# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 15:09:56 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-{6-amino-5-[4-(methylsulfonyl)phenyl]pyridin-3-yl}phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc(cc1)c2cc(cnc2N)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
 5DF  5DF  4-{6-amino-5-[4-(methylsulfonyl)phenyl]pyridin-3-yl}phenol  ligand  40  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 PERFECT
;

data_comp_5DF
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
 5DF  C7   C  CR6   0   0.061  -3.7906  -0.0856   0.1027
 5DF  C6   C  CR6   0   0.001  -2.6402   0.8313   0.1415
 5DF  C9   C  CR16  0  -0.322  -4.8298  -2.1866   0.7330
 5DF  C8   C  CR16  0  -0.303  -3.7534  -1.3176   0.7598
 5DF  C18  C  CR16  0  -0.211   3.3402   0.6987  -0.8899
 5DF  C16  C  CR16  0  -0.214   2.7643  -0.8980   0.8298
 5DF  C19  C  CR16  0  -0.292   2.0669   1.2361  -0.8106
 5DF  C1   C  CR16  0  -0.245  -1.3227   0.3741   0.1070
 5DF  C2   C  CR6   0  -0.038  -0.2508   1.2479   0.1468
 5DF  C3   C  CR6   0   0.404  -0.5424   2.6289   0.2470
 5DF  N4   N  N     0  -0.444  -1.7960   3.0737   0.2727
 5DF  C5   C  CR16  0  -0.107  -2.7975   2.2099   0.2168
 5DF  C10  C  CR6   0   0.343  -5.9894  -1.8391   0.0431
 5DF  C11  C  CR16  0  -0.368  -6.0467  -0.6145  -0.6170
 5DF  C12  C  CR16  0  -0.301  -4.9583   0.2431  -0.5858
 5DF  N13  N  NH2   0  -0.829   0.4374   3.5748   0.3017
 5DF  C14  C  CR6   0   0.065   1.1258   0.7208   0.0844
 5DF  C15  C  CR16  0  -0.289   1.4958  -0.3484   0.9023
 5DF  C17  C  CR6   0  -0.217   3.6783  -0.3686  -0.0694
 5DF  S20  S  S     0   1.215   5.3011  -1.0741  -0.1792
 5DF  O21  O  OS    0  -0.668   6.2273  -0.0363  -0.6275
 5DF  O22  O  OS    0  -0.668   5.5820  -1.7741   1.0726
 5DF  C23  C  CH3   0  -0.789   5.1499  -2.2841  -1.4732
 5DF  O24  O  OH1   0  -0.631  -7.0116  -2.7171   0.0457
 5DF  H28  H  HCR6  0   0.264  -4.7787  -3.1330   1.2572
 5DF  H27  H  HCR6  0   0.252  -2.8729  -1.6029   1.3230
 5DF  H34  H  HCR6  0   0.286   3.0284  -1.7234   1.4767
 5DF  H36  H  HCR6  0   0.278   1.8049   2.0570  -1.4649
 5DF  H25  H  HCR6  0   0.266  -1.1282  -0.6877   0.0080
 5DF  H26  H  HCR6  0   0.257  -3.7931   2.6414   0.2561
 5DF  H29  H  HCR6  0   0.272  -6.9360  -0.3305  -1.1685
 5DF  H30  H  HCR6  0   0.255  -5.0201   1.1791  -1.1275
 5DF  H32  H  HNH2  0   0.395   1.3416   3.3088   0.6555
 5DF  H31  H  HNH2  0   0.388   0.1362   4.4882   0.6013
 5DF  H33  H  HCR6  0   0.272   0.7895  -0.7521   1.6162
 5DF  H38  H  HCH3  0   0.311   6.1238  -2.7599  -1.5870
 5DF  H39  H  HCH3  0   0.296   4.4044  -3.0241  -1.1911
 5DF  H37  H  HCH3  0   0.296   4.8646  -1.7912  -2.3998
