# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:40:27 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: 4-{2-[(2R,3R)-3-(2,5-difluorophenyl)-3-hydroxy-4-(1H-1,2,4-triazol-1-yl)butan-2-yl]-1,3-thiazol-4-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](c1scc(n1)c2ccc(cc2)C#N)[C@](O)(Cn3cncn3)c4cc(F)ccc4F
#
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
 QKM  QKM  4-{2-[(2R,3R)-3-(2,5-difluorophenyl)-3-hydroxy-4-(1H-1,2,4-triazol-1-yl)butan-2-yl]-1,3-thiazol-4-yl}benzonitrile  ligand  48  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QKM
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
 QKM  CD1  C  CH3   0  -0.647  -20.0999  25.8175  -19.6267
 QKM  CE1  C  CH1   0  -0.359  -19.3132  26.2155  -18.3760
 QKM  C3   C  CR5   0   0.072  -17.8420  26.0360  -18.5970
 QKM  N    N  N     0  -0.394  -17.1205  25.1872  -17.9421
 QKM  CA   C  CR5   0   0.372  -15.8174  25.1801  -18.3626
 QKM  C    C  CR15  0  -0.577  -15.5513  26.0543  -19.3766
 QKM  S1   S  S2    0   0.278  -16.9608  26.9167  -19.7990
 QKM  CB   C  CR6   0   0.068  -14.8549  24.2904  -17.7074
 QKM  C7   C  CR16  0  -0.320  -13.5491  24.1556  -18.1871
 QKM  C8   C  CR16  0  -0.217  -12.6428  23.3291  -17.5542
 QKM  C9   C  CR6   0  -0.011  -13.0334  22.6138  -16.4214
 QKM  C10  C  CR16  0  -0.220  -14.3345  22.7326  -15.9345
 QKM  C11  C  CR16  0  -0.286  -15.2334  23.5631  -16.5762
 QKM  C12  C  CSP   0   0.054  -12.1019  21.7590  -15.7625
 QKM  N2   N  NS    0  -0.253  -11.3500  21.0659  -15.2307
 QKM  CZ   C  CT    0   0.197  -19.6475  27.6493  -17.8942
 QKM  C14  C  CH2   0  -0.304  -18.7836  27.9848  -16.6564
 QKM  N3   N  NR5   0  -0.269  -19.1179  29.2637  -16.0790
 QKM  C15  C  CR15  0   0.084  -18.5847  30.4620  -16.3482
 QKM  N4   N  N     0  -0.455  -19.1952  31.3928  -15.6526
 QKM  C16  C  CR15  0   0.009  -20.1152  30.6910  -14.9569
 QKM  N5   N  N     0  -0.242  -20.1027  29.4004  -15.1859
 QKM  CE2  C  CR6   0  -0.104  -21.1393  27.7670  -17.5878
 QKM  CD2  C  CR6   0   0.550  -21.7596  27.0858  -16.5474
 QKM  C19  C  CR16  0  -0.392  -23.1061  27.1968  -16.2721
 QKM  C20  C  CR16  0  -0.406  -23.8990  28.0203  -17.0566
 QKM  C21  C  CR6   0   0.548  -23.2977  28.6964  -18.0962
 QKM  C22  C  CR16  0  -0.459  -21.9498  28.5801  -18.3734
 QKM  F1   F  F     0  -0.315  -24.0460  29.4936  -18.8758
 QKM  F2   F  F     0  -0.313  -21.0324  26.2748  -15.7575
 QKM  OH   O  OH1   0  -0.648  -19.2902  28.4921  -18.9563
 QKM  H1   H  HCH3  0   0.250  -21.1726  25.8487  -19.4394
 QKM  H2   H  HCH3  0   0.238  -19.8846  26.4685  -20.4729
