  119.48  3.000
 IRH  O24  C17  C16  121.34  3.000
 IRH  C18  C17  C16  119.18  3.000
 IRH  H5   O24  C17  110.39  3.000
 IRH  H6   C18  C19  119.97  3.000
 IRH  H6   C18  C17  119.24  3.000
 IRH  C19  C18  C17  120.79  3.000
 IRH  H7   C19  C14  121.08  3.000
 IRH  H7   C19  C18  118.45  3.000
 IRH  C14  C19  C18  120.45  3.000
 IRH  C11  C14  C19  121.78  3.000
 IRH  C19  C14  C15  118.91  3.000
 IRH  C11  C14  C15  119.30  3.000
 IRH  C10  C11  O12  120.34  3.000
 IRH  O12  C11  C14  112.44  3.000
 IRH  C10  C11  C14  127.22  3.000
 IRH  C4   O12  C11  122.82  3.000
 IRH  C3   C4   C5   122.42  3.000
 IRH  C5   C4   O12  117.36  3.000
 IRH  C3   C4   O12  120.22  3.000
 IRH  H8   C5   C6   121.68  3.000
 IRH  H8   C5   C4   120.49  3.000
 IRH  C6   C5   C4   117.83  3.000
 IRH  C1   C6   O29  116.52  3.000
 IRH  O29  C6   C5   121.83  3.000
 IRH  C1   C6   C5   121.65  3.000
 IRH  H9   O29  C6   110.98  3.000
 IRH  H10  C1   C2   120.22  3.000
 IRH  H10  C1   C6   120.07  3.000
 IRH  C2   C1   C6   119.71  3.000
 IRH  C3   C2   O30  120.54  3.000
 IRH  C3   C2   C1   120.02  3.000
 IRH  O30  C2   C1   119.44  3.000
 IRH  H11  O30  C2   108.35  3.000
 IRH  C9   C3   C2   121.98  3.000
 IRH  C9   C3   C4   119.65  3.000
 IRH  C2   C3   C4   118.37  3.000
 IRH  C10  C9   O13  119.88  3.000
 IRH  C10  C9   C3   116.28  3.000
 IRH  O13  C9   C3   123.84  3.000
 IRH  O27  C10  C9   117.27  3.000
 IRH  O27  C10  C11  122.03  3.000
 IRH  C9   C10  C11  120.69  3.000
 IRH  H12  O27  C10  107.74  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
 IRH  CONST_01  C19  C14  C15  C16     0.00   0.0  0
 IRH  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 IRH  CONST_03  C18  C19  C14  C15     0.00   0.0  0
 IRH  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 IRH  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 IRH  CONST_06  C14  C19  C18  C17     0.00   0.0  0
 IRH  CONST_07  C1   C2   C3   C4      0.00   0.0  0
 IRH  CONST_08  C1   C6   C5   C4      0.00   0.0  0
 IRH  CONST_09  C2   C1   C6   C5      0.00   0.0  0
 IRH  CONST_10  C2   C3   C4   C5      0.00   0.0  0
 IRH  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 IRH  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 IRH  CONST_13  C11  C14  C15  C16   180.00   0.0  0
 IRH  CONST_14  C11  C14  C19  C18   180.00   0.0  0
 IRH  CONST_15  C14  C15  C16  O25   180.00   0.0  0
 IRH  CONST_16  C18  C17  C16  O25   180.00   0.0  0
 IRH  CONST_17  O24  C17  C16  C15   180.00   0.0  0
 IRH  CONST_18  C19  C18  C17  O24   180.00   0.0  0
 IRH  CONST_19  O30  C2   C3   C4    180.00   0.0  0
 IRH  CONST_20  O29  C6   C5   C4    180.00   0.0  0
 IRH  CONST_21  O30  C2   C1   C6    180.00   0.0  0
 IRH  CONST_22  C2   C1   C6   O29   180.00   0.0  0
 IRH  CONST_23  C9   C3   C2   O30     0.00   0.0  0
 IRH  CONST_24  H6   C18  C17  C16   180.00   0.0  0
 IRH  CONST_25  H7   C19  C14  C15   180.00   0.0  0
 IRH  CONST_26  H4   C15  C16  C17   180.00   0.0  0
 IRH  CONST_27  H8   C5   C4   O12     0.00   0.0  0
 IRH  CONST_28  H10  C1   C6   C5    180.00   0.0  0
 IRH  Var_01    C10  C11  C14  C15  -149.93  30.0  2
 IRH  Var_02    C9   C10  C11  C14   179.65  30.0  1
 IRH  Var_03    C3   C9   C10  C11    -0.94  30.0  1
 IRH  Var_04    C3   C4   O12  C11    -0.97  30.0  1
 IRH  Var_05    C10  C9   C3   C4      0.04  30.0  1
 IRH  Var_06    C15  C16  O25  C01     0.53  30.0  2
 IRH  Var_07    H1   C01  O25  C16    60.98  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
 IRH  plan-1  O25  0.020
 IRH  plan-1  C16  0.020
 IRH  plan-1  C15  0.020
 IRH  plan-1  C17  0.020
 IRH  plan-1  O24  0.020
 IRH  plan-1  C18  0.020
 IRH  plan-1  C19  0.020
 IRH  plan-1  C14  0.020
 IRH  plan-1  C11  0.020
 IRH  plan-1  H4   0.020
 IRH  plan-1  H6   0.020
 IRH  plan-1  H7   0.020
 IRH  plan-2  O12  0.020
 IRH  plan-2  C4   0.020
 IRH  plan-2  C5   0.020
 IRH  plan-2  C6   0.020
 IRH  plan-2  O29  0.020
 IRH  plan-2  C1   0.020
 IRH  plan-2  C2   0.020
 IRH  plan-2  O30  0.020
 IRH  plan-2  C3   0.020
 IRH  plan-2  C9   0.020
 IRH  plan-2  H8   0.020
 IRH  plan-2  H10  0.020
 IRH  plan-3  C3   0.020
 IRH  plan-3  C9   0.020
 IRH  plan-3  O13  0.020
 IRH  plan-3  C10  0.020

