# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 04:05:55 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 6-(3-methoxyphenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(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
 KRX  KRX  6-(3-methoxyphenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide  ligand  50  28  .  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_KRX
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
 KRX  C1    C  CH3   0  -0.437   8.5302   3.1850  -0.0674
 KRX  O2    O  O2    0  -0.472   7.2004   2.7055  -0.0986
 KRX  C3    C  CR6   0   0.412   6.9935   1.3782  -0.0091
 KRX  C4    C  CR16  0  -0.387   8.0076   0.4326   0.1266
 KRX  C5    C  CR16  0  -0.224   7.6712  -0.9132   0.2146
 KRX  C6    C  CR16  0  -0.343   6.3529  -1.3290   0.1752
 KRX  C7    C  CR6   0   0.092   5.3330  -0.3828   0.0400
 KRX  C8    C  CR16  0  -0.388   5.6635   0.9635  -0.0579
 KRX  C9    C  CR6   0   0.236   3.9120  -0.7899  -0.0106
 KRX  C10   C  CR16  0  -0.324   3.4769  -2.0112   0.5076
 KRX  C11   C  CR16  0  -0.150   2.1389  -2.3400   0.4221
 KRX  C12   C  CR6   0  -0.136   1.2478  -1.4388  -0.1502
 KRX  C13   C  CR16  0  -0.087   1.7764  -0.2461  -0.6341
 KRX  N14   N  N     0  -0.427   3.0591   0.0668  -0.5701
 KRX  C15   C  C     0   0.539  -0.1943  -1.8065  -0.2675
 KRX  O16   O  O     0  -0.486  -0.5341  -2.9809  -0.3173
 KRX  N17   N  NH1   0  -0.657  -1.0588  -0.7808  -0.3250
 KRX  C18   C  CH1   0  -0.071  -2.4938  -0.9516  -0.4409
 KRX  C19   C  CH2   0  -0.448  -3.1044   0.2451  -1.1582
 KRX  C20   C  CH2   0  -0.291  -4.6155   0.1048  -1.2364
 KRX  N21   N  NT    0  -0.434  -5.1933  -0.0628   0.0838
 KRX  C22   C  CH2   0  -0.289  -4.6723  -1.2303   0.7712
 KRX  C23   C  CH2   0  -0.432  -3.1621  -1.1398   0.9179
 KRX  C24   C  CH2   0  -0.475  -6.6333   0.0330   0.0989
 KRX  C25   C  CT    0   0.986  -7.0567   1.3136   0.7778
 KRX  F26   F  F     0  -0.313  -6.5735   2.4015   0.1597
 KRX  F27   F  F     0  -0.315  -8.3930   1.4434   0.8071
 KRX  F28   F  F     0  -0.312  -6.6309   1.3737   2.0474
 KRX  H11C  H  HCH3  0   0.260   8.4706   4.2680  -0.1396
 KRX  H12C  H  HCH3  0   0.229   9.0371   2.9211   0.8642
 KRX  H13C  H  HCH3  0   0.229   9.1188   2.8082  -0.9079
 KRX  H4    H  HCR6  0   0.282   9.0501   0.7181   0.1628
 KRX  H8    H  HCR6  0   0.260   4.8824   1.7050  -0.1650
 KRX  H5    H  HCR6  0   0.264   8.4611  -1.6465   0.3099
 KRX  H6    H  HCR6  0   0.253   6.1300  -2.3859   0.2271
 KRX  H10   H  HCR6  0   0.275   4.1662  -2.6939   0.9838
 KRX  H11   H  HCR6  0   0.275   1.7874  -3.2856   0.8128
 KRX  H13   H  HCR6  0   0.264   1.1412   0.4858  -1.1225
 KRX  H17   H  HNH1  0   0.403  -0.7296   0.1450  -0.0985
 KRX  H18   H  HCH1  0   0.244  -2.6694  -1.8441  -1.0471
 KRX  H191  H  HCH2  0   0.228  -2.8515   1.1677  -0.6254
 KRX  H192  H  HCH2  0   0.249  -2.6982   0.3291  -2.1684
