# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:17:53 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: [2,3-bis(oxidanyl)phenyl]-[6-(2-fluoranyl-3-oxidanyl-phenyl)pyridin-2-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(c1O)C(=O)c2cccc(n2)c3cccc(O)c3F
#
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
 5Q6  5Q6  '[2,3-bis(oxidanyl)phenyl]-[6-(2-fluoranyl-3-oxidanyl-phenyl)pyridin-2-yl]methanone'  ligand  36  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5Q6
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
 5Q6  C1   C  CR16  0  -0.334   3.5944   2.0350  -1.1644
 5Q6  C2   C  CR16  0  -0.263   2.4267   1.5258  -1.7331
 5Q6  C3   C  CR16  0  -0.295   1.8510   0.3826  -1.2287
 5Q6  C4   C  CR6   0  -0.148   2.4383  -0.2870  -0.1426
 5Q6  C5   C  C     0   0.396   1.8764  -1.5190   0.4151
 5Q6  C6   C  CR6   0   0.124   0.4987  -1.9752   0.0483
 5Q6  C7   C  CR16  0  -0.295   0.2653  -3.3283  -0.1649
 5Q6  C8   C  CR16  0  -0.151  -1.0318  -3.7233  -0.4486
 5Q6  C9   C  CR16  0  -0.308  -2.0345  -2.7695  -0.4751
 5Q6  C10  C  CR6   0   0.221  -1.7050  -1.4386  -0.2218
 5Q6  C17  C  CR6   0   0.265   3.6346   0.2095   0.4044
 5Q6  C16  C  CR6   0   0.429  -2.6103   0.8110  -0.8365
 5Q6  C15  C  CR6   0   0.246  -3.5848   1.8041  -0.8058
 5Q6  O2   O  OH1   0  -0.628  -3.4431   2.9779  -1.4448
 5Q6  C14  C  CR16  0  -0.346  -4.7499   1.5610  -0.0880
 5Q6  C13  C  CR16  0  -0.246  -4.9244   0.3507   0.5656
 5Q6  C12  C  CR16  0  -0.300  -3.9434  -0.6266   0.5170
 5Q6  C11  C  CR6   0  -0.149  -2.7596  -0.4029  -0.1864
 5Q6  N    N  N     0  -0.412  -0.4562  -1.0557   0.0187
 5Q6  O1   O  O     0  -0.439   2.5115  -2.2139   1.2025
 5Q6  O3   O  OH1   0  -0.634   4.2937  -0.3700   1.4120
 5Q6  C    C  CR6   0   0.299   4.2003   1.3905  -0.1041
 5Q6  O    O  OH1   0  -0.632   5.3341   1.8972   0.4191
 5Q6  H1   H  HCR6  0   0.276   4.0452   2.9390  -1.5554
 5Q6  H2   H  HCR6  0   0.262   1.9764   2.0373  -2.5725
 5Q6  H3   H  HCR6  0   0.262   0.9511  -0.0039  -1.6793
 5Q6  H4   H  HCR6  0   0.284   1.0720  -4.0465  -0.1253
 5Q6  H5   H  HCR6  0   0.284  -1.2593  -4.7619  -0.6463
 5Q6  H6   H  HCR6  0   0.284  -3.0551  -3.0475  -0.6999
 5Q6  H7   H  HOH1  0   0.478  -2.6058   3.0195  -1.9215
 5Q6  H8   H  HCR6  0   0.280  -5.5154   2.3257  -0.0519
 5Q6  H9   H  HCR6  0   0.266  -5.8338   0.1731   1.1235
 5Q6  H10  H  HCR6  0   0.267  -4.0806  -1.5622   1.0432
 5Q6  H11  H  HOH1  0   0.487   3.8571  -1.2266   1.6090
 5Q6  H12  H  HOH1  0   0.475   5.6550   1.3379   1.1369
 5Q6  F    F  F     0  -0.305  -1.5081   1.0588  -1.5667

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
 5Q6  F    C16  single    1.345  0.020  1.345
 5Q6  O2   C15  single    1.344  0.020  1.344
 5Q6  O1   C5   double    1.227  0.020  1.227
 5Q6  C16  C15  aromatic  1.392  0.020  1.392
 5Q6  C16  C11  aromatic  1.385  0.020  1.385
 5Q6  O3   C17  single    1.336  0.020  1.336
 5Q6  C15  C14  aromatic  1.390  0.020  1.390
 5Q6  C5   C6   single    1.497  0.020  1.497
 5Q6  C5   C4   single    1.464  0.020  1.464
 5Q6  C7   C8   aromatic  1.385  0.020  1.385
 5Q6  C7   C6   aromatic  1.390  0.020  1.390
 5Q6  C8   C9   aromatic  1.384  0.020  1.384
 5Q6  C6   N    aromatic  1.326  0.020  1.326
 5Q6  N    C10  aromatic  1.328  0.020  1.328
