# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 15:52:18 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc2OC(=CC(=O)c2c(O)c1O)c3ccccc3
#
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
 3WL  3WL  5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one  ligand  30  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3WL
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
 3WL  C4   C  CR16  0  -0.336  -3.2827   1.3592   0.3018
 3WL  C5   C  CR16  0  -0.243  -4.6294   1.6873   0.2753
 3WL  C6   C  CR6   0   0.318  -1.4484  -0.3095   0.0627
 3WL  C7   C  CR16  0  -0.441  -0.9576  -1.5628   0.1745
 3WL  C8   C  CR6   0   0.444   0.4623  -1.8255   0.2097
 3WL  C10  C  CR6   0   0.195   2.7069  -0.7010   0.0178
 3WL  C13  C  CR16  0  -0.422   1.4370   1.7888  -0.0778
 3WL  O    O  O     0  -0.455   0.9202  -2.9555   0.3835
 3WL  C9   C  CR66  0  -0.392   1.2994  -0.6418   0.0575
 3WL  C14  C  CR66  0   0.483   0.7024   0.6173  -0.0076
 3WL  C12  C  CR6   0   0.332   2.8189   1.7070  -0.0897
 3WL  O2   O  OH1   0  -0.657   3.5275   2.8385  -0.1593
 3WL  C11  C  CR6   0   0.221   3.4590   0.4573  -0.0365
 3WL  O3   O  OH1   0  -0.650   4.8094   0.4619  -0.0658
 3WL  O4   O  OH1   0  -0.619   3.3885  -1.8634  -0.0423
 3WL  O1   O  O     0  -0.464  -0.6429   0.7555  -0.0072
 3WL  C3   C  CR6   0   0.213  -2.8708   0.0530   0.0260
 3WL  C2   C  CR16  0  -0.366  -3.8341  -0.9092  -0.2858
 3WL  C1   C  CR16  0  -0.217  -5.1776  -0.5756  -0.3114
 3WL  C    C  CR16  0  -0.269  -5.5805   0.7239  -0.0302
 3WL  H1   H  HCR6  0   0.267  -2.5617   2.1257   0.5497
 3WL  H2   H  HCR6  0   0.256  -4.9349   2.7013   0.4965
 3WL  H3   H  HCR6  0   0.276  -1.6332  -2.4003   0.2695
 3WL  H4   H  HCR6  0   0.294   0.9435   2.7508  -0.1229
 3WL  H5   H  HOH1  0   0.484   4.4746   2.6588  -0.1033
 3WL  H6   H  HOH1  0   0.484   5.1488  -0.4411  -0.0254
 3WL  H7   H  HOH1  0   0.469   2.9959  -2.5121   0.5585
 3WL  H8   H  HCR6  0   0.259  -3.5397  -1.9208  -0.5312
 3WL  H9   H  HCR6  0   0.283  -5.9112  -1.3314  -0.5586
 3WL  H10  H  HCR6  0   0.256  -6.6309   0.9831  -0.0514

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
 3WL  C5   C    aromatic  1.388  0.020  1.388
 3WL  C5   C4   aromatic  1.386  0.020  1.386
 3WL  C    C1   aromatic  1.389  0.020  1.389
 3WL  C4   C3   aromatic  1.397  0.020  1.397
 3WL  C1   C2   aromatic  1.385  0.020  1.385
 3WL  C3   C2   aromatic  1.397  0.020  1.397
 3WL  C3   C6   single    1.468  0.020  1.468
 3WL  C7   C6   double    1.351  0.020  1.351
 3WL  C7   C8   single    1.444  0.020  1.444
 3WL  O    C8   double    1.232  0.020  1.232
 3WL  C6   O1   single    1.337  0.020  1.337
 3WL  C8   C9   single    1.458  0.020  1.458
 3WL  O1   C14  single    1.352  0.020  1.352
 3WL  C9   C14  aromatic  1.395  0.020  1.395
 3WL  C9   C10  aromatic  1.409  0.020  1.409
 3WL  O4   C10  single    1.349  0.020  1.349
 3WL  C14  C13  aromatic  1.385  0.020  1.385
 3WL  C10  C11  aromatic  1.382  0.020  1.382
 3WL  C13  C12  aromatic  1.384  0.020  1.384
 3WL  C11  C12  aromatic  1.405  0.020  1.405
 3WL  C11  O3   single    1.351  0.020  1.351
 3WL  C12  O2   single    1.337  0.020  1.337
 3WL  C4   H1   single    0.930  0.020  1.080
 3WL  C5   H2   single    0.930  0.020  1.080
 3WL  C7   H3   single    0.930  0.020  1.080
 3WL  C13  H4   single    0.930  0.020  1.080
 3WL  O2   H5   single    0.850  0.020  0.980
 3WL  O3   H6   single    0.850  0.020  0.980
 3WL  O4   H7   single    0.850  0.020  0.980
 3WL  C2   H8   single    0.930  0.020  1.080
 3WL  C1   H9   single    0.930  0.020  1.080
 3WL  C    H10  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
 3WL  H1   C4   C3   120.77  3.000
 3WL  H1   C4   C5   118.97  3.000
 3WL  C3   C4   C5   120.26  3.000
 3WL  H2   C5   C    120.14  3.000
 3WL  H2   C5   C4   119.48  3.000
 3WL  C    C5   C4   120.37  3.000
 3WL  C3   C6   O1   112.68  3.000
 3WL  O1   C6   C7   121.63  3.000
