# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 11:04:41 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: 5-[(3~{R},5~{S})-3-azanyl-5-(trifluoromethyl)piperidin-1-yl]quinoline-8-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C[C@@H](CN(C1)c2ccc(C#N)c3ncccc23)C(F)(F)F
#
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
 QLH  QLH  5-[(3~{R},5~{S})-3-azanyl-5-(trifluoromethyl)piperidin-1-yl]quinoline-8-carbonitrile  ligand  38  23  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QLH
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
 QLH  C1   C  CR16  0  -0.357  136.2160  -0.7884  40.2927
 QLH  C2   C  CR16  0  -0.249  135.6491  -0.1914  41.4232
 QLH  C3   C  CR6   0  -0.064  134.2857  -0.0482  41.5386
 QLH  C8   C  CR16  0  -0.067  131.3052  -0.9827  39.8131
 QLH  C9   C  CR16  0  -0.323  131.7643  -1.7049  38.6971
 QLH  C10  C  CR16  0  -0.178  133.1121  -1.8151  38.4990
 QLH  C12  C  CSP   0   0.057  133.7157   0.5942  42.6715
 QLH  C14  C  CH2   0  -0.309  137.2982  -2.3892  38.1796
 QLH  C15  C  CH1   0  -0.073  137.4781  -3.4092  37.0599
 QLH  C16  C  CH2   0  -0.457  137.2273  -2.7484  35.7103
 QLH  C19  C  CT    0   1.044  135.5644  -1.4066  34.3789
 QLH  C4   C  CR6   0   0.336  135.4271  -1.2633  39.2633
 QLH  C5   C  CR66  0   0.024  134.0031  -1.2008  39.4040
 QLH  C6   C  CR66  0   0.231  133.4301  -0.5609  40.5268
 QLH  N7   N  N     0  -0.428  132.0989  -0.4453  40.7026
 QLH  N11  N  NT    0  -0.515  135.9589  -1.8336  38.1157
 QLH  N13  N  NS    0  -0.261  133.2819   1.1221  43.6005
 QLH  C17  C  CH1   0  -0.510  135.8475  -2.0908  35.6953
 QLH  C18  C  CH2   0  -0.330  135.7272  -1.1154  36.8665
 QLH  F21  F  F     0  -0.310  135.6280  -2.2600  33.3470
 QLH  F22  F  F     0  -0.312  134.3385  -0.8606  34.3501
 QLH  F23  F  F     0  -0.312  136.4296  -0.4164  34.1113
 QLH  H1   H  HCR6  0   0.288  137.2937  -0.8361  40.2253
 QLH  H2   H  HCR6  0   0.288  136.2993   0.1886  42.1998
 QLH  H3   H  HCR6  0   0.275  130.2397  -0.8677  39.9790
 QLH  H4   H  HCR6  0   0.280  131.0579  -2.1701  38.0245
 QLH  H5   H  HCR6  0   0.288  133.4931  -2.3942  37.6690
 QLH  H6   H  HCH2  0   0.265  137.4353  -2.8799  39.1446
 QLH  H7   H  HCH2  0   0.222  138.0722  -1.6133  38.0808
 QLH  H8   H  HCH1  0   0.213  136.7166  -4.1910  37.2022
 QLH  H9   H  HCH2  0   0.264  137.3118  -3.4954  34.9180
 QLH  H10  H  HCH2  0   0.241  138.0062  -1.9977  35.5424
 QLH  H11  H  HCH1  0   0.297  135.0819  -2.8662  35.8145
 QLH  H12  H  HCH2  0   0.259  136.4681  -0.3096  36.7643
 QLH  H13  H  HCH2  0   0.284  134.7465  -0.6439  36.8879
 QLH  N20  N  NH2   0  -0.803  138.8368  -3.9198  37.1072
 QLH  H14  H  HNH2  0   0.349  138.9656  -4.4554  37.9573
 QLH  H15  H  HNH2  0   0.350  138.9752  -4.5789  36.3505

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
 QLH  F21  C19  single    1.341  0.020  1.341
 QLH  F23  C19  single    1.342  0.020  1.342
 QLH  C19  F22  single    1.342  0.020  1.342
 QLH  C19  C17  single    1.510  0.020  1.510
 QLH  C17  C16  single    1.529  0.020  1.529
 QLH  C17  C18  single    1.529  0.020  1.529
 QLH  C16  C15  single    1.524  0.020  1.524
 QLH  C18  N11  single    1.460  0.020  1.460