 5Q6  C9   C10  aromatic  1.394  0.020  1.394
 5Q6  C10  C11  single    1.479  0.020  1.479
 5Q6  C11  C12  aromatic  1.395  0.020  1.395
 5Q6  C17  C4   aromatic  1.406  0.020  1.406
 5Q6  C17  C    aromatic  1.405  0.020  1.405
 5Q6  C14  C13  aromatic  1.387  0.020  1.387
 5Q6  C4   C3   aromatic  1.405  0.020  1.405
 5Q6  O    C    single    1.348  0.020  1.348
 5Q6  C12  C13  aromatic  1.386  0.020  1.386
 5Q6  C    C1   aromatic  1.381  0.020  1.381
 5Q6  C3   C2   aromatic  1.376  0.020  1.376
 5Q6  C1   C2   aromatic  1.395  0.020  1.395
 5Q6  C1   H1   single    0.930  0.020  1.080
 5Q6  C2   H2   single    0.930  0.020  1.080
 5Q6  C3   H3   single    0.930  0.020  1.080
 5Q6  C7   H4   single    0.930  0.020  1.080
 5Q6  C8   H5   single    0.930  0.020  1.080
 5Q6  C9   H6   single    0.930  0.020  1.080
 5Q6  O2   H7   single    0.850  0.020  0.980
 5Q6  C14  H8   single    0.930  0.020  1.080
 5Q6  C13  H9   single    0.930  0.020  1.080
 5Q6  C12  H10  single    0.930  0.020  1.080
 5Q6  O3   H11  single    0.850  0.020  0.980
 5Q6  O    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
 5Q6  H1   C1   C    118.95  3.000
 5Q6  H1   C1   C2   120.39  3.000
 5Q6  C    C1   C2   120.66  3.000
 5Q6  H2   C2   C3   120.23  3.000
 5Q6  H2   C2   C1   119.49  3.000
 5Q6  C3   C2   C1   120.27  3.000
 5Q6  H3   C3   C4   120.09  3.000
 5Q6  H3   C3   C2   119.60  3.000
 5Q6  C4   C3   C2   120.31  3.000
 5Q6  C17  C4   C5   118.39  3.000
 5Q6  C17  C4   C3   119.22  3.000
 5Q6  C5   C4   C3   122.35  3.000
 5Q6  O1   C5   C6   117.45  3.000
 5Q6  C6   C5   C4   121.08  3.000
 5Q6  O1   C5   C4   121.47  3.000
 5Q6  N    C6   C7   123.43  3.000
 5Q6  N    C6   C5   117.19  3.000
 5Q6  C7   C6   C5   119.27  3.000
 5Q6  H4   C7   C8   121.12  3.000
 5Q6  H4   C7   C6   121.07  3.000
 5Q6  C8   C7   C6   117.80  3.000
 5Q6  H5   C8   C9   120.39  3.000
 5Q6  H5   C8   C7   120.55  3.000
 5Q6  C9   C8   C7   119.06  3.000
 5Q6  H6   C9   C10  120.41  3.000
 5Q6  H6   C9   C8   120.70  3.000
 5Q6  C10  C9   C8   118.89  3.000
 5Q6  N    C10  C11  117.67  3.000
 5Q6  C11  C10  C9   120.29  3.000
 5Q6  N    C10  C9   122.03  3.000
 5Q6  C    C17  O3   116.04  3.000
 5Q6  C    C17  C4   119.91  3.000
 5Q6  O3   C17  C4   124.05  3.000
 5Q6  C11  C16  C15  122.65  3.000
 5Q6  C11  C16  F    120.30  3.000
 5Q6  C15  C16  F    117.02  3.000
 5Q6  C14  C15  O2   119.12  3.000
 5Q6  C14  C15  C16  118.27  3.000
 5Q6  O2   C15  C16  122.61  3.000
 5Q6  H7   O2   C15  111.36  3.000
 5Q6  H8   C14  C13  120.79  3.000
 5Q6  H8   C14  C15  119.11  3.000
 5Q6  C13  C14  C15  120.10  3.000
 5Q6  H9   C13  C12  119.83  3.000
 5Q6  H9   C13  C14  119.49  3.000
 5Q6  C12  C13  C14  120.67  3.000
 5Q6  H10  C12  C11  119.43  3.000
 5Q6  H10  C12  C13  120.21  3.000
 5Q6  C11  C12  C13  120.35  3.000
 5Q6  C12  C11  C16  117.95  3.000
 5Q6  C12  C11  C10  120.33  3.000
 5Q6  C16  C11  C10  121.72  3.000
 5Q6  C10  N    C6   118.77  3.000
 5Q6  H11  O3   C17  108.08  3.000
 5Q6  O    C    C17  120.95  3.000
 5Q6  O    C    C1   119.46  3.000
 5Q6  C17  C    C1   119.58  3.000
 5Q6  H12  O    C    110.53  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
 5Q6  CONST_01  C4   C17  C    C1     0.00   0.0  0
 5Q6  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 5Q6  CONST_03  C17  C4   C3   C2     0.00   0.0  0