 3WL  C3   C6   C7   125.68  3.000
 3WL  H3   C7   C8   118.14  3.000
 3WL  H3   C7   C6   119.97  3.000
 3WL  C8   C7   C6   121.87  3.000
 3WL  C9   C8   O    123.11  3.000
 3WL  C9   C8   C7   114.47  3.000
 3WL  O    C8   C7   122.40  3.000
 3WL  O4   C10  C11  116.45  3.000
 3WL  C11  C10  C9   120.62  3.000
 3WL  O4   C10  C9   122.83  3.000
 3WL  H4   C13  C12  120.49  3.000
 3WL  H4   C13  C14  120.82  3.000
 3WL  C12  C13  C14  118.69  3.000
 3WL  C14  C9   C10  117.65  3.000
 3WL  C10  C9   C8   122.84  3.000
 3WL  C14  C9   C8   119.47  3.000
 3WL  O1   C14  C9   121.19  3.000
 3WL  C9   C14  C13  122.62  3.000
 3WL  O1   C14  C13  116.19  3.000
 3WL  C11  C12  O2   120.88  3.000
 3WL  O2   C12  C13  118.65  3.000
 3WL  C11  C12  C13  120.46  3.000
 3WL  H5   O2   C12  111.06  3.000
 3WL  O3   C11  C12  116.85  3.000
 3WL  O3   C11  C10  123.21  3.000
 3WL  C12  C11  C10  119.93  3.000
 3WL  H6   O3   C11  110.33  3.000
 3WL  H7   O4   C10  110.19  3.000
 3WL  C14  O1   C6   121.19  3.000
 3WL  C2   C3   C6   120.24  3.000
 3WL  C6   C3   C4   120.76  3.000
 3WL  C2   C3   C4   119.00  3.000
 3WL  H8   C2   C1   119.02  3.000
 3WL  H8   C2   C3   120.48  3.000
 3WL  C1   C2   C3   120.49  3.000
 3WL  H9   C1   C    120.20  3.000
 3WL  H9   C1   C2   119.60  3.000
 3WL  C    C1   C2   120.20  3.000
 3WL  H10  C    C1   120.11  3.000
 3WL  H10  C    C5   120.21  3.000
 3WL  C1   C    C5   119.68  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
 3WL  CONST_01  C1   C    C5   C4      0.00   0.0  0
 3WL  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 3WL  CONST_03  C2   C1   C    C5      0.00   0.0  0
 3WL  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 3WL  CONST_05  C13  C14  C9   C10     0.00   0.0  0
 3WL  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 3WL  CONST_07  C12  C13  C14  C9      0.00   0.0  0
 3WL  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 3WL  CONST_09  C11  C10  C9   C14     0.00   0.0  0
 3WL  CONST_10  C11  C12  C13  C14     0.00   0.0  0
 3WL  CONST_11  C    C5   C4   C3      0.00   0.0  0
 3WL  CONST_12  C    C1   C2   C3      0.00   0.0  0
 3WL  CONST_13  C6   C3   C4   C5    180.00   0.0  0
 3WL  CONST_14  C1   C2   C3   C6    180.00   0.0  0
 3WL  CONST_15  O4   C10  C9   C8      0.00   0.0  0
 3WL  CONST_16  O2   C12  C11  C10   180.00   0.0  0
 3WL  CONST_17  O3   C11  C12  C13   180.00   0.0  0
 3WL  CONST_18  O3   C11  C10  C9    180.00   0.0  0
 3WL  CONST_19  O4   C10  C9   C14   180.00   0.0  0
 3WL  CONST_20  O2   C12  C13  C14   180.00   0.0  0
 3WL  CONST_21  O4   C10  C11  C12   180.00   0.0  0
 3WL  CONST_22  H10  C    C5   C4    180.00   0.0  0
 3WL  CONST_23  H8   C2   C3   C4    180.00   0.0  0
 3WL  CONST_24  H9   C1   C    C5    180.00   0.0  0
 3WL  CONST_25  H1   C4   C3   C6      0.00   0.0  0
 3WL  CONST_26  H4   C13  C14  C9    180.00   0.0  0
 3WL  CONST_27  H2   C5   C4   C3    180.00   0.0  0
 3WL  Var_01    C7   C6   C3   C4    161.02  30.0  2
 3WL  Var_02    C9   C8   C7   C6     -2.51  30.0  1
 3WL  Var_03    C9   C14  O1   C6      0.36  30.0  1
 3WL  Var_04    C14  C9   C8   C7      4.60  30.0  1
 3WL  Var_05    C3   C6   C7   C8   -179.66  30.0  1

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
 3WL  plan-1  C4   0.020
 3WL  plan-1  C5   0.020
 3WL  plan-1  C6   0.020
 3WL  plan-1  C3   0.020
 3WL  plan-1  C2   0.020
 3WL  plan-1  C1   0.020
 3WL  plan-1  C    0.020
 3WL  plan-1  H1   0.020
 3WL  plan-1  H2   0.020
 3WL  plan-1  H8   0.020
 3WL  plan-1  H9   0.020
 3WL  plan-1  H10  0.020
 3WL  plan-2  C8   0.020
 3WL  plan-2  C10  0.020
 3WL  plan-2  C13  0.020
 3WL  plan-2  C9   0.020
 3WL  plan-2  C14  0.020
 3WL  plan-2  C12  0.020
 3WL  plan-2  O2   0.020
 3WL  plan-2  C11  0.020
 3WL  plan-2  O3   0.020
 3WL  plan-2  O4   0.020
 3WL  plan-2  O1   0.020
 3WL  plan-2  H4   0.020
 3WL  plan-3  C7   0.020
 3WL  plan-3  C8   0.020
 3WL  plan-3  O    0.020
 3WL  plan-3  C9   0.020

