# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 19:55:58 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 6-(3-fluorophenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(c1)c2ccc(cn2)C(=O)NC3CCN(CC3)CC(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
 KXO  KXO  6-(3-fluorophenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide  ligand  46  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KXO
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
 KXO  C4    C  CR16  0  -0.117   2.3971   2.5985  -0.0915
 KXO  C5    C  CR16  0  -0.300   3.6450   2.0116  -0.1263
 KXO  C6    C  CR16  0  -0.432   5.0707  -1.4776  -0.2017
 KXO  C7    C  CR16  0  -0.052   1.4615   0.4220  -0.1674
 KXO  C8    C  CH2   0  -0.462  -3.1650   1.3350   1.6836
 KXO  C10   C  CH2   0  -0.276  -3.3780  -0.1169   1.2829
 KXO  C13   C  CR6   0   0.094   5.0479  -0.0822  -0.2143
 KXO  C15   C  CR6   0  -0.127   1.2630   1.7956  -0.0881
 KXO  C17   C  CH1   0  -0.098  -2.4431   2.1366   0.6072
 KXO  C1    C  CR16  0  -0.194   7.4640  -0.0809  -0.2715
 KXO  C2    C  CR16  0  -0.322   6.2609   0.6065  -0.2517
 KXO  C3    C  CR16  0  -0.394   7.4908  -1.4669  -0.2563
 KXO  C9    C  CH2   0  -0.423  -3.1605   1.9463  -0.7280
 KXO  C11   C  CH2   0  -0.280  -3.3509   0.4775  -1.0610
 KXO  C14   C  CR6   0   0.569   6.2816  -2.1325  -0.2236
 KXO  C16   C  CR6   0   0.273   3.7460   0.6211  -0.1843
 KXO  C18   C  C     0   0.558  -0.0873   2.4213  -0.0575
 KXO  C19   C  CT    0   0.991  -5.9729  -1.5994  -0.5214
 KXO  N20   N  N     0  -0.454   2.6542  -0.1421  -0.2160
 KXO  N21   N  NH1   0  -0.650  -1.0525   1.7083   0.5370
 KXO  N22   N  NT    0  -0.424  -4.0563  -0.2084   0.0063
 KXO  O23   O  O     0  -0.521  -0.2773   3.5298  -0.5460
 KXO  F24   F  F     0  -0.320   6.2821  -3.4758  -0.2111
 KXO  F25   F  F     0  -0.306  -6.6226  -1.2839   0.6056
 KXO  F26   F  F     0  -0.306  -6.3998  -0.7525  -1.4670
 KXO  F27   F  F     0  -0.308  -6.3745  -2.8267  -0.8810
 KXO  H4    H  HCR6  0   0.260   2.3108   3.6755  -0.0524
 KXO  H5    H  HCR6  0   0.251   4.5183   2.6446  -0.1060
 KXO  H6    H  HCR6  0   0.260   4.1513  -2.0450  -0.1746
 KXO  H7    H  HCR6  0   0.237   0.6219  -0.2633  -0.2254
 KXO  H8    H  HCH2  0   0.253  -4.1370   1.7999   1.8569
 KXO  H8A   H  HCH2  0   0.247  -2.6214   1.3791   2.6300
 KXO  H10   H  HCH2  0   0.177  -2.4195  -0.6681   1.2781
 KXO  H10A  H  HCH2  0   0.249  -3.9876  -0.6004   2.0473
 KXO  H17   H  HCH1  0   0.264  -2.4602   3.1933   0.8809
 KXO  H1    H  HCR6  0   0.254   8.3933   0.4704  -0.2995
 KXO  H2    H  HCR6  0   0.228   6.2935   1.6862  -0.2694
 KXO  H3    H  HCR6  0   0.264   8.4244  -2.0123  -0.2700
 KXO  H9    H  HCH2  0   0.235  -4.1368   2.4321  -0.6625
 KXO  H9A   H  HCH2  0   0.241  -2.6157   2.4381  -1.5339
 KXO  H11   H  HCH2  0   0.244  -3.9309   0.3987  -1.9809
 KXO  H11A  H  HCH2  0   0.191  -2.3734   0.0095  -1.2716
