# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 11:18:05 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)C=C(Oc2c1)c3cc(O)c(O)c(O)c3
#
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
 MYF  MYF  5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one  ligand  32  22  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MYF
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
 MYF  O22   O  OC    0  -0.510   5.6127   2.3636  -0.0810
 MYF  C7    C  CR6   0   0.533   4.4889   2.8767  -0.2116
 MYF  C6    C  CR66  0  -0.353   3.2788   2.0889  -0.1473
 MYF  C1    C  CR6   0   0.404   3.3080   0.6895   0.0658
 MYF  O21   O  OH1   0  -0.630   4.4684   0.0613   0.2211
 MYF  C2    C  CR16  0  -0.454   2.1288  -0.0307   0.1142
 MYF  C3    C  CR6   0   0.398   0.9073   0.6286  -0.0469
 MYF  O20   O  OH1   0  -0.616  -0.1947  -0.1248   0.0153
 MYF  C5    C  CR66  0   0.421   2.0366   2.7024  -0.3052
 MYF  C4    C  CR16  0  -0.515   0.8452   2.0035  -0.2608
 MYF  O10   O  O     0  -0.469   1.9551   4.0347  -0.5053
 MYF  C9    C  CR6   0   0.408   3.0519   4.8011  -0.5807
 MYF  C8    C  CR16  0  -0.519   4.2945   4.2807  -0.4513
 MYF  C11   C  CR6   0   0.033   2.7400   6.2097  -0.8260
 MYF  C12   C  CR16  0  -0.472   3.6798   7.1918  -0.5095
 MYF  C13   C  CR6   0   0.314   3.3972   8.5226  -0.7608
 MYF  O19   O  OH1   0  -0.641   4.2369   9.5394  -0.4796
 MYF  C14   C  CR6   0   0.186   2.1761   8.8905  -1.3302
 MYF  O18   O  OH1   0  -0.631   1.8494  10.1695  -1.6012
 MYF  C15   C  CR6   0   0.327   1.2362   7.9070  -1.6365
 MYF  C16   C  CR16  0  -0.403   1.5148   6.5723  -1.3817
 MYF  O17   O  OH1   0  -0.632   0.0486   8.2226  -2.1869
 MYF  HO21  H  HOH1  0   0.476   5.1827   0.7419   0.1509
 MYF  H2    H  HCR6  0   0.281   2.1501  -1.1007   0.2774
 MYF  HO20  H  HOH1  0   0.484  -0.9875   0.4139  -0.0915
 MYF  H4    H  HCR6  0   0.295  -0.0987   2.5178  -0.3904
 MYF  H8    H  HCR6  0   0.284   5.1617   4.9177  -0.5483
 MYF  H12   H  HCR6  0   0.280   4.6218   6.9298  -0.0444
 MYF  HO19  H  HOH1  0   0.487   5.0547   9.2171  -0.0839
 MYF  HO18  H  HOH1  0   0.485   2.5426  10.7756  -1.3136
 MYF  H16   H  HCR6  0   0.271   0.7682   5.8335  -1.6390
 MYF  HO17  H  HOH1  0   0.476  -0.0481   9.1783  -2.2741

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
 MYF  O22  C7    double    1.242  0.020  1.242
 MYF  C7   C6    aromatic  1.445  0.020  1.445
 MYF  C7   C8    aromatic  1.438  0.020  1.438
 MYF  C6   C1    aromatic  1.416  0.020  1.416
 MYF  C6   C5    aromatic  1.394  0.020  1.394
 MYF  C1   O21   single    1.329  0.020  1.329
 MYF  C1   C2    aromatic  1.383  0.020  1.383
 MYF  O21  HO21  single    0.850  0.020  0.980
 MYF  C2   C3    aromatic  1.397  0.020  1.397
 MYF  C2   H2    single    0.930  0.020  1.080
 MYF  C3   O20   single    1.336  0.020  1.336
 MYF  C3   C4    aromatic  1.393  0.020  1.393
 MYF  O20  HO20  single    0.850  0.020  0.980
 MYF  C5   C4    aromatic  1.382  0.020  1.382