 5DF  H40  H  HOH1  0   0.475  -7.7572  -2.3671  -0.4545
 5DF  H35  H  HCR6  0   0.287   4.0518   1.1129  -1.5915

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
 5DF  C23  S20  single    1.778  0.020  1.778
 5DF  O22  S20  double    1.461  0.020  1.461
 5DF  S20  O21  double    1.461  0.020  1.461
 5DF  S20  C17  single    1.773  0.020  1.773
 5DF  C17  C16  aromatic  1.387  0.020  1.387
 5DF  C17  C18  aromatic  1.388  0.020  1.388
 5DF  C16  C15  aromatic  1.384  0.020  1.384
 5DF  C18  C19  aromatic  1.384  0.020  1.384
 5DF  C15  C14  aromatic  1.396  0.020  1.396
 5DF  C19  C14  aromatic  1.397  0.020  1.397
 5DF  N13  C3   single    1.363  0.020  1.363
 5DF  C14  C2   single    1.475  0.020  1.475
 5DF  C3   C2   aromatic  1.415  0.020  1.415
 5DF  C3   N4   aromatic  1.330  0.020  1.330
 5DF  C2   C1   aromatic  1.383  0.020  1.383
 5DF  N4   C5   aromatic  1.324  0.020  1.324
 5DF  C1   C6   aromatic  1.395  0.020  1.395
 5DF  C5   C6   aromatic  1.390  0.020  1.390
 5DF  C6   C7   single    1.472  0.020  1.472
 5DF  C8   C7   aromatic  1.397  0.020  1.397
 5DF  C8   C9   aromatic  1.384  0.020  1.384
 5DF  C7   C12  aromatic  1.395  0.020  1.395
 5DF  C9   C10  aromatic  1.393  0.020  1.393
 5DF  C12  C11  aromatic  1.386  0.020  1.386
 5DF  C10  C11  aromatic  1.392  0.020  1.392
 5DF  C10  O24  single    1.348  0.020  1.348
 5DF  C9   H28  single    0.930  0.020  1.080
 5DF  C8   H27  single    0.930  0.020  1.080
 5DF  C18  H35  single    0.930  0.020  1.080
 5DF  C16  H34  single    0.930  0.020  1.080
 5DF  C19  H36  single    0.930  0.020  1.080
 5DF  C1   H25  single    0.930  0.020  1.080
 5DF  C5   H26  single    0.930  0.020  1.080
 5DF  C11  H29  single    0.930  0.020  1.080
 5DF  C12  H30  single    0.930  0.020  1.080
 5DF  N13  H32  single    0.890  0.020  1.040
 5DF  N13  H31  single    0.890  0.020  1.040
 5DF  C15  H33  single    0.930  0.020  1.080
 5DF  C23  H38  single    0.970  0.020  1.090
 5DF  C23  H39  single    0.970  0.020  1.090
 5DF  C23  H37  single    0.970  0.020  1.090
 5DF  O24  H40  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
 5DF  C12  C7   C8   117.54  3.000
 5DF  C12  C7   C6   121.37  3.000
 5DF  C8   C7   C6   121.08  3.000
 5DF  C5   C6   C1   115.68  3.000
 5DF  C5   C6   C7   122.08  3.000
 5DF  C1   C6   C7   122.24  3.000
 5DF  H28  C9   C10  119.79  3.000
 5DF  H28  C9   C8   120.18  3.000
 5DF  C10  C9   C8   120.02  3.000
 5DF  H27  C8   C9   118.48  3.000
 5DF  H27  C8   C7   119.90  3.000
 5DF  C9   C8   C7   121.61  3.000
 5DF  H35  C18  C17  121.17  3.000
 5DF  H35  C18  C19  119.57  3.000
 5DF  C17  C18  C19  119.25  3.000
 5DF  H34  C16  C17  121.20  3.000