 KXO  H12   H  HCH2  0   0.258  -4.1997  -2.2635   0.4370
 KXO  H12A  H  HCH2  0   0.249  -3.9974  -1.8991  -1.2622
 KXO  HN21  H  HNH1  0   0.384  -0.7930   0.8659   1.0234
 KXO  C12   C  CH2   0  -0.464  -4.4727  -1.5436  -0.3407

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
 KXO  C5   C4    aromatic  1.379  0.020  1.379
 KXO  C4   C15   aromatic  1.390  0.020  1.390
 KXO  C4   H4    single    0.930  0.020  1.080
 KXO  C5   C16   aromatic  1.395  0.020  1.395
 KXO  C5   H5    single    0.930  0.020  1.080
 KXO  C13  C6    aromatic  1.396  0.020  1.396
 KXO  C6   C14   aromatic  1.377  0.020  1.377
 KXO  C6   H6    single    0.930  0.020  1.080
 KXO  C15  C7    aromatic  1.390  0.020  1.390
 KXO  N20  C7    aromatic  1.320  0.020  1.320
 KXO  C7   H7    single    0.930  0.020  1.080
 KXO  C8   C10   single    1.521  0.020  1.521
 KXO  C8   C17   single    1.524  0.020  1.524
 KXO  C8   H8    single    0.970  0.020  1.090
 KXO  C8   H8A   single    0.970  0.020  1.090
 KXO  C10  N22   single    1.449  0.020  1.449
 KXO  C10  H10   single    0.970  0.020  1.090
 KXO  C10  H10A  single    0.970  0.020  1.090
 KXO  C2   C13   aromatic  1.395  0.020  1.395
 KXO  C16  C13   single    1.480  0.020  1.480
 KXO  C15  C18   single    1.488  0.020  1.488
 KXO  N21  C17   single    1.457  0.020  1.457
 KXO  C17  C9    single    1.528  0.020  1.528
 KXO  C17  H17   single    0.970  0.020  1.090
 KXO  C2   C1    aromatic  1.386  0.020  1.386
 KXO  C1   C3    aromatic  1.386  0.020  1.386
 KXO  C1   H1    single    0.930  0.020  1.080
 KXO  C2   H2    single    0.930  0.020  1.080
 KXO  C3   C14   aromatic  1.381  0.020  1.381
 KXO  C3   H3    single    0.930  0.020  1.080
 KXO  C9   C11   single    1.518  0.020  1.518
 KXO  C9   H9    single    0.970  0.020  1.090
 KXO  C9   H9A   single    0.970  0.020  1.090
 KXO  N22  C11   single    1.452  0.020  1.452
 KXO  C11  H11   single    0.970  0.020  1.090
 KXO  C11  H11A  single    0.970  0.020  1.090
 KXO  N22  C12   single    1.441  0.020  1.441
 KXO  C12  C19   single    1.512  0.020  1.512
 KXO  C12  H12   single    0.970  0.020  1.090
 KXO  C12  H12A  single    0.970  0.020  1.090
 KXO  C14  F24   single    1.343  0.020  1.343
 KXO  C16  N20   aromatic  1.332  0.020  1.332
 KXO  N21  C18   single    1.339  0.020  1.339
 KXO  C18  O23   double    1.226  0.020  1.226
 KXO  F27  C19   single    1.340  0.020  1.340
 KXO  C19  F26   single    1.339  0.020  1.339
 KXO  C19  F25   single    1.339  0.020  1.339
 KXO  N21  HN21  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
 KXO  H4    C4   C15  120.68  3.000
 KXO  H4    C4   C5   119.80  3.000
 KXO  C15   C4   C5   119.51  3.000
 KXO  H5    C5   C16  121.80  3.000
 KXO  H5    C5   C4   118.83  3.000
 KXO  C16   C5   C4   119.37  3.000
 KXO  H6    C6   C14  119.93  3.000
 KXO  H6    C6   C13  120.75  3.000
 KXO  C14   C6   C13  119.32  3.000
 KXO  H7    C7   N20  115.28  3.000
