# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:14:07 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-(4-hydroxyphenyl)-7-methoxy-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2C(=O)C(=COc2c1)c3ccc(O)cc3
#
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
 HMO  HMO  3-(4-hydroxyphenyl)-7-methoxy-4H-chromen-4-one  ligand  32  20  .  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_HMO
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
 HMO  C1    C  CR6   0   0.405  -0.0988  -0.0472   4.1340
 HMO  C2    C  CR16  0  -0.372   1.2441   0.0871   3.7419
 HMO  C3    C  CR16  0  -0.276   1.5641   0.0985   2.4038
 HMO  C4    C  CR66  0  -0.142   0.5844  -0.0218   1.4142
 HMO  C5    C  CR66  0   0.393  -0.7399  -0.1516   1.8336
 HMO  C6    C  CR16  0  -0.436  -1.0946  -0.1669   3.1717
 HMO  C7    C  CR6   0   0.428   0.9173  -0.0026  -0.0094
 HMO  C8    C  CR6   0  -0.224  -0.2343  -0.1345  -0.9018
 HMO  C9    C  CR16  0   0.038  -1.4647  -0.2623  -0.3687
 HMO  O10   O  O     0  -0.430  -1.7433  -0.2702   0.9366
 HMO  C11   C  CR6   0   0.067  -0.0689  -0.0854  -2.3652
 HMO  C12   C  CR16  0  -0.290  -0.8501   0.7709  -3.1376
 HMO  C13   C  CR16  0  -0.370  -0.7288   0.8129  -4.5184
 HMO  C14   C  CR6   0   0.347   0.1961  -0.0056  -5.1586
 HMO  C15   C  CR16  0  -0.326   0.9880  -0.8670  -4.3994
 HMO  C16   C  CR16  0  -0.275   0.8550  -0.9003  -3.0231
 HMO  O17   O  OH1   0  -0.630   0.3684  -0.0072  -6.4942
 HMO  O18   O  OC    0  -0.427   2.0641   0.1244  -0.4147
 HMO  O19   O  O2    0  -0.461  -0.5057  -0.0693   5.4062
 HMO  C20   C  CH3   0  -0.442   0.4577   0.0203   6.4431
 HMO  H2    H  HCR6  0   0.292   2.0356   0.1808   4.4713
 HMO  H3    H  HCR6  0   0.275   2.5991   0.2029   2.1066
 HMO  H6    H  HCR6  0   0.290  -2.1323  -0.2712   3.4633
 HMO  H9    H  HCR6  0   0.306  -2.3609  -0.3747  -0.9654
 HMO  H12   H  HCR6  0   0.258  -1.5629   1.4293  -2.6559
 HMO  H13   H  HCR6  0   0.272  -1.3485   1.4926  -5.0922
 HMO  H15   H  HCR6  0   0.264   1.7066  -1.5096  -4.8932
 HMO  H16   H  HCR6  0   0.252   1.4695  -1.5882  -2.4581
 HMO  H17   H  HOH1  0   0.475  -0.2073   0.6449  -6.9093
 HMO  H201  H  HCH3  0   0.266  -0.0955  -0.0342   7.3768
 HMO  H202  H  HCH3  0   0.237   1.1713  -0.8053   6.4058
 HMO  H203  H  HCH3  0   0.237   1.0012   0.9670   6.4118

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
 HMO  C1   C2    aromatic  1.405  0.020  1.405
 HMO  C1   C6    aromatic  1.390  0.020  1.390
 HMO  C1   O19   single    1.336  0.020  1.336
 HMO  C2   C3    aromatic  1.376  0.020  1.376
 HMO  C2   H2    single    0.930  0.020  1.080
 HMO  C3   C4    aromatic  1.398  0.020  1.398
 HMO  C3   H3    single    0.930  0.020  1.080
 HMO  C4   C5    aromatic  1.395  0.020  1.395
 HMO  C4   C7    aromatic  1.462  0.020  1.462
 HMO  C5   C6    aromatic  1.384  0.020  1.384
 HMO  C5   O10   aromatic  1.351  0.020  1.351
 HMO  C6   H6    single    0.930  0.020  1.080
 HMO  C7   C8    aromatic  1.463  0.020  1.463
 HMO  C7   O18   double    1.223  0.020  1.223
 HMO  C8   C9    aromatic  1.347  0.020  1.347