 5DF  H34  C16  C15  119.70  3.000
 5DF  C17  C16  C15  119.09  3.000
 5DF  H36  C19  C14  120.27  3.000
 5DF  H36  C19  C18  118.86  3.000
 5DF  C14  C19  C18  120.86  3.000
 5DF  H25  C1   C2   118.83  3.000
 5DF  H25  C1   C6   119.52  3.000
 5DF  C2   C1   C6   121.61  3.000
 5DF  C14  C2   C3   122.95  3.000
 5DF  C3   C2   C1   117.30  3.000
 5DF  C14  C2   C1   119.75  3.000
 5DF  N13  C3   N4   116.40  3.000
 5DF  N4   C3   C2   121.46  3.000
 5DF  N13  C3   C2   122.14  3.000
 5DF  C5   N4   C3   119.59  3.000
 5DF  H26  C5   N4   115.65  3.000
 5DF  H26  C5   C6   120.00  3.000
 5DF  N4   C5   C6   124.34  3.000
 5DF  O24  C10  C11  122.87  3.000
 5DF  O24  C10  C9   117.89  3.000
 5DF  C11  C10  C9   119.23  3.000
 5DF  H29  C11  C12  119.57  3.000
 5DF  H29  C11  C10  120.35  3.000
 5DF  C12  C11  C10  120.08  3.000
 5DF  H30  C12  C11  118.60  3.000
 5DF  H30  C12  C7   119.88  3.000
 5DF  C11  C12  C7   121.51  3.000
 5DF  H31  N13  H32  113.81  3.000
 5DF  H31  N13  C3   115.23  3.000
 5DF  H32  N13  C3   118.45  3.000
 5DF  C15  C14  C2   119.74  3.000
 5DF  C2   C14  C19  121.58  3.000
 5DF  C15  C14  C19  118.64  3.000
 5DF  H33  C15  C14  119.94  3.000
 5DF  H33  C15  C16  118.98  3.000
 5DF  C14  C15  C16  121.07  3.000
 5DF  S20  C17  C16  119.43  3.000
 5DF  C16  C17  C18  121.07  3.000
 5DF  S20  C17  C18  119.49  3.000
 5DF  C23  S20  O22  108.28  3.000
 5DF  O22  S20  O21  118.76  3.000
 5DF  C23  S20  O21  108.30  3.000
 5DF  O21  S20  C17  108.45  3.000
 5DF  O22  S20  C17  108.27  3.000
 5DF  C23  S20  C17  103.77  3.000
 5DF  H37  C23  H39  110.45  3.000
 5DF  H37  C23  H38  110.08  3.000
 5DF  H39  C23  H38  110.03  3.000
 5DF  H37  C23  S20  109.51  3.000
 5DF  H39  C23  S20  109.43  3.000
 5DF  H38  C23  S20  107.28  3.000
 5DF  H40  O24  C10  110.44  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
 5DF  CONST_01  C2   C1   C6   C7    180.00   0.0  0
 5DF  CONST_02  N4   C5   C6   C7    180.00   0.0  0
 5DF  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 5DF  CONST_04  C10  C11  C12  C7      0.00   0.0  0
 5DF  CONST_05  C14  C2   C1   C6    180.00   0.0  0
 5DF  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 5DF  CONST_07  C3   N4   C5   C6      0.00   0.0  0
 5DF  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 5DF  CONST_09  C11  C12  C7   C6    180.00   0.0  0
 5DF  CONST_10  C12  C7   C8   C9      0.00   0.0  0
 5DF  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 5DF  CONST_14  C11  C12  C7   C8      0.00   0.0  0
 5DF  CONST_15  C11  C10  C9   C8      0.00   0.0  0
 5DF  CONST_16  C15  C16  C17  C18     0.00   0.0  0
 5DF  CONST_17  C15  C14  C19  C18     0.00   0.0  0