 QLH  C15  N20  single    1.452  0.020  1.452
 QLH  C15  C14  single    1.525  0.020  1.525
 QLH  N11  C14  single    1.451  0.020  1.451
 QLH  N11  C4   single    1.387  0.020  1.387
 QLH  C10  C9   aromatic  1.367  0.020  1.367
 QLH  C10  C5   aromatic  1.411  0.020  1.411
 QLH  C9   C8   aromatic  1.406  0.020  1.406
 QLH  C4   C5   aromatic  1.432  0.020  1.432
 QLH  C4   C1   aromatic  1.381  0.020  1.381
 QLH  C5   C6   aromatic  1.414  0.020  1.414
 QLH  C8   N7   aromatic  1.308  0.020  1.308
 QLH  C1   C2   aromatic  1.398  0.020  1.398
 QLH  C6   N7   aromatic  1.348  0.020  1.348
 QLH  C6   C3   aromatic  1.421  0.020  1.421
 QLH  C2   C3   aromatic  1.376  0.020  1.376
 QLH  C3   C12  single    1.422  0.020  1.422
 QLH  C12  N13  triple    1.153  0.020  1.153
 QLH  C1   H1   single    0.930  0.020  1.080
 QLH  C2   H2   single    0.930  0.020  1.080
 QLH  C8   H3   single    0.930  0.020  1.080
 QLH  C9   H4   single    0.930  0.020  1.080
 QLH  C10  H5   single    0.930  0.020  1.080
 QLH  C14  H6   single    0.970  0.020  1.090
 QLH  C14  H7   single    0.970  0.020  1.090
 QLH  C15  H8   single    0.970  0.020  1.090
 QLH  C16  H9   single    0.970  0.020  1.090
 QLH  C16  H10  single    0.970  0.020  1.090
 QLH  C17  H11  single    0.970  0.020  1.090
 QLH  C18  H12  single    0.970  0.020  1.090
 QLH  C18  H13  single    0.970  0.020  1.090
 QLH  N20  H14  single    0.890  0.020  1.040
 QLH  N20  H15  single    0.890  0.020  1.040

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
 QLH  H1   C1   C4   120.52  3.000
 QLH  H1   C1   C2   118.25  3.000
 QLH  C4   C1   C2   121.18  3.000
 QLH  H2   C2   C3   119.93  3.000
 QLH  H2   C2   C1   119.12  3.000
 QLH  C3   C2   C1   120.92  3.000
 QLH  C6   C3   C12  119.28  3.000
 QLH  C12  C3   C2   120.74  3.000
 QLH  C6   C3   C2   119.97  3.000
 QLH  H3   C8   N7   116.66  3.000
 QLH  H3   C8   C9   119.78  3.000
 QLH  N7   C8   C9   123.55  3.000
 QLH  H4   C9   C10  121.31  3.000
 QLH  H4   C9   C8   120.10  3.000
 QLH  C10  C9   C8   118.58  3.000
 QLH  H5   C10  C5   120.20  3.000
 QLH  H5   C10  C9   120.12  3.000
 QLH  C5   C10  C9   119.65  3.000
 QLH  N13  C12  C3   180.00  3.000
 QLH  H7   C14  H6   107.95  3.000
 QLH  H7   C14  N11  112.03  3.000
 QLH  H6   C14  N11  109.09  3.000
 QLH  H7   C14  C15  108.82  3.000
 QLH  H6   C14  C15  109.49  3.000
 QLH  N11  C14  C15  109.42  3.000
 QLH  H8   C15  N20  113.16  3.000
 QLH  H8   C15  C16  107.98  3.000
 QLH  N20  C15  C16  109.59  3.000
 QLH  H8   C15  C14  107.37  3.000
 QLH  N20  C15  C14  108.76  3.000
 QLH  C16  C15  C14  109.93  3.000
 QLH  H10  C16  H9   107.61  3.000
 QLH  H10  C16  C17  110.23  3.000
 QLH  H9   C16  C17  110.91  3.000
 QLH  H10  C16  C15  108.43  3.000
 QLH  H9   C16  C15  109.46  3.000
 QLH  C17  C16  C15  110.12  3.000
 QLH  F23  C19  F22  106.52  3.000
 QLH  F22  C19  F21  106.61  3.000
 QLH  F23  C19  F21  106.60  3.000
 QLH  F22  C19  C17  111.97  3.000
 QLH  F23  C19  C17  112.78  3.000
 QLH  F21  C19  C17  111.94  3.000
 QLH  N11  C4   C5   118.70  3.000
 QLH  C5   C4   C1   118.66  3.000
 QLH  N11  C4   C1   122.61  3.000
 QLH  C6   C5   C4   120.05  3.000