 KRX  H231  H  HCH2  0   0.245  -2.7891  -2.0461   1.3988
 KRX  H232  H  HCH2  0   0.224  -2.9112  -0.2947   1.5659
 KRX  H201  H  HCH2  0   0.249  -5.0348   0.9990  -1.6996
 KRX  H202  H  HCH2  0   0.202  -4.8658  -0.7414  -1.8992
 KRX  H221  H  HCH2  0   0.247  -5.1250  -1.2891   1.7624
 KRX  H222  H  HCH2  0   0.201  -4.9359  -2.1645   0.2466
 KRX  H241  H  HCH2  0   0.271  -7.0639   0.0138  -0.9077
 KRX  H242  H  HCH2  0   0.280  -7.0885  -0.8013   0.6398

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
 KRX  C1   O2    single    1.414  0.020  1.414
 KRX  O2   C3    single    1.346  0.020  1.346
 KRX  C3   C4    aromatic  1.393  0.020  1.393
 KRX  C3   C8    aromatic  1.394  0.020  1.394
 KRX  C4   C5    aromatic  1.390  0.020  1.390
 KRX  C5   C6    aromatic  1.383  0.020  1.383
 KRX  C6   C7    aromatic  1.398  0.020  1.398
 KRX  C7   C8    aromatic  1.390  0.020  1.390
 KRX  C7   C9    single    1.479  0.020  1.479
 KRX  C9   C10   aromatic  1.396  0.020  1.396
 KRX  C9   N14   aromatic  1.332  0.020  1.332
 KRX  C10  C11   aromatic  1.380  0.020  1.380
 KRX  C11  C12   aromatic  1.391  0.020  1.391
 KRX  C12  C13   aromatic  1.391  0.020  1.391
 KRX  C12  C15   single    1.493  0.020  1.493
 KRX  C13  N14   aromatic  1.322  0.020  1.322
 KRX  C15  O16   double    1.224  0.020  1.224
 KRX  C15  N17   single    1.343  0.020  1.343
 KRX  N17  C18   single    1.450  0.020  1.450
 KRX  C18  C19   single    1.523  0.020  1.523
 KRX  C18  C23   single    1.526  0.020  1.526
 KRX  C19  C20   single    1.520  0.020  1.520
 KRX  C20  N21   single    1.451  0.020  1.451
 KRX  N21  C22   single    1.451  0.020  1.451
 KRX  N21  C24   single    1.443  0.020  1.443
 KRX  C22  C23   single    1.520  0.020  1.520
 KRX  C24  C25   single    1.510  0.020  1.510
 KRX  C25  F26   single    1.341  0.020  1.341
 KRX  C25  F27   single    1.343  0.020  1.343
 KRX  C25  F28   single    1.341  0.020  1.341
 KRX  C1   H11C  single    0.970  0.020  1.090
 KRX  C1   H12C  single    0.970  0.020  1.090
 KRX  C1   H13C  single    0.970  0.020  1.090
 KRX  C4   H4    single    0.930  0.020  1.080
 KRX  C8   H8    single    0.930  0.020  1.080
 KRX  C5   H5    single    0.930  0.020  1.080
 KRX  C6   H6    single    0.930  0.020  1.080
 KRX  C10  H10   single    0.930  0.020  1.080
 KRX  C11  H11   single    0.930  0.020  1.080
 KRX  C13  H13   single    0.930  0.020  1.080
 KRX  N17  H17   single    0.860  0.020  1.020
 KRX  C18  H18   single    0.970  0.020  1.090
 KRX  C19  H191  single    0.970  0.020  1.090
 KRX  C19  H192  single    0.970  0.020  1.090
 KRX  C23  H231  single    0.970  0.020  1.090
 KRX  C23  H232  single    0.970  0.020  1.090
 KRX  C20  H201  single    0.970  0.020  1.090
 KRX  C20  H202  single    0.970  0.020  1.090
 KRX  C22  H221  single    0.970  0.020  1.090
 KRX  C22  H222  single    0.970  0.020  1.090