 5Q6  CONST_04  C17  C    C1   C2     0.00   0.0  0
 5Q6  CONST_05  C    C17  C4   C3     0.00   0.0  0
 5Q6  CONST_06  C    C1   C2   C3     0.00   0.0  0
 5Q6  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 5Q6  CONST_08  C9   C10  N    C6     0.00   0.0  0
 5Q6  CONST_09  C11  C10  N    C6   180.00   0.0  0
 5Q6  CONST_10  C10  C9   C8   C7     0.00   0.0  0
 5Q6  CONST_11  C10  N    C6   C7     0.00   0.0  0
 5Q6  CONST_12  N    C6   C7   C8     0.00   0.0  0
 5Q6  CONST_13  N    C10  C9   C8     0.00   0.0  0
 5Q6  CONST_14  C11  C10  C9   C8   180.00   0.0  0
 5Q6  CONST_17  C15  C16  C11  C10  180.00   0.0  0
 5Q6  CONST_18  C13  C12  C11  C10  180.00   0.0  0
 5Q6  CONST_19  C13  C14  C15  C16    0.00   0.0  0
 5Q6  CONST_21  C13  C12  C11  C16    0.00   0.0  0
 5Q6  CONST_22  C12  C11  C16  C15    0.00   0.0  0
 5Q6  CONST_23  C12  C13  C14  C15    0.00   0.0  0
 5Q6  CONST_24  C11  C16  C15  C14    0.00   0.0  0
 5Q6  CONST_25  C11  C12  C13  C14    0.00   0.0  0
 5Q6  CONST_27  O3   C17  C    C1   180.00   0.0  0
 5Q6  CONST_28  C5   C4   C3   C2   180.00   0.0  0
 5Q6  CONST_29  O    C    C1   C2   180.00   0.0  0
 5Q6  CONST_30  O3   C17  C4   C3   180.00   0.0  0
 5Q6  CONST_31  O    C    C17  C4   180.00   0.0  0
 5Q6  CONST_32  C8   C7   C6   C5   180.00   0.0  0
 5Q6  CONST_33  C10  N    C6   C5   180.00   0.0  0
 5Q6  CONST_34  C    C17  C4   C5   180.00   0.0  0
 5Q6  CONST_35  F    C16  C11  C10    0.00   0.0  0
 5Q6  CONST_36  C14  C15  C16  F    180.00   0.0  0
 5Q6  CONST_37  C12  C11  C16  F    180.00   0.0  0
 5Q6  CONST_38  C11  C16  C15  O2   180.00   0.0  0
 5Q6  CONST_39  C13  C14  C15  O2   180.00   0.0  0
 5Q6  CONST_40  H3   C3   C2   C1   180.00   0.0  0
 5Q6  CONST_41  H1   C1   C2   C3   180.00   0.0  0
 5Q6  CONST_42  H2   C2   C3   C4   180.00   0.0  0
 5Q6  CONST_43  H5   C8   C7   C6   180.00   0.0  0
 5Q6  CONST_44  H6   C9   C8   C7   180.00   0.0  0
 5Q6  CONST_45  H4   C7   C8   C9   180.00   0.0  0
 5Q6  CONST_46  H10  C12  C11  C10    0.00   0.0  0
 5Q6  CONST_47  H8   C14  C15  C16  180.00   0.0  0
 5Q6  CONST_48  H9   C13  C14  C15  180.00   0.0  0
 5Q6  Var_01    C6   C5   C4   C3   -12.91  30.0  2
 5Q6  Var_02    C7   C6   C5   C4   140.06  30.0  2

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
 5Q6  plan-1  C5   0.020
 5Q6  plan-1  C6   0.020
 5Q6  plan-1  C7   0.020
 5Q6  plan-1  C8   0.020
 5Q6  plan-1  C9   0.020
 5Q6  plan-1  C10  0.020
 5Q6  plan-1  C11  0.020
 5Q6  plan-1  N    0.020
 5Q6  plan-1  H4   0.020
 5Q6  plan-1  H5   0.020
 5Q6  plan-1  H6   0.020
 5Q6  plan-2  C1   0.020
 5Q6  plan-2  C2   0.020
 5Q6  plan-2  C3   0.020
 5Q6  plan-2  C4   0.020
 5Q6  plan-2  C5   0.020
 5Q6  plan-2  C17  0.020
 5Q6  plan-2  O3   0.020
 5Q6  plan-2  C    0.020
 5Q6  plan-2  O    0.020
 5Q6  plan-2  H1   0.020
 5Q6  plan-2  H2   0.020
 5Q6  plan-2  H3   0.020
 5Q6  plan-3  C10  0.020
 5Q6  plan-3  C16  0.020
 5Q6  plan-3  C15  0.020
 5Q6  plan-3  O2   0.020
 5Q6  plan-3  C14  0.020
 5Q6  plan-3  C13  0.020
 5Q6  plan-3  C12  0.020
 5Q6  plan-3  C11  0.020
 5Q6  plan-3  H8   0.020
 5Q6  plan-3  H9   0.020
 5Q6  plan-3  H10  0.020
 5Q6  plan-3  F    0.020
 5Q6  plan-4  C4   0.020
 5Q6  plan-4  C5   0.020
 5Q6  plan-4  C6   0.020
 5Q6  plan-4  O1   0.020