 MYF  C5   O10   aromatic  1.350  0.020  1.350
 MYF  C4   H4    single    0.930  0.020  1.080
 MYF  O10  C9    aromatic  1.340  0.020  1.340
 MYF  C9   C8    aromatic  1.353  0.020  1.353
 MYF  C9   C11   single    1.463  0.020  1.463
 MYF  C8   H8    single    0.930  0.020  1.080
 MYF  C11  C12   aromatic  1.396  0.020  1.396
 MYF  C11  C16   aromatic  1.393  0.020  1.393
 MYF  C12  C13   aromatic  1.383  0.020  1.383
 MYF  C12  H12   single    0.930  0.020  1.080
 MYF  C13  O19   single    1.348  0.020  1.348
 MYF  C13  C14   aromatic  1.397  0.020  1.397
 MYF  O19  HO19  single    0.850  0.020  0.980
 MYF  C14  C15   aromatic  1.394  0.020  1.394
 MYF  C14  O18   single    1.348  0.020  1.348
 MYF  O18  HO18  single    0.850  0.020  0.980
 MYF  C15  C16   aromatic  1.387  0.020  1.387
 MYF  C15  O17   single    1.346  0.020  1.346
 MYF  C16  H16   single    0.930  0.020  1.080
 MYF  O17  HO17  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
 MYF  C8    C7   C6   115.25  3.000
 MYF  C8    C7   O22  122.91  3.000
 MYF  C6    C7   O22  121.84  3.000
 MYF  C5    C6   C1   118.06  3.000
 MYF  C5    C6   C7   120.06  3.000
 MYF  C1    C6   C7   121.88  3.000
 MYF  C2    C1   O21  119.64  3.000
 MYF  C2    C1   C6   120.17  3.000
 MYF  O21   C1   C6   120.19  3.000
 MYF  HO21  O21  C1   107.29  3.000
 MYF  H2    C2   C3   120.06  3.000
 MYF  H2    C2   C1   120.22  3.000
 MYF  C3    C2   C1   119.72  3.000
 MYF  C4    C3   O20  121.80  3.000
 MYF  C4    C3   C2   121.49  3.000
 MYF  O20   C3   C2   116.71  3.000
 MYF  HO20  O20  C3   110.97  3.000
 MYF  O10   C5   C4   116.87  3.000
 MYF  O10   C5   C6   120.33  3.000
 MYF  C4    C5   C6   122.80  3.000
 MYF  H4    C4   C5   120.49  3.000
 MYF  H4    C4   C3   121.75  3.000
 MYF  C5    C4   C3   117.76  3.000
 MYF  C9    O10  C5   121.56  3.000
 MYF  C11   C9   C8   125.58  3.000
 MYF  C11   C9   O10  112.67  3.000
 MYF  C8    C9   O10  121.74  3.000
 MYF  H8    C8   C9   120.11  3.000
 MYF  H8    C8   C7   118.83  3.000
 MYF  C9    C8   C7   121.05  3.000
 MYF  C16   C11  C12  119.96  3.000
 MYF  C16   C11  C9   120.32  3.000
 MYF  C12   C11  C9   119.72  3.000
 MYF  H12   C12  C13  119.24  3.000
 MYF  H12   C12  C11  120.86  3.000
 MYF  C13   C12  C11  119.88  3.000
 MYF  C14   C13  O19  115.53  3.000
 MYF  C14   C13  C12  120.40  3.000
 MYF  O19   C13  C12  124.07  3.000
 MYF  HO19  O19  C13  111.21  3.000
 MYF  C15   C14  O18  117.50  3.000
 MYF  O18   C14  C13  122.95  3.000
 MYF  C15   C14  C13  119.54  3.000
 MYF  HO18  O18  C14  111.24  3.000
 MYF  O17   C15  C16  118.54  3.000
 MYF  O17   C15  C14  121.26  3.000
 MYF  C16   C15  C14  120.19  3.000
 MYF  H16   C16  C15  118.35  3.000
 MYF  H16   C16  C11  121.62  3.000
 MYF  C15   C16  C11  120.02  3.000
 MYF  HO17  O17  C15  110.95  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
 MYF  CONST_01  C2   C1   C6   C7   180.00  0.0  0
 MYF  CONST_02  C4   C5   C6   C7   180.00  0.0  0
 MYF  CONST_03  O10  C5   C6   C7     0.00  0.0  0