 HMO  C8   C11   single    1.474  0.020  1.474
 HMO  C9   O10   aromatic  1.335  0.020  1.335
 HMO  C9   H9    single    0.930  0.020  1.080
 HMO  C11  C12   aromatic  1.393  0.020  1.393
 HMO  C11  C16   aromatic  1.397  0.020  1.397
 HMO  C12  C13   aromatic  1.387  0.020  1.387
 HMO  C12  H12   single    0.930  0.020  1.080
 HMO  C13  C14   aromatic  1.391  0.020  1.391
 HMO  C13  H13   single    0.930  0.020  1.080
 HMO  C14  C15   aromatic  1.395  0.020  1.395
 HMO  C14  O17   single    1.347  0.020  1.347
 HMO  C15  C16   aromatic  1.383  0.020  1.383
 HMO  C15  H15   single    0.930  0.020  1.080
 HMO  C16  H16   single    0.930  0.020  1.080
 HMO  O17  H17   single    0.850  0.020  0.980
 HMO  O19  C20   single    1.418  0.020  1.418
 HMO  C20  H201  single    0.970  0.020  1.090
 HMO  C20  H202  single    0.970  0.020  1.090
 HMO  C20  H203  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
 HMO  O19   C1   C6    116.08  3.000
 HMO  O19   C1   C2    123.94  3.000
 HMO  C6    C1   C2    119.97  3.000
 HMO  H2    C2   C3    119.04  3.000
 HMO  H2    C2   C1    121.33  3.000
 HMO  C3    C2   C1    119.63  3.000
 HMO  H3    C3   C4    118.97  3.000
 HMO  H3    C3   C2    119.37  3.000
 HMO  C4    C3   C2    121.66  3.000
 HMO  C7    C4   C5    120.67  3.000
 HMO  C7    C4   C3    121.91  3.000
 HMO  C5    C4   C3    117.42  3.000
 HMO  O10   C5   C6    116.77  3.000
 HMO  O10   C5   C4    120.90  3.000
 HMO  C6    C5   C4    122.33  3.000
 HMO  H6    C6   C5    120.45  3.000
 HMO  H6    C6   C1    120.56  3.000
 HMO  C5    C6   C1    118.99  3.000
 HMO  O18   C7   C8    123.05  3.000
 HMO  O18   C7   C4    122.52  3.000
 HMO  C8    C7   C4    114.43  3.000
 HMO  C11   C8   C9    119.92  3.000
 HMO  C11   C8   C7    120.96  3.000
 HMO  C9    C8   C7    119.09  3.000
 HMO  H9    C9   O10   111.45  3.000
 HMO  H9    C9   C8    123.23  3.000
 HMO  O10   C9   C8    125.33  3.000
 HMO  C9    O10  C5    119.59  3.000
 HMO  C16   C11  C12   117.94  3.000
 HMO  C16   C11  C8    121.51  3.000
 HMO  C12   C11  C8    120.55  3.000
 HMO  H12   C12  C13   118.80  3.000
 HMO  H12   C12  C11   119.74  3.000
 HMO  C13   C12  C11   121.45  3.000
 HMO  H13   C13  C14   120.36  3.000
 HMO  H13   C13  C12   119.74  3.000
 HMO  C14   C13  C12   119.90  3.000
 HMO  O17   C14  C15   117.81  3.000
 HMO  O17   C14  C13   122.83  3.000
 HMO  C15   C14  C13   119.36  3.000
 HMO  H15   C15  C16   120.21  3.000
 HMO  H15   C15  C14   119.66  3.000
 HMO  C16   C15  C14   120.13  3.000
 HMO  H16   C16  C15   118.72  3.000
 HMO  H16   C16  C11   120.05  3.000
 HMO  C15   C16  C11   121.22  3.000
 HMO  H17   O17  C14   110.48  3.000
 HMO  C20   O19  C1    119.23  3.000
 HMO  H203  C20  H202  109.22  3.000
 HMO  H203  C20  H201  108.76  3.000
 HMO  H202  C20  H201  108.91  3.000
 HMO  H203  C20  O19   111.83  3.000
 HMO  H202  C20  O19   111.79  3.000
 HMO  H201  C20  O19   106.22  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
 HMO  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 HMO  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 HMO  CONST_03  O10   C5   C6   C1    180.00   0.0  0