 KXO  H7    C7   C15  121.10  3.000
 KXO  N20   C7   C15  123.59  3.000
 KXO  H8A   C8   H8   106.77  3.000
 KXO  H8A   C8   C17  110.80  3.000
 KXO  H8    C8   C17  108.06  3.000
 KXO  H8A   C8   C10  109.66  3.000
 KXO  H8    C8   C10  108.89  3.000
 KXO  C17   C8   C10  112.48  3.000
 KXO  H10A  C10  H10  105.46  3.000
 KXO  H10A  C10  N22  109.14  3.000
 KXO  H10   C10  N22  111.75  3.000
 KXO  H10A  C10  C8   108.47  3.000
 KXO  H10   C10  C8   110.83  3.000
 KXO  N22   C10  C8   110.98  3.000
 KXO  C16   C13  C2   122.05  3.000
 KXO  C16   C13  C6   119.29  3.000
 KXO  C2    C13  C6   118.65  3.000
 KXO  C18   C15  C7   123.10  3.000
 KXO  C18   C15  C4   119.84  3.000
 KXO  C7    C15  C4   117.01  3.000
 KXO  H17   C17  N21  108.16  3.000
 KXO  H17   C17  C9   109.41  3.000
 KXO  N21   C17  C9   111.69  3.000
 KXO  H17   C17  C8   108.95  3.000
 KXO  C9    C17  C8   109.23  3.000
 KXO  N21   C17  C8   109.36  3.000
 KXO  H1    C1   C3   119.57  3.000
 KXO  H1    C1   C2   119.59  3.000
 KXO  C3    C1   C2   120.83  3.000
 KXO  H2    C2   C1   117.99  3.000
 KXO  H2    C2   C13  121.33  3.000
 KXO  C1    C2   C13  120.68  3.000
 KXO  H3    C3   C14  120.88  3.000
 KXO  H3    C3   C1   121.39  3.000
 KXO  C14   C3   C1   117.73  3.000
 KXO  H9A   C9   H9   106.88  3.000
 KXO  H9A   C9   C11  109.70  3.000
 KXO  H9    C9   C11  109.35  3.000
 KXO  H9A   C9   C17  110.81  3.000
 KXO  H9    C9   C17  108.17  3.000
 KXO  C11   C9   C17  111.79  3.000
 KXO  H11A  C11  H11  106.22  3.000
 KXO  H11A  C11  N22  111.73  3.000
 KXO  H11   C11  N22  109.13  3.000
 KXO  H11A  C11  C9   109.93  3.000
 KXO  H11   C11  C9   108.77  3.000
 KXO  N22   C11  C9   110.91  3.000
 KXO  F24   C14  C3   118.81  3.000
 KXO  F24   C14  C6   118.41  3.000
 KXO  C3    C14  C6   122.78  3.000
 KXO  N20   C16  C13  116.62  3.000
 KXO  N20   C16  C5   120.83  3.000
 KXO  C13   C16  C5   122.55  3.000
 KXO  O23   C18  N21  123.13  3.000
 KXO  O23   C18  C15  120.82  3.000
 KXO  N21   C18  C15  116.05  3.000
 KXO  F27   C19  F26  107.10  3.000
 KXO  F26   C19  F25  106.90  3.000
 KXO  F27   C19  F25  107.23  3.000
 KXO  F25   C19  C12  111.85  3.000
 KXO  F26   C19  C12  112.17  3.000
 KXO  F27   C19  C12  111.29  3.000
 KXO  C16   N20  C7   119.64  3.000
 KXO  HN21  N21  C18  118.31  3.000
 KXO  HN21  N21  C17  117.95  3.000
 KXO  C18   N21  C17  123.56  3.000
 KXO  C12   N22  C11  113.65  3.000
 KXO  C12   N22  C10  113.96  3.000
 KXO  C11   N22  C10  112.99  3.000
 KXO  H12A  C12  H12  106.02  3.000
 KXO  H12A  C12  N22  112.19  3.000
 KXO  H12   C12  N22  111.49  3.000
 KXO  H12A  C12  C19  108.53  3.000
 KXO  H12   C12  C19  107.95  3.000
 KXO  N22   C12  C19  110.46  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
 KXO  CONST_01  C13   C16  C5   C4    180.00   0.0  0
 KXO  CONST_02  N20   C16  C5   C4      0.00   0.0  0
 KXO  CONST_03  N20   C7   C15  C4      0.00   0.0  0
