# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:03:03 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-5-(1-methyl-1H-imidazol-4-yl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc(c1)c2cnc(O[C@H]3CCN(C[C@H]3F)C(=O)Cc4ccc(OC(F)(F)F)cc4)c(c2)C(N)=O
#
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
 FKY  FKY  2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-5-(1-methyl-1H-imidazol-4-yl)pyridine-3-carboxamide  ligand  60  37  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FKY
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
 FKY  C5   C  CR15  0  -0.098   -7.9784   2.2291   0.2104
 FKY  C6   C  CH3   0  -0.518  -10.1868   3.3267   0.6601
 FKY  C7   C  CR6   0  -0.059   -6.1227   0.4718   0.2416
 FKY  C8   C  CR16  0  -0.184   -5.7358  -0.7965   0.6843
 FKY  C10  C  CR6   0   0.539   -3.6437  -0.5016  -0.4091
 FKY  C15  C  CH1   0   0.183   -0.5733  -1.1707  -2.1308
 FKY  C20  C  C     0   0.571    2.4232   0.1565  -1.5435
 FKY  C22  C  CH2   0  -0.720    2.9887   1.0257  -0.4271
 FKY  C24  C  CR16  0  -0.306    4.3713  -0.3260   1.1702
 FKY  C26  C  CR6   0   0.296    6.7431  -0.4650   0.9632
 FKY  C28  C  CR16  0  -0.297    5.4911   0.8427  -0.5914
 FKY  C1   C  CR5   0   0.126   -7.4367   1.0177   0.5630
 FKY  N2   N  N     0  -0.467   -8.3388   0.3128   1.3096
 FKY  C3   C  CR15  0   0.095   -9.3936   1.0791   1.4038
 FKY  N4   N  NR5   0  -0.402   -9.2268   2.2494   0.7555
 FKY  C9   C  CR6   0  -0.212   -4.4970  -1.3105   0.3587
 FKY  N11  N  N     0  -0.454   -3.9874   0.6972  -0.8222
 FKY  C12  C  CR16  0  -0.107   -5.1917   1.1659  -0.5170
 FKY  O13  O  O2    0  -0.478   -2.4332  -0.9841  -0.6911
 FKY  C14  C  CH1   0  -0.004   -1.5228  -0.2015  -1.4528
 FKY  C16  C  CH2   0  -0.392    0.4925  -0.4125  -2.9017
 FKY  N17  N  NT    0  -0.450    1.1953   0.4888  -2.0109
 FKY  C18  C  CH2   0  -0.351    0.3186   1.4788  -1.4104
 FKY  C19  C  CH2   0  -0.471   -0.7725   0.8016  -0.5853
 FKY  O21  O  O     0  -0.476    3.0684  -0.7708  -2.0022
 FKY  C23  C  CR6   0   0.181    4.3084   0.5108   0.0615
 FKY  C25  C  CR16  0  -0.284    5.5841  -0.8191   1.6296
 FKY  C27  C  CR16  0  -0.287    6.7129   0.3611  -0.1475
 FKY  C30  C  CT    0   1.071    8.6628  -0.3049   2.2872
 FKY  F31  F  F     0  -0.300    9.0139   0.9075   1.8529
 FKY  F32  F  F     0  -0.300    7.9998  -0.1247   3.4315
 FKY  F33  F  F     0  -0.277    9.7660  -0.9881   2.5481
 FKY  F34  F  F     0  -0.372    0.0528  -1.9478  -1.1595
 FKY  C35  C  C     0   0.470   -4.1162  -2.7042   0.7501
 FKY  N36  N  NH2   0  -0.791   -4.2832  -2.9799   2.0511
 FKY  O37  O  O     0  -0.467   -3.7203  -3.5159  -0.0705
 FKY  H1   H  HCR5  0   0.287   -7.5967   3.0572  -0.3638
 FKY  H2   H  HCH3  0   0.264  -10.4064   3.5491  -0.3818
 FKY  H3   H  HCH3  0   0.265  -11.1065   3.0260   1.1541
 FKY  H4   H  HCH3  0   0.264   -9.8058   4.2237   1.1439
 FKY  H5   H  HCR6  0   0.273   -6.4270  -1.3854   1.2744
 FKY  H6   H  HCH1  0   0.247   -1.1186  -1.8418  -2.7997
 FKY  H7   H  HCH2  0   0.303    3.0920   2.0529  -0.7887