 KRX  C24  H241  single    0.970  0.020  1.090
 KRX  C24  H242  single    0.970  0.020  1.090

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
 KRX  H13C  C1   H12C  108.81  3.000
 KRX  H13C  C1   H11C  108.78  3.000
 KRX  H12C  C1   H11C  108.82  3.000
 KRX  H13C  C1   O2    111.88  3.000
 KRX  H12C  C1   O2    111.91  3.000
 KRX  H11C  C1   O2    106.54  3.000
 KRX  C3    O2   C1    118.51  3.000
 KRX  C8    C3   C4    119.73  3.000
 KRX  C8    C3   O2    115.95  3.000
 KRX  C4    C3   O2    124.32  3.000
 KRX  H4    C4   C5    119.13  3.000
 KRX  H4    C4   C3    121.71  3.000
 KRX  C5    C4   C3    119.16  3.000
 KRX  H5    C5   C6    119.65  3.000
 KRX  H5    C5   C4    119.02  3.000
 KRX  C6    C5   C4    121.33  3.000
 KRX  H6    C6   C7    121.05  3.000
 KRX  H6    C6   C5    119.27  3.000
 KRX  C7    C6   C5    119.66  3.000
 KRX  C9    C7   C8    119.52  3.000
 KRX  C9    C7   C6    121.20  3.000
 KRX  C8    C7   C6    119.28  3.000
 KRX  H8    C8   C7    119.94  3.000
 KRX  H8    C8   C3    119.23  3.000
 KRX  C7    C8   C3    120.84  3.000
 KRX  N14   C9   C10   121.26  3.000
 KRX  N14   C9   C7    116.90  3.000
 KRX  C10   C9   C7    121.84  3.000
 KRX  H10   C10  C11   119.67  3.000
 KRX  H10   C10  C9    121.15  3.000
 KRX  C11   C10  C9    119.17  3.000
 KRX  H11   C11  C12   120.46  3.000
 KRX  H11   C11  C10   120.04  3.000
 KRX  C12   C11  C10   119.49  3.000
 KRX  C15   C12  C13   123.42  3.000
 KRX  C15   C12  C11   119.45  3.000
 KRX  C13   C12  C11   117.08  3.000
 KRX  H13   C13  N14   115.48  3.000
 KRX  H13   C13  C12   120.81  3.000
 KRX  N14   C13  C12   123.69  3.000
 KRX  C13   N14  C9    119.30  3.000
 KRX  N17   C15  O16   123.55  3.000
 KRX  N17   C15  C12   115.93  3.000
 KRX  O16   C15  C12   120.52  3.000
 KRX  H17   N17  C18   116.70  3.000
 KRX  H17   N17  C15   118.78  3.000
 KRX  C18   N17  C15   123.42  3.000
 KRX  H18   C18  C23   108.83  3.000
 KRX  H18   C18  C19   108.42  3.000
 KRX  C23   C18  C19   109.92  3.000
 KRX  H18   C18  N17   107.43  3.000
 KRX  C23   C18  N17   112.14  3.000
 KRX  C19   C18  N17   110.00  3.000
 KRX  H192  C19  H191  107.43  3.000
 KRX  H192  C19  C20   109.23  3.000
 KRX  H191  C19  C20   109.42  3.000
 KRX  H192  C19  C18   110.30  3.000
 KRX  H191  C19  C18   109.89  3.000
 KRX  C20   C19  C18   110.51  3.000
 KRX  H202  C20  H201  106.63  3.000
 KRX  H202  C20  N21   111.57  3.000
 KRX  H201  C20  N21   109.15  3.000
 KRX  H202  C20  C19   109.10  3.000
 KRX  H201  C20  C19   109.17  3.000
 KRX  N21   C20  C19   111.10  3.000
 KRX  C24   N21  C22   113.99  3.000
 KRX  C24   N21  C20   113.53  3.000
 KRX  C22   N21  C20   112.39  3.000
 KRX  H222  C22  H221  106.68  3.000
 KRX  H222  C22  C23   109.49  3.000
 KRX  H221  C22  C23   109.13  3.000
 KRX  H222  C22  N21   111.72  3.000
 KRX  H221  C22  N21   108.94  3.000
 KRX  C23   C22  N21   110.76  3.000
 KRX  H232  C23  H231  107.58  3.000