 HMO  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 HMO  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 HMO  CONST_06  C7    C4   C3   C2    180.00   0.0  0
 HMO  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 HMO  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 HMO  CONST_09  O10   C5   C4   C3    180.00   0.0  0
 HMO  CONST_10  C8    C7   C4   C3    180.00   0.0  0
 HMO  CONST_11  C9    O10  C5   C4      0.00   0.0  0
 HMO  CONST_12  C9    C8   C7   C4      0.00   0.0  0
 HMO  CONST_13  C11   C8   C7   C4    180.00   0.0  0
 HMO  CONST_14  C8    C7   C4   C5      0.00   0.0  0
 HMO  CONST_15  C8    C9   O10  C5      0.00   0.0  0
 HMO  CONST_16  C7    C4   C5   C6    180.00   0.0  0
 HMO  CONST_17  C9    O10  C5   C6    180.00   0.0  0
 HMO  CONST_18  O10   C5   C4   C7      0.00   0.0  0
 HMO  CONST_19  O10   C9   C8   C7      0.00   0.0  0
 HMO  CONST_22  C13   C12  C11  C8    180.00   0.0  0
 HMO  CONST_23  C15   C16  C11  C8    180.00   0.0  0
 HMO  CONST_26  C11   C8   C9   O10   180.00   0.0  0
 HMO  CONST_27  C14   C13  C12  C11     0.00   0.0  0
 HMO  CONST_28  C14   C15  C16  C11     0.00   0.0  0
 HMO  CONST_29  C15   C16  C11  C12     0.00   0.0  0
 HMO  CONST_30  C15   C14  C13  C12     0.00   0.0  0
 HMO  CONST_31  C16   C11  C12  C13     0.00   0.0  0
 HMO  CONST_32  C16   C15  C14  C13     0.00   0.0  0
 HMO  CONST_33  O19   C1   C2   C3    180.00   0.0  0
 HMO  CONST_34  O18   C7   C4   C3      0.00   0.0  0
 HMO  CONST_35  O18   C7   C4   C5    180.00   0.0  0
 HMO  CONST_36  O19   C1   C6   C5    180.00   0.0  0
 HMO  CONST_37  O18   C7   C8   C9    180.00   0.0  0
 HMO  CONST_38  O18   C7   C8   C11     0.00   0.0  0
 HMO  CONST_39  O17   C14  C13  C12   180.00   0.0  0
 HMO  CONST_40  O17   C14  C15  C16   180.00   0.0  0
 HMO  CONST_41  H3    C3   C2   C1    180.00   0.0  0
 HMO  CONST_42  H6    C6   C1   C2    180.00   0.0  0
 HMO  CONST_43  H2    C2   C3   C4    180.00   0.0  0
 HMO  CONST_44  H9    C9   O10  C5    180.00   0.0  0
 HMO  CONST_45  H12   C12  C11  C8      0.00   0.0  0
 HMO  CONST_46  H16   C16  C11  C8      0.00   0.0  0
 HMO  CONST_47  H13   C13  C12  C11   180.00   0.0  0
 HMO  CONST_48  H15   C15  C16  C11   180.00   0.0  0
 HMO  Var_01    H201  C20  O19  C1   -179.06  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
 HMO  plan-1  C8   0.020
 HMO  plan-1  C11  0.020
 HMO  plan-1  C12  0.020
 HMO  plan-1  C13  0.020
 HMO  plan-1  C14  0.020
 HMO  plan-1  C15  0.020
 HMO  plan-1  C16  0.020
 HMO  plan-1  O17  0.020
 HMO  plan-1  H12  0.020
 HMO  plan-1  H13  0.020
 HMO  plan-1  H15  0.020
 HMO  plan-1  H16  0.020
 HMO  plan-2  C1   0.020
 HMO  plan-2  C2   0.020
 HMO  plan-2  C3   0.020
 HMO  plan-2  C4   0.020
 HMO  plan-2  C5   0.020
 HMO  plan-2  C6   0.020
 HMO  plan-2  C7   0.020
 HMO  plan-2  O10  0.020
 HMO  plan-2  O19  0.020
 HMO  plan-2  H2   0.020
 HMO  plan-2  H3   0.020
 HMO  plan-2  H6   0.020
 HMO  plan-3  C4   0.020
 HMO  plan-3  C7   0.020
 HMO  plan-3  C8   0.020
 HMO  plan-3  O18  0.020