 FKY  H8   H  HCH2  0   0.292    2.2792   1.0684   0.4026
 FKY  H9   H  HCR6  0   0.260    3.4620  -0.5997   1.6912
 FKY  H10  H  HCR6  0   0.261    5.4658   1.4920  -1.4576
 FKY  H11  H  HCR5  0   0.284  -10.3064   0.8390   1.9281
 FKY  H12  H  HCR6  0   0.256   -5.4179   2.1552  -0.9001
 FKY  H13  H  HCH1  0   0.255   -2.0573   0.3339  -2.2449
 FKY  H14  H  HCH2  0   0.292    1.1914  -1.1002  -3.3704
 FKY  H15  H  HCH2  0   0.268    0.0146   0.1621  -3.7002
 FKY  H16  H  HCH2  0   0.289    0.8783   2.1815  -0.7999
 FKY  H17  H  HCH2  0   0.265   -0.1308   2.0680  -2.2158
 FKY  H18  H  HCH2  0   0.264   -1.4604   1.5575  -0.2047
 FKY  H19  H  HCH2  0   0.248   -0.3265   0.2975   0.2761
 FKY  H20  H  HCR6  0   0.279    5.6180  -1.4803   2.4853
 FKY  H21  H  HCR6  0   0.279    7.6256   0.6146  -0.6705
 FKY  H22  H  HNH2  0   0.406   -4.0912  -3.9043   2.4033
 FKY  H23  H  HNH2  0   0.414   -4.5333  -2.2715   2.7193
 FKY  O29  O  O2    0  -0.523    7.9599  -0.9963   1.3834

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
 FKY  C15  C16  single    1.518  0.020  1.518
 FKY  C15  F34  single    1.393  0.020  1.393
 FKY  C15  C14  single    1.517  0.020  1.517
 FKY  C16  N17  single    1.449  0.020  1.449
 FKY  C22  C23  single    1.498  0.020  1.498
 FKY  C22  C20  single    1.524  0.020  1.524
 FKY  O13  C14  single    1.422  0.020  1.422
 FKY  O13  C10  single    1.333  0.020  1.333
 FKY  C14  C19  single    1.524  0.020  1.524
 FKY  C23  C28  aromatic  1.391  0.020  1.391
 FKY  C23  C24  aromatic  1.390  0.020  1.390
 FKY  N36  C35  single    1.340  0.020  1.340
 FKY  N17  C20  single    1.355  0.020  1.355
 FKY  N17  C18  single    1.452  0.020  1.452
 FKY  C28  C27  aromatic  1.386  0.020  1.386
 FKY  C24  C25  aromatic  1.387  0.020  1.387
 FKY  C35  O37  double    1.220  0.020  1.220
 FKY  C35  C9   single    1.497  0.020  1.497
 FKY  C10  C9   aromatic  1.404  0.020  1.404
 FKY  C10  N11  aromatic  1.314  0.020  1.314
 FKY  C20  O21  double    1.219  0.020  1.219
 FKY  C27  C26  aromatic  1.384  0.020  1.384
 FKY  C9   C8   aromatic  1.380  0.020  1.380
 FKY  N11  C12  aromatic  1.328  0.020  1.328
 FKY  C25  C26  aromatic  1.383  0.020  1.383
 FKY  C26  O29  single    1.393  0.020  1.393
 FKY  C18  C19  single    1.526  0.020  1.526
 FKY  C8   C7   aromatic  1.398  0.020  1.398
 FKY  C12  C7   aromatic  1.387  0.020  1.387
 FKY  O29  C30  single    1.337  0.020  1.337
 FKY  C7   C1   single    1.459  0.020  1.459
 FKY  C1   N2   aromatic  1.367  0.020  1.367
 FKY  C1   C5   aromatic  1.373  0.020  1.373
 FKY  N2   C3   aromatic  1.307  0.020  1.307
 FKY  C30  F32  single    1.335  0.020  1.335
 FKY  C30  F31  single    1.335  0.020  1.335
 FKY  C30  F33  single    1.324  0.020  1.324
 FKY  C5   N4   aromatic  1.362  0.020  1.362
 FKY  C3   N4   aromatic  1.348  0.020  1.348
 FKY  N4   C6   single    1.446  0.020  1.446
 FKY  C5   H1   single    0.930  0.020  1.080
 FKY  C6   H2   single    0.970  0.020  1.090
 FKY  C6   H3   single    0.970  0.020  1.090