 QKM  H3   H  HCH3  0   0.253  -19.8431  24.7981  -19.9124
 QKM  H4   H  HCH1  0   0.297  -19.5666  25.5184  -17.5758
 QKM  H5   H  HCR5  0   0.309  -14.6127  26.2513  -19.8705
 QKM  H6   H  HCR6  0   0.265  -13.2283  24.6941  -19.0686
 QKM  H7   H  HCR6  0   0.284  -11.6355  23.2359  -17.9361
 QKM  H8   H  HCR6  0   0.283  -14.6400  22.1798  -15.0566
 QKM  H9   H  HCR6  0   0.270  -16.2402  23.6523  -16.1936
 QKM  H10  H  HCH2  0   0.294  -18.8674  27.2284  -15.8816
 QKM  H11  H  HCH2  0   0.298  -17.7370  28.0301  -16.9571
 QKM  H12  H  HCR5  0   0.314  -17.7564  30.5997  -17.0277
 QKM  H13  H  HCR5  0   0.275  -20.8063  31.1409  -14.2606
 QKM  H14  H  HCR6  0   0.292  -23.5336  26.6469  -15.4443
 QKM  H15  H  HCR6  0   0.292  -24.9568  28.1255  -16.8575
 QKM  H16  H  HCR6  0   0.285  -21.5408  29.1204  -19.2158
 QKM  H17  H  HOH1  0   0.462  -19.3474  29.4204  -18.7001

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
 QKM  CD1  CE1  single    1.530  0.020  1.530
 QKM  F1   C21  single    1.343  0.020  1.343
 QKM  S1   C    aromatic  1.705  0.020  1.705
 QKM  S1   C3   aromatic  1.731  0.020  1.731
 QKM  OH   CZ   single    1.402  0.020  1.402
 QKM  C    CA   aromatic  1.365  0.020  1.365
 QKM  C22  C21  aromatic  1.381  0.020  1.381
 QKM  C22  CE2  aromatic  1.391  0.020  1.391
 QKM  C21  C20  aromatic  1.378  0.020  1.378
 QKM  C7   C8   aromatic  1.380  0.020  1.380
 QKM  C7   CB   aromatic  1.398  0.020  1.398
 QKM  C3   CE1  single    1.499  0.020  1.499
 QKM  C3   N    aromatic  1.292  0.020  1.292
 QKM  CE1  CZ   single    1.549  0.020  1.549
 QKM  C8   C9   aromatic  1.396  0.020  1.396
 QKM  CA   N    aromatic  1.369  0.020  1.369
 QKM  CA   CB   single    1.465  0.020  1.465
 QKM  CZ   CE2  single    1.527  0.020  1.527
 QKM  CZ   C14  single    1.546  0.020  1.546
 QKM  CE2  CD2  aromatic  1.390  0.020  1.390
 QKM  CB   C11  aromatic  1.397  0.020  1.397
 QKM  C20  C19  aromatic  1.386  0.020  1.386
 QKM  C9   C12  single    1.426  0.020  1.426
 QKM  C9   C10  aromatic  1.394  0.020  1.394
 QKM  CD2  C19  aromatic  1.379  0.020  1.379
 QKM  CD2  F2   single    1.346  0.020  1.346
 QKM  C15  N3   aromatic  1.339  0.020  1.339
 QKM  C15  N4   aromatic  1.313  0.020  1.313
 QKM  C14  N3   single    1.442  0.020  1.442
 QKM  C12  N2   triple    1.153  0.020  1.153
 QKM  C11  C10  aromatic  1.382  0.020  1.382
 QKM  N3   N5   aromatic  1.336  0.020  1.336
 QKM  N4   C16  aromatic  1.350  0.020  1.350
 QKM  N5   C16  aromatic  1.311  0.020  1.311
 QKM  CD1  H1   single    0.970  0.020  1.090