 MYF  CONST_04  O10  C9   C8   C7     0.00  0.0  0
 MYF  CONST_05  C11  C9   C8   C7   180.00  0.0  0
 MYF  CONST_06  C9   C8   C7   C6     0.00  0.0  0
 MYF  CONST_07  C3   C2   C1   C6     0.00  0.0  0
 MYF  CONST_08  C3   C4   C5   C6     0.00  0.0  0
 MYF  CONST_09  C9   O10  C5   C6     0.00  0.0  0
 MYF  CONST_10  C8   C7   C6   C1   180.00  0.0  0
 MYF  CONST_11  C4   C5   C6   C1     0.00  0.0  0
 MYF  CONST_12  O10  C5   C6   C1   180.00  0.0  0
 MYF  CONST_13  C4   C3   C2   C1     0.00  0.0  0
 MYF  CONST_14  C5   C6   C1   C2     0.00  0.0  0
 MYF  CONST_15  C5   C4   C3   C2     0.00  0.0  0
 MYF  CONST_16  O10  C5   C4   C3   180.00  0.0  0
 MYF  CONST_17  C8   C7   C6   C5     0.00  0.0  0
 MYF  CONST_18  C8   C9   O10  C5     0.00  0.0  0
 MYF  CONST_19  C11  C9   O10  C5   180.00  0.0  0
 MYF  CONST_20  C9   O10  C5   C4   180.00  0.0  0
 MYF  CONST_23  C13  C12  C11  C9   180.00  0.0  0
 MYF  CONST_24  C15  C16  C11  C9   180.00  0.0  0
 MYF  CONST_27  C14  C13  C12  C11    0.00  0.0  0
 MYF  CONST_28  C14  C15  C16  C11    0.00  0.0  0
 MYF  CONST_29  C15  C16  C11  C12    0.00  0.0  0
 MYF  CONST_30  C15  C14  C13  C12    0.00  0.0  0
 MYF  CONST_31  C16  C11  C12  C13    0.00  0.0  0
 MYF  CONST_32  C16  C15  C14  C13    0.00  0.0  0
 MYF  CONST_33  C1   C6   C7   O22    0.00  0.0  0
 MYF  CONST_34  C5   C6   C7   O22  180.00  0.0  0
 MYF  CONST_35  C9   C8   C7   O22  180.00  0.0  0
 MYF  CONST_36  O21  C1   C6   C7     0.00  0.0  0
 MYF  CONST_37  O20  C3   C2   C1   180.00  0.0  0
 MYF  CONST_38  C5   C6   C1   O21  180.00  0.0  0
 MYF  CONST_39  C3   C2   C1   O21  180.00  0.0  0
 MYF  CONST_40  C5   C4   C3   O20  180.00  0.0  0
 MYF  CONST_41  O19  C13  C12  C11  180.00  0.0  0
 MYF  CONST_42  O17  C15  C16  C11  180.00  0.0  0
 MYF  CONST_43  O18  C14  C13  C12  180.00  0.0  0
 MYF  CONST_44  O17  C15  C14  C13  180.00  0.0  0
 MYF  CONST_45  C15  C14  C13  O19  180.00  0.0  0
 MYF  CONST_46  C16  C15  C14  O18  180.00  0.0  0
 MYF  CONST_47  H8   C8   C7   C6   180.00  0.0  0
 MYF  CONST_48  H2   C2   C1   C6   180.00  0.0  0
 MYF  CONST_49  H4   C4   C5   C6   180.00  0.0  0
 MYF  CONST_50  H12  C12  C11  C9     0.00  0.0  0
 MYF  CONST_51  H16  C16  C11  C9     0.00  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
 MYF  plan-1  C9   0.020
 MYF  plan-1  C11  0.020
 MYF  plan-1  C12  0.020
 MYF  plan-1  C13  0.020
 MYF  plan-1  O19  0.020
 MYF  plan-1  C14  0.020
 MYF  plan-1  O18  0.020
 MYF  plan-1  C15  0.020
 MYF  plan-1  C16  0.020
 MYF  plan-1  O17  0.020
 MYF  plan-1  H12  0.020
 MYF  plan-1  H16  0.020
 MYF  plan-2  C7   0.020
 MYF  plan-2  C6   0.020
 MYF  plan-2  C1   0.020
 MYF  plan-2  O21  0.020
 MYF  plan-2  C2   0.020
 MYF  plan-2  C3   0.020
 MYF  plan-2  O20  0.020
 MYF  plan-2  C5   0.020
 MYF  plan-2  C4   0.020
 MYF  plan-2  O10  0.020
 MYF  plan-2  H2   0.020
 MYF  plan-2  H4   0.020
 MYF  plan-3  O22  0.020
 MYF  plan-3  C7   0.020
 MYF  plan-3  C6   0.020
 MYF  plan-3  C8   0.020