 FKY  C6   H4   single    0.970  0.020  1.090
 FKY  C8   H5   single    0.930  0.020  1.080
 FKY  C15  H6   single    0.970  0.020  1.090
 FKY  C22  H7   single    0.970  0.020  1.090
 FKY  C22  H8   single    0.970  0.020  1.090
 FKY  C24  H9   single    0.930  0.020  1.080
 FKY  C28  H10  single    0.930  0.020  1.080
 FKY  C3   H11  single    0.930  0.020  1.080
 FKY  C12  H12  single    0.930  0.020  1.080
 FKY  C14  H13  single    0.970  0.020  1.090
 FKY  C16  H14  single    0.970  0.020  1.090
 FKY  C16  H15  single    0.970  0.020  1.090
 FKY  C18  H16  single    0.970  0.020  1.090
 FKY  C18  H17  single    0.970  0.020  1.090
 FKY  C19  H18  single    0.970  0.020  1.090
 FKY  C19  H19  single    0.970  0.020  1.090
 FKY  C25  H20  single    0.930  0.020  1.080
 FKY  C27  H21  single    0.930  0.020  1.080
 FKY  N36  H22  single    0.860  0.020  1.020
 FKY  N36  H23  single    0.860  0.020  1.020

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
 FKY  H1   C5   N4   121.76  3.000
 FKY  H1   C5   C1   132.46  3.000
 FKY  N4   C5   C1   105.78  3.000
 FKY  H4   C6   H3   108.81  3.000
 FKY  H4   C6   H2   109.15  3.000
 FKY  H3   C6   H2   108.74  3.000
 FKY  H4   C6   N4   110.63  3.000
 FKY  H3   C6   N4   109.01  3.000
 FKY  H2   C6   N4   110.46  3.000
 FKY  C12  C7   C1   122.54  3.000
 FKY  C1   C7   C8   121.26  3.000
 FKY  C12  C7   C8   116.20  3.000
 FKY  H5   C8   C9   119.93  3.000
 FKY  H5   C8   C7   119.29  3.000
 FKY  C9   C8   C7   120.77  3.000
 FKY  O13  C10  N11  120.08  3.000
 FKY  N11  C10  C9   122.59  3.000
 FKY  O13  C10  C9   117.32  3.000
 FKY  H6   C15  F34  107.96  3.000
 FKY  H6   C15  C16  110.25  3.000
 FKY  F34  C15  C16  108.49  3.000
 FKY  H6   C15  C14  110.70  3.000
 FKY  F34  C15  C14  109.04  3.000
 FKY  C16  C15  C14  110.32  3.000
 FKY  O21  C20  N17  122.43  3.000
 FKY  O21  C20  C22  120.87  3.000
 FKY  N17  C20  C22  116.69  3.000
 FKY  H8   C22  H7   106.00  3.000
 FKY  H8   C22  C23  109.74  3.000
 FKY  H7   C22  C23  110.33  3.000
 FKY  H8   C22  C20  109.74  3.000
 FKY  H7   C22  C20  109.18  3.000
 FKY  C23  C22  C20  111.70  3.000
 FKY  H9   C24  C25  118.99  3.000
 FKY  H9   C24  C23  119.84  3.000
 FKY  C25  C24  C23  121.17  3.000
 FKY  O29  C26  C27  119.26  3.000
 FKY  O29  C26  C25  119.28  3.000
 FKY  C27  C26  C25  121.40  3.000
 FKY  H10  C28  C27  119.02  3.000
 FKY  H10  C28  C23  119.91  3.000
 FKY  C27  C28  C23  121.07  3.000
 FKY  N2   C1   C7   121.46  3.000
 FKY  N2   C1   C5   109.57  3.000
 FKY  C7   C1   C5   128.97  3.000
 FKY  C3   N2   C1   105.64  3.000
 FKY  H11  C3   N4   122.08  3.000
 FKY  H11  C3   N2   125.93  3.000
 FKY  N4   C3   N2   111.99  3.000
 FKY  C3   N4   C6   126.60  3.000
 FKY  C6   N4   C5   126.37  3.000
 FKY  C3   N4   C5   107.02  3.000
 FKY  C35  C9   C10  121.65  3.000
 FKY  C10  C9   C8   117.38  3.000
 FKY  C35  C9   C8   120.89  3.000
 FKY  C12  N11  C10  119.15  3.000
 FKY  H12  C12  N11  115.46  3.000
 FKY  H12  C12  C7   120.63  3.000
 FKY  N11  C12  C7   123.91  3.000