 KXO  CONST_04  C7    C15  C4   C5      0.00   0.0  0
 KXO  CONST_05  C6    C13  C16  C5    180.00   0.0  0
 KXO  CONST_06  C2    C13  C16  C5      0.00   0.0  0
 KXO  CONST_07  C7    N20  C16  C5      0.00   0.0  0
 KXO  CONST_08  C1    C2   C13  C6      0.00   0.0  0
 KXO  CONST_09  N20   C16  C13  C6      0.00   0.0  0
 KXO  CONST_10  C1    C3   C14  C6      0.00   0.0  0
 KXO  CONST_11  C13   C16  N20  C7    180.00   0.0  0
 KXO  CONST_12  C3    C14  C6   C13     0.00   0.0  0
 KXO  CONST_13  C3    C1   C2   C13     0.00   0.0  0
 KXO  CONST_14  C16   C5   C4   C15     0.00   0.0  0
 KXO  CONST_15  C16   N20  C7   C15     0.00   0.0  0
 KXO  CONST_16  C16   C13  C2   C1    180.00   0.0  0
 KXO  CONST_17  C14   C6   C13  C2      0.00   0.0  0
 KXO  CONST_18  N20   C16  C13  C2    180.00   0.0  0
 KXO  CONST_19  C14   C3   C1   C2      0.00   0.0  0
 KXO  CONST_20  C16   C13  C6   C14   180.00   0.0  0
 KXO  CONST_21  C18   C15  C4   C5    180.00   0.0  0
 KXO  CONST_22  F24   C14  C6   C13   180.00   0.0  0
 KXO  CONST_23  F24   C14  C3   C1    180.00   0.0  0
 KXO  CONST_24  N20   C7   C15  C18   180.00   0.0  0
 KXO  CONST_25  H7    C7   C15  C4    180.00   0.0  0
 KXO  CONST_26  H2    C2   C13  C6    180.00   0.0  0
 KXO  CONST_27  H3    C3   C14  C6    180.00   0.0  0
 KXO  CONST_28  H4    C4   C15  C7    180.00   0.0  0
 KXO  CONST_29  H1    C1   C2   C13   180.00   0.0  0
 KXO  CONST_30  H5    C5   C16  C13     0.00   0.0  0
 KXO  CONST_31  H6    C6   C13  C2    180.00   0.0  0
 KXO  CONST_32  C17   N21  C18  C15   180.00   0.0  0
 KXO  CONST_33  O23   C18  N21  C17     0.00   0.0  0
 KXO  CONST_34  HN21  N21  C18  C15     0.00   0.0  0
 KXO  Var_01    C11   N22  C10  C8     57.23  30.0  1
 KXO  Var_02    C9    C11  N22  C10   -58.25  30.0  1
 KXO  Var_03    N22   C10  C8   C17   -54.23  30.0  1
 KXO  Var_04    N22   C11  C9   C17    55.76  30.0  1
 KXO  Var_05    N21   C18  C15  C4   -150.53  30.0  2
 KXO  Var_06    C19   C12  N22  C10   120.17  30.0  3
 KXO  Var_07    F27   C19  C12  N22   178.29  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
 KXO  chir_01  C17  C8  N21  C9  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
 KXO  plan-1  C4    0.020
 KXO  plan-1  C5    0.020
 KXO  plan-1  C7    0.020
 KXO  plan-1  C13   0.020
 KXO  plan-1  C15   0.020
 KXO  plan-1  C16   0.020
 KXO  plan-1  C18   0.020
 KXO  plan-1  N20   0.020
 KXO  plan-1  H4    0.020
 KXO  plan-1  H5    0.020
 KXO  plan-1  H7    0.020
 KXO  plan-2  C6    0.020
 KXO  plan-2  C13   0.020
 KXO  plan-2  C1    0.020
 KXO  plan-2  C2    0.020
 KXO  plan-2  C3    0.020
 KXO  plan-2  C14   0.020
 KXO  plan-2  C16   0.020
 KXO  plan-2  F24   0.020
 KXO  plan-2  H6    0.020
 KXO  plan-2  H1    0.020
 KXO  plan-2  H2    0.020
 KXO  plan-2  H3    0.020
 KXO  plan-3  C15   0.020
 KXO  plan-3  C17   0.020
 KXO  plan-3  C18   0.020
 KXO  plan-3  N21   0.020
 KXO  plan-3  O23   0.020
 KXO  plan-3  HN21  0.020