 QLH  C6   C5   C10  116.78  3.000
 QLH  C4   C5   C10  123.09  3.000
 QLH  N7   C6   C5   122.87  3.000
 QLH  N7   C6   C3   118.10  3.000
 QLH  C5   C6   C3   119.00  3.000
 QLH  C6   N7   C8   118.40  3.000
 QLH  C18  N11  C4   116.42  3.000
 QLH  C4   N11  C14  118.34  3.000
 QLH  C18  N11  C14  111.87  3.000
 QLH  H11  C17  C18  108.24  3.000
 QLH  H11  C17  C19  106.52  3.000
 QLH  C18  C17  C19  111.34  3.000
 QLH  H11  C17  C16  108.97  3.000
 QLH  C18  C17  C16  109.75  3.000
 QLH  C19  C17  C16  111.88  3.000
 QLH  H13  C18  H12  106.95  3.000
 QLH  H13  C18  C17  111.24  3.000
 QLH  H12  C18  C17  110.09  3.000
 QLH  H13  C18  N11  109.84  3.000
 QLH  H12  C18  N11  109.46  3.000
 QLH  C17  C18  N11  109.22  3.000
 QLH  H15  N20  H14  105.40  3.000
 QLH  H15  N20  C15  109.41  3.000
 QLH  H14  N20  C15  109.40  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
 QLH  CONST_01  C10  C5   C4   C1    180.00   0.0  0
 QLH  CONST_02  C6   C5   C4   C1      0.00   0.0  0
 QLH  CONST_03  C6   C3   C2   C1      0.00   0.0  0
 QLH  CONST_04  C5   C4   C1   C2      0.00   0.0  0
 QLH  CONST_05  C5   C6   C3   C2      0.00   0.0  0
 QLH  CONST_06  N7   C6   C3   C2    180.00   0.0  0
 QLH  CONST_07  C10  C5   C6   C3    180.00   0.0  0
 QLH  CONST_08  C4   C5   C6   C3      0.00   0.0  0
 QLH  CONST_09  C8   N7   C6   C3    180.00   0.0  0
 QLH  CONST_10  C4   C1   C2   C3      0.00   0.0  0
 QLH  CONST_11  C5   C10  C9   C8      0.00   0.0  0
 QLH  CONST_12  C5   C6   N7   C8      0.00   0.0  0
 QLH  CONST_13  C4   C5   C10  C9    180.00   0.0  0
 QLH  CONST_14  C6   C5   C10  C9      0.00   0.0  0
 QLH  CONST_15  C6   N7   C8   C9      0.00   0.0  0
 QLH  CONST_16  N7   C8   C9   C10     0.00   0.0  0
 QLH  CONST_17  N7   C6   C5   C10     0.00   0.0  0
 QLH  CONST_18  N7   C6   C5   C4    180.00   0.0  0
 QLH  CONST_19  N11  C4   C1   C2    180.00   0.0  0
 QLH  CONST_20  N11  C4   C5   C10     0.00   0.0  0
 QLH  CONST_21  N11  C4   C5   C6    180.00   0.0  0
 QLH  CONST_22  C12  C3   C2   C1    180.00   0.0  0
 QLH  CONST_23  C5   C6   C3   C12   180.00   0.0  0
 QLH  CONST_24  N7   C6   C3   C12     0.00   0.0  0
 QLH  CONST_25  H1   C1   C2   C3    180.00   0.0  0
 QLH  CONST_26  H5   C10  C9   C8    180.00   0.0  0
 QLH  CONST_27  H3   C8   C9   C10   180.00   0.0  0
 QLH  CONST_28  H2   C2   C1   C4    180.00   0.0  0
 QLH  CONST_29  H4   C9   C10  C5    180.00   0.0  0
 QLH  Var_01    C18  N11  C4   C1   -115.07  30.0  2
 QLH  Var_02    C17  C18  N11  C14    62.41  30.0  1

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
 QLH  chir_01  C15  C16  N20  C14  negativ
 QLH  chir_02  C17  C18  C16  C19  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
 QLH  plan-1  C1   0.020
 QLH  plan-1  C2   0.020
 QLH  plan-1  C3   0.020
 QLH  plan-1  C8   0.020
 QLH  plan-1  C9   0.020
 QLH  plan-1  C10  0.020
 QLH  plan-1  C12  0.020
 QLH  plan-1  C4   0.020
 QLH  plan-1  C5   0.020
 QLH  plan-1  C6   0.020
 QLH  plan-1  N7   0.020
 QLH  plan-1  N11  0.020
 QLH  plan-1  N13  0.020
 QLH  plan-1  H1   0.020
 QLH  plan-1  H2   0.020
 QLH  plan-1  H3   0.020
 QLH  plan-1  H4   0.020
 QLH  plan-1  H5   0.020