 QKM  CD1  H2   single    0.970  0.020  1.090
 QKM  CD1  H3   single    0.970  0.020  1.090
 QKM  CE1  H4   single    0.970  0.020  1.090
 QKM  C    H5   single    0.930  0.020  1.080
 QKM  C7   H6   single    0.930  0.020  1.080
 QKM  C8   H7   single    0.930  0.020  1.080
 QKM  C10  H8   single    0.930  0.020  1.080
 QKM  C11  H9   single    0.930  0.020  1.080
 QKM  C14  H10  single    0.970  0.020  1.090
 QKM  C14  H11  single    0.970  0.020  1.090
 QKM  C15  H12  single    0.930  0.020  1.080
 QKM  C16  H13  single    0.930  0.020  1.080
 QKM  C19  H14  single    0.930  0.020  1.080
 QKM  C20  H15  single    0.930  0.020  1.080
 QKM  C22  H16  single    0.930  0.020  1.080
 QKM  OH   H17  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
 QKM  H3   CD1  H2   107.99  3.000
 QKM  H3   CD1  H1   107.70  3.000
 QKM  H2   CD1  H1   108.13  3.000
 QKM  H3   CD1  CE1  109.67  3.000
 QKM  H2   CD1  CE1  112.21  3.000
 QKM  H1   CD1  CE1  110.99  3.000
 QKM  H4   CE1  CZ   108.25  3.000
 QKM  H4   CE1  C3   105.05  3.000
 QKM  CZ   CE1  C3   111.63  3.000
 QKM  H4   CE1  CD1  108.29  3.000
 QKM  CZ   CE1  CD1  112.59  3.000
 QKM  C3   CE1  CD1  110.67  3.000
 QKM  S1   C3   N    113.69  3.000
 QKM  N    C3   CE1  123.51  3.000
 QKM  S1   C3   CE1  122.77  3.000
 QKM  CA   N    C3   112.28  3.000
 QKM  CB   CA   C    126.37  3.000
 QKM  CB   CA   N    119.40  3.000
 QKM  C    CA   N    114.22  3.000
 QKM  H5   C    S1   120.89  3.000
 QKM  H5   C    CA   128.80  3.000
 QKM  S1   C    CA   110.29  3.000
 QKM  C    S1   C3    89.51  3.000
 QKM  C11  CB   C7   118.74  3.000
 QKM  C11  CB   CA   120.01  3.000
 QKM  C7   CB   CA   121.25  3.000
 QKM  H6   C7   C8   118.50  3.000
 QKM  H6   C7   CB   120.58  3.000
 QKM  C8   C7   CB   120.92  3.000
 QKM  H7   C8   C9   120.22  3.000
 QKM  H7   C8   C7   120.08  3.000
 QKM  C9   C8   C7   119.70  3.000
 QKM  C12  C9   C10  119.96  3.000
 QKM  C10  C9   C8   120.06  3.000
 QKM  C12  C9   C8   119.97  3.000
 QKM  H8   C10  C11  120.03  3.000
 QKM  H8   C10  C9   120.23  3.000
 QKM  C11  C10  C9   119.74  3.000
 QKM  H9   C11  C10  119.42  3.000
 QKM  H9   C11  CB   119.74  3.000
 QKM  C10  C11  CB   120.84  3.000
 QKM  N2   C12  C9   180.00  3.000
 QKM  OH   CZ   CE2  110.76  3.000
 QKM  CE2  CZ   C14  111.62  3.000
 QKM  OH   CZ   C14  109.48  3.000
 QKM  C14  CZ   CE1  109.22  3.000
 QKM  CE2  CZ   CE1  110.15  3.000
 QKM  OH   CZ   CE1  105.41  3.000
 QKM  H11  C14  H10  107.45  3.000
 QKM  H11  C14  N3   107.23  3.000
 QKM  H10  C14  N3   108.30  3.000
 QKM  H11  C14  CZ   108.95  3.000