 FKY  C14  O13  C10  119.70  3.000
 FKY  H13  C14  C19  109.28  3.000
 FKY  H13  C14  O13  110.12  3.000
 FKY  C19  C14  O13  111.88  3.000
 FKY  H13  C14  C15  107.13  3.000
 FKY  C19  C14  C15  111.52  3.000
 FKY  O13  C14  C15  106.77  3.000
 FKY  H15  C16  H14  107.38  3.000
 FKY  H15  C16  N17  109.51  3.000
 FKY  H14  C16  N17  110.30  3.000
 FKY  H15  C16  C15  109.05  3.000
 FKY  H14  C16  C15  110.75  3.000
 FKY  N17  C16  C15  109.81  3.000
 FKY  C18  N17  C16  112.67  3.000
 FKY  C18  N17  C20  124.85  3.000
 FKY  C16  N17  C20  119.93  3.000
 FKY  H17  C18  H16  106.08  3.000
 FKY  H17  C18  C19  110.07  3.000
 FKY  H16  C18  C19  110.58  3.000
 FKY  H17  C18  N17  108.09  3.000
 FKY  H16  C18  N17  111.24  3.000
 FKY  C19  C18  N17  110.64  3.000
 FKY  H19  C19  H18  107.57  3.000
 FKY  H19  C19  C18  109.81  3.000
 FKY  H18  C19  C18  109.39  3.000
 FKY  H19  C19  C14  110.24  3.000
 FKY  H18  C19  C14  110.15  3.000
 FKY  C18  C19  C14  109.65  3.000
 FKY  C28  C23  C24  118.64  3.000
 FKY  C24  C23  C22  120.44  3.000
 FKY  C28  C23  C22  120.91  3.000
 FKY  H20  C25  C26  120.75  3.000
 FKY  H20  C25  C24  120.44  3.000
 FKY  C26  C25  C24  118.81  3.000
 FKY  H21  C27  C28  120.48  3.000
 FKY  H21  C27  C26  120.61  3.000
 FKY  C28  C27  C26  118.91  3.000
 FKY  F33  C30  F32  108.34  3.000
 FKY  F33  C30  F31  108.28  3.000
 FKY  F32  C30  F31  106.67  3.000
 FKY  F33  C30  O29  107.72  3.000
 FKY  F31  C30  O29  112.82  3.000
 FKY  F32  C30  O29  112.84  3.000
 FKY  O37  C35  N36  123.80  3.000
 FKY  O37  C35  C9   121.74  3.000
 FKY  N36  C35  C9   114.43  3.000
 FKY  H23  N36  H22  117.48  3.000
 FKY  H23  N36  C35  122.08  3.000
 FKY  H22  N36  C35  120.28  3.000
 FKY  C30  O29  C26  117.76  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
 FKY  CONST_01  C8   C7   C1   C5   180.00   0.0  0
 FKY  CONST_02  C12  C7   C1   C5     0.00   0.0  0
 FKY  CONST_03  C3   N2   C1   C5     0.00   0.0  0
 FKY  CONST_04  N2   C3   N4   C5     0.00   0.0  0
 FKY  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 FKY  CONST_06  C10  N11  C12  C7     0.00   0.0  0
 FKY  CONST_07  C3   N2   C1   C7   180.00   0.0  0
 FKY  CONST_08  N4   C5   C1   C7   180.00   0.0  0
 FKY  CONST_09  N11  C10  C9   C8     0.00   0.0  0
 FKY  CONST_10  N11  C12  C7   C8     0.00   0.0  0
 FKY  CONST_11  N2   C1   C7   C8     0.00   0.0  0
 FKY  CONST_12  C27  C28  C23  C24    0.00   0.0  0
 FKY  CONST_13  C27  C26  C25  C24    0.00   0.0  0
 FKY  CONST_14  C23  C28  C27  C26    0.00   0.0  0
 FKY  CONST_15  C23  C24  C25  C26    0.00   0.0  0
 FKY  CONST_16  C25  C24  C23  C28    0.00   0.0  0
 FKY  CONST_17  C25  C26  C27  C28    0.00   0.0  0
 FKY  CONST_18  C9   C8   C7   C1   180.00   0.0  0
 FKY  CONST_19  N11  C12  C7   C1   180.00   0.0  0
 FKY  CONST_20  N4   C3   N2   C1     0.00   0.0  0
 FKY  CONST_21  C3   N4   C5   C1     0.00   0.0  0
 FKY  CONST_22  C12  C7   C1   N2   180.00   0.0  0
 FKY  CONST_23  N4   C5   C1   N2     0.00   0.0  0
 FKY  CONST_24  C12  N11  C10  C9     0.00   0.0  0