 5DF  CONST_18  C2   C14  C19  C18   180.00   0.0  0
 5DF  CONST_19  C19  C18  C17  C16     0.00   0.0  0
 5DF  CONST_20  C19  C14  C15  C16     0.00   0.0  0
 5DF  CONST_21  C2   C14  C15  C16   180.00   0.0  0
 5DF  CONST_25  N4   C3   C2   C1      0.00   0.0  0
 5DF  CONST_26  N4   C5   C6   C1      0.00   0.0  0
 5DF  CONST_28  C5   N4   C3   C2      0.00   0.0  0
 5DF  CONST_29  C5   C6   C1   C2      0.00   0.0  0
 5DF  CONST_31  C14  C2   C3   N4    180.00   0.0  0
 5DF  CONST_33  C17  C16  C15  C14     0.00   0.0  0
 5DF  CONST_34  C17  C18  C19  C14     0.00   0.0  0
 5DF  CONST_35  O24  C10  C9   C8    180.00   0.0  0
 5DF  CONST_36  S20  C17  C18  C19   180.00   0.0  0
 5DF  CONST_37  N13  C3   C2   C1    180.00   0.0  0
 5DF  CONST_38  N13  C3   N4   C5    180.00   0.0  0
 5DF  CONST_39  O24  C10  C11  C12   180.00   0.0  0
 5DF  CONST_40  C14  C2   C3   N13     0.00   0.0  0
 5DF  CONST_41  S20  C17  C16  C15   180.00   0.0  0
 5DF  CONST_42  H25  C1   C6   C7      0.00   0.0  0
 5DF  CONST_43  H26  C5   C6   C7      0.00   0.0  0
 5DF  CONST_44  H28  C9   C8   C7    180.00   0.0  0
 5DF  CONST_45  H29  C11  C12  C7    180.00   0.0  0
 5DF  CONST_46  H27  C8   C7   C6      0.00   0.0  0
 5DF  CONST_47  H30  C12  C7   C6      0.00   0.0  0
 5DF  CONST_48  H34  C16  C17  C18   180.00   0.0  0
 5DF  CONST_49  H35  C18  C17  C16   180.00   0.0  0
 5DF  CONST_50  H33  C15  C14  C19   180.00   0.0  0
 5DF  CONST_51  H36  C19  C14  C2      0.00   0.0  0
 5DF  CONST_53  H31  N13  C3   C2    180.00   0.0  0
 5DF  Var_01    C23  S20  C17  C18   -86.96  30.0  2
 5DF  Var_02    H38  C23  S20  C17  -179.79  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
 5DF  plan-1  C7   0.020
 5DF  plan-1  C6   0.020
 5DF  plan-1  C9   0.020
 5DF  plan-1  C8   0.020
 5DF  plan-1  C10  0.020
 5DF  plan-1  C11  0.020
 5DF  plan-1  C12  0.020
 5DF  plan-1  O24  0.020
 5DF  plan-1  H28  0.020
 5DF  plan-1  H27  0.020
 5DF  plan-1  H29  0.020
 5DF  plan-1  H30  0.020
 5DF  plan-2  C7   0.020
 5DF  plan-2  C6   0.020
 5DF  plan-2  C1   0.020
 5DF  plan-2  C2   0.020
 5DF  plan-2  C3   0.020
 5DF  plan-2  N4   0.020
 5DF  plan-2  C5   0.020
 5DF  plan-2  N13  0.020
 5DF  plan-2  C14  0.020
 5DF  plan-2  H25  0.020
 5DF  plan-2  H26  0.020
 5DF  plan-3  C18  0.020
 5DF  plan-3  C16  0.020
 5DF  plan-3  C19  0.020
 5DF  plan-3  C2   0.020
 5DF  plan-3  C14  0.020
 5DF  plan-3  C15  0.020
 5DF  plan-3  C17  0.020
 5DF  plan-3  S20  0.020
 5DF  plan-3  H34  0.020
 5DF  plan-3  H36  0.020
 5DF  plan-3  H33  0.020
 5DF  plan-3  H35  0.020
 5DF  plan-4  C3   0.020
 5DF  plan-4  N13  0.020
 5DF  plan-4  H32  0.020
 5DF  plan-4  H31  0.020