 QKM  H10  C14  CZ   112.14  3.000
 QKM  N3   C14  CZ   112.54  3.000
 QKM  N5   N3   C15  109.65  3.000
 QKM  N5   N3   C14  121.94  3.000
 QKM  C15  N3   C14  128.36  3.000
 QKM  H12  C15  N4   126.84  3.000
 QKM  H12  C15  N3   123.09  3.000
 QKM  N4   C15  N3   110.05  3.000
 QKM  C16  N4   C15  102.79  3.000
 QKM  H13  C16  N5   121.96  3.000
 QKM  H13  C16  N4   123.51  3.000
 QKM  N5   C16  N4   114.53  3.000
 QKM  C16  N5   N3   102.97  3.000
 QKM  C22  CE2  CD2  116.69  3.000
 QKM  CD2  CE2  CZ   123.25  3.000
 QKM  C22  CE2  CZ   120.05  3.000
 QKM  F2   CD2  C19  117.33  3.000
 QKM  F2   CD2  CE2  119.58  3.000
 QKM  C19  CD2  CE2  123.09  3.000
 QKM  H14  C19  C20  120.60  3.000
 QKM  H14  C19  CD2  119.84  3.000
 QKM  C20  C19  CD2  119.56  3.000
 QKM  H15  C20  C21  121.19  3.000
 QKM  H15  C20  C19  120.86  3.000
 QKM  C21  C20  C19  117.95  3.000
 QKM  F1   C21  C22  118.51  3.000
 QKM  C22  C21  C20  122.41  3.000
 QKM  F1   C21  C20  119.08  3.000
 QKM  H16  C22  C21  118.91  3.000
 QKM  H16  C22  CE2  120.78  3.000
 QKM  C21  C22  CE2  120.30  3.000
 QKM  H17  OH   CZ   111.23  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
 QKM  CONST_01  CA   C    S1   C3     0.00   0.0  0
 QKM  CONST_02  C    CA   N    C3     0.00   0.0  0
 QKM  CONST_03  CB   CA   N    C3   180.00   0.0  0
 QKM  CONST_04  C    S1   C3   N      0.00   0.0  0
 QKM  CONST_05  S1   C    CA   N      0.00   0.0  0
 QKM  CONST_06  C7   CB   CA   N    180.00   0.0  0
 QKM  CONST_07  C11  CB   CA   N      0.00   0.0  0
 QKM  CONST_08  S1   C3   N    CA     0.00   0.0  0
 QKM  CONST_09  C8   C7   CB   CA   180.00   0.0  0
 QKM  CONST_10  C10  C11  CB   CA   180.00   0.0  0
 QKM  CONST_11  C7   CB   CA   C      0.00   0.0  0
 QKM  CONST_12  C11  CB   CA   C    180.00   0.0  0
 QKM  CONST_13  CB   CA   C    S1   180.00   0.0  0
 QKM  CONST_14  C9   C8   C7   CB     0.00   0.0  0
 QKM  CONST_15  C9   C10  C11  CB     0.00   0.0  0
 QKM  CONST_16  C10  C9   C8   C7     0.00   0.0  0
 QKM  CONST_17  C10  C11  CB   C7     0.00   0.0  0
 QKM  CONST_18  C11  CB   C7   C8     0.00   0.0  0
 QKM  CONST_19  C11  C10  C9   C8     0.00   0.0  0
 QKM  CONST_20  C16  N4   C15  N3     0.00   0.0  0
 QKM  CONST_21  N4   C16  N5   N3     0.00   0.0  0
 QKM  CONST_22  C16  N5   N3   C15    0.00   0.0  0
 QKM  CONST_23  N5   C16  N4   C15    0.00   0.0  0
 QKM  CONST_24  N5   N3   C15  N4     0.00   0.0  0
 QKM  CONST_25  C20  C21  C22  CE2    0.00   0.0  0
 QKM  CONST_26  C20  C19  CD2  CE2    0.00   0.0  0
 QKM  CONST_27  C21  C22  CE2  CD2    0.00   0.0  0