 FKY  CONST_25  C12  C7   C8   C9     0.00   0.0  0
 FKY  CONST_26  C1   C5   N4   C6   180.00   0.0  0
 FKY  CONST_27  N2   C3   N4   C6   180.00   0.0  0
 FKY  CONST_28  C35  C9   C8   C7   180.00   0.0  0
 FKY  CONST_29  O13  C10  C9   C8   180.00   0.0  0
 FKY  CONST_30  C27  C28  C23  C22  180.00   0.0  0
 FKY  CONST_31  C25  C24  C23  C22  180.00   0.0  0
 FKY  CONST_32  O29  C26  C25  C24  180.00   0.0  0
 FKY  CONST_33  O29  C26  C27  C28  180.00   0.0  0
 FKY  CONST_34  C35  C9   C10  N11  180.00   0.0  0
 FKY  CONST_35  O13  C10  N11  C12  180.00   0.0  0
 FKY  CONST_36  H11  C3   N4   C5   180.00   0.0  0
 FKY  CONST_37  H1   C5   C1   C7     0.00   0.0  0
 FKY  CONST_38  H12  C12  C7   C8   180.00   0.0  0
 FKY  CONST_39  H5   C8   C9   C10  180.00   0.0  0
 FKY  CONST_40  H10  C28  C23  C24  180.00   0.0  0
 FKY  CONST_41  H9   C24  C25  C26  180.00   0.0  0
 FKY  CONST_42  H21  C27  C28  C23  180.00   0.0  0
 FKY  CONST_43  H20  C25  C24  C23  180.00   0.0  0
 FKY  CONST_44  C16  N17  C20  C22  180.00   0.0  0
 FKY  CONST_45  C18  N17  C20  C22    0.00   0.0  0
 FKY  CONST_46  O21  C20  N17  C16    0.00   0.0  0
 FKY  CONST_47  O21  C20  N17  C18  180.00   0.0  0
 FKY  CONST_48  H22  N36  C35  C9   180.00   0.0  0
 FKY  CONST_49  H23  N36  C35  C9     0.00   0.0  0
 FKY  Var_01    C18  N17  C16  C15  -60.77  30.0  1
 FKY  Var_02    N17  C18  C19  C14  -55.00  30.0  1
 FKY  Var_03    C19  C18  N17  C16   60.42  30.0  1
 FKY  Var_04    N36  C35  C9   C8   -52.42  30.0  2
 FKY  Var_05    C28  C23  C22  C20   84.09  30.0  2
 FKY  Var_06    C23  C22  C20  N17  176.49  30.0  1
 FKY  Var_07    H2   C6   N4   C5    57.76  30.0  2
 FKY  Var_08    F32  C30  O29  C26   60.01  30.0  3

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
 FKY  chir_01  C15  C16  F34  C14  negativ
 FKY  chir_02  C14  O13  C19  C15  negativ

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
 FKY  plan-1  C5   0.020
 FKY  plan-1  C6   0.020
 FKY  plan-1  C7   0.020
 FKY  plan-1  C1   0.020
 FKY  plan-1  N2   0.020
 FKY  plan-1  C3   0.020
 FKY  plan-1  N4   0.020
 FKY  plan-1  H1   0.020
 FKY  plan-1  H11  0.020
 FKY  plan-2  C7   0.020
 FKY  plan-2  C8   0.020
 FKY  plan-2  C10  0.020
 FKY  plan-2  C1   0.020
 FKY  plan-2  C9   0.020
 FKY  plan-2  N11  0.020
 FKY  plan-2  C12  0.020
 FKY  plan-2  O13  0.020
 FKY  plan-2  C35  0.020
 FKY  plan-2  H5   0.020
 FKY  plan-2  H12  0.020
 FKY  plan-3  C22  0.020
 FKY  plan-3  C24  0.020
 FKY  plan-3  C26  0.020
 FKY  plan-3  C28  0.020
 FKY  plan-3  C23  0.020
 FKY  plan-3  C25  0.020
 FKY  plan-3  C27  0.020
 FKY  plan-3  H9   0.020
 FKY  plan-3  H10  0.020
 FKY  plan-3  H20  0.020
 FKY  plan-3  H21  0.020
 FKY  plan-3  O29  0.020
 FKY  plan-4  C9   0.020
 FKY  plan-4  C35  0.020
 FKY  plan-4  N36  0.020
 FKY  plan-4  O37  0.020
 FKY  plan-4  H22  0.020
 FKY  plan-4  H23  0.020
 FKY  plan-5  C20  0.020
 FKY  plan-5  C22  0.020
 FKY  plan-5  C16  0.020
 FKY  plan-5  N17  0.020
 FKY  plan-5  C18  0.020
 FKY  plan-5  O21  0.020