 QKM  CONST_28  C21  C20  C19  CD2    0.00   0.0  0
 QKM  CONST_29  C22  C21  C20  C19    0.00   0.0  0
 QKM  CONST_30  C22  CE2  CD2  C19    0.00   0.0  0
 QKM  CONST_31  C    S1   C3   CE1  180.00   0.0  0
 QKM  CONST_32  CA   N    C3   CE1  180.00   0.0  0
 QKM  CONST_33  C12  C9   C8   C7   180.00   0.0  0
 QKM  CONST_34  C12  C9   C10  C11  180.00   0.0  0
 QKM  CONST_35  C21  C22  CE2  CZ   180.00   0.0  0
 QKM  CONST_36  C19  CD2  CE2  CZ   180.00   0.0  0
 QKM  CONST_37  N4   C15  N3   C14  180.00   0.0  0
 QKM  CONST_38  C16  N5   N3   C14  180.00   0.0  0
 QKM  CONST_39  F1   C21  C22  CE2  180.00   0.0  0
 QKM  CONST_40  F1   C21  C20  C19  180.00   0.0  0
 QKM  CONST_41  F2   CD2  C19  C20  180.00   0.0  0
 QKM  CONST_42  F2   CD2  CE2  C22  180.00   0.0  0
 QKM  CONST_43  H5   C    S1   C3   180.00   0.0  0
 QKM  CONST_44  H6   C7   CB   CA     0.00   0.0  0
 QKM  CONST_45  H9   C11  CB   CA     0.00   0.0  0
 QKM  CONST_46  H7   C8   C7   CB   180.00   0.0  0
 QKM  CONST_47  H8   C10  C11  CB   180.00   0.0  0
 QKM  CONST_48  H13  C16  N5   N3   180.00   0.0  0
 QKM  CONST_49  H12  C15  N4   C16  180.00   0.0  0
 QKM  CONST_50  H14  C19  CD2  CE2  180.00   0.0  0
 QKM  CONST_51  H16  C22  CE2  CD2  180.00   0.0  0
 QKM  CONST_52  H15  C20  C19  CD2  180.00   0.0  0
 QKM  Var_01    C15  N3   C14  CZ   -91.41  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 QKM  chir_01  CE1  CD1  C3   CZ   negativ
 QKM  chir_02  CZ   C14  CE2  CE1  positiv

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
 QKM  plan-1  CE1  0.020
 QKM  plan-1  C3   0.020
 QKM  plan-1  N    0.020
 QKM  plan-1  CA   0.020
 QKM  plan-1  C    0.020
 QKM  plan-1  S1   0.020
 QKM  plan-1  CB   0.020
 QKM  plan-1  H5   0.020
 QKM  plan-2  C14  0.020
 QKM  plan-2  N3   0.020
 QKM  plan-2  C15  0.020
 QKM  plan-2  N4   0.020
 QKM  plan-2  C16  0.020
 QKM  plan-2  N5   0.020
 QKM  plan-2  H12  0.020
 QKM  plan-2  H13  0.020
 QKM  plan-3  CA   0.020
 QKM  plan-3  CB   0.020
 QKM  plan-3  C7   0.020
 QKM  plan-3  C8   0.020
 QKM  plan-3  C9   0.020
 QKM  plan-3  C10  0.020
 QKM  plan-3  C11  0.020
 QKM  plan-3  C12  0.020
 QKM  plan-3  N2   0.020
 QKM  plan-3  H6   0.020
 QKM  plan-3  H7   0.020
 QKM  plan-3  H8   0.020
 QKM  plan-3  H9   0.020
 QKM  plan-4  CZ   0.020
 QKM  plan-4  CE2  0.020
 QKM  plan-4  CD2  0.020
 QKM  plan-4  C19  0.020
 QKM  plan-4  C20  0.020
 QKM  plan-4  C21  0.020
 QKM  plan-4  C22  0.020
 QKM  plan-4  F1   0.020
 QKM  plan-4  F2   0.020
 QKM  plan-4  H14  0.020
 QKM  plan-4  H15  0.020
 QKM  plan-4  H16  0.020