 KRX  H232  C23  C22   109.33  3.000
 KRX  H231  C23  C22   109.42  3.000
 KRX  H232  C23  C18   109.38  3.000
 KRX  H231  C23  C18   110.18  3.000
 KRX  C22   C23  C18   110.89  3.000
 KRX  H242  C24  H241  106.12  3.000
 KRX  H242  C24  C25   107.94  3.000
 KRX  H241  C24  C25   108.53  3.000
 KRX  H242  C24  N21   111.70  3.000
 KRX  H241  C24  N21   112.43  3.000
 KRX  C25   C24  N21   109.92  3.000
 KRX  F28   C25  F27   106.92  3.000
 KRX  F28   C25  F26   106.59  3.000
 KRX  F27   C25  F26   106.87  3.000
 KRX  F28   C25  C24   112.01  3.000
 KRX  F27   C25  C24   111.77  3.000
 KRX  F26   C25  C24   112.32  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
 KRX  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 KRX  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 KRX  CONST_03  C9    C7   C8   C3    180.00   0.0  0
 KRX  CONST_04  C7    C8   C3   C4      0.00   0.0  0
 KRX  CONST_05  C7    C6   C5   C4      0.00   0.0  0
 KRX  CONST_06  C8    C3   C4   C5      0.00   0.0  0
 KRX  CONST_07  C8    C7   C6   C5      0.00   0.0  0
 KRX  CONST_08  C9    C7   C6   C5    180.00   0.0  0
 KRX  CONST_11  C11   C10  C9   C7    180.00   0.0  0
 KRX  CONST_12  C13   N14  C9   C7    180.00   0.0  0
 KRX  CONST_15  C12   C11  C10  C9      0.00   0.0  0
 KRX  CONST_16  C12   C13  N14  C9      0.00   0.0  0
 KRX  CONST_17  C13   N14  C9   C10     0.00   0.0  0
 KRX  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 KRX  CONST_19  N14   C9   C10  C11     0.00   0.0  0
 KRX  CONST_20  N14   C13  C12  C11     0.00   0.0  0
 KRX  CONST_21  C5    C4   C3   O2    180.00   0.0  0
 KRX  CONST_22  C7    C8   C3   O2    180.00   0.0  0
 KRX  CONST_23  C15   C12  C11  C10   180.00   0.0  0
 KRX  CONST_24  C15   C12  C13  N14   180.00   0.0  0
 KRX  CONST_25  H5    C5   C4   C3    180.00   0.0  0
 KRX  CONST_26  H8    C8   C3   C4    180.00   0.0  0
 KRX  CONST_27  H6    C6   C5   C4    180.00   0.0  0
 KRX  CONST_28  H4    C4   C5   C6    180.00   0.0  0
 KRX  CONST_29  H10   C10  C9   C7      0.00   0.0  0
 KRX  CONST_30  H11   C11  C10  C9    180.00   0.0  0
 KRX  CONST_31  H13   C13  N14  C9    180.00   0.0  0
 KRX  CONST_32  C18   N17  C15  C12   180.00   0.0  0
 KRX  CONST_33  C18   N17  C15  O16     0.00   0.0  0
 KRX  CONST_34  H17   N17  C15  C12     0.00   0.0  0
 KRX  Var_01    N21   C20  C19  C18    56.23  30.0  1
 KRX  Var_02    N21   C22  C23  C18   -55.88  30.0  1
 KRX  Var_03    C22   N21  C20  C19   -59.01  30.0  1
 KRX  Var_04    C23   C22  N21  C20    58.65  30.0  1
 KRX  Var_05    C4    C3   O2   C1      0.66  30.0  2
 KRX  Var_06    O16   C15  C12  C11   -25.50  30.0  2
 KRX  Var_07    C25   C24  N21  C20  -109.43  30.0  3
 KRX  Var_08    F26   C25  C24  N21    59.62  30.0  3
 KRX  Var_09    H11C  C1   O2   C3   -179.32  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
 KRX  chir_01  C18  N17  C19  C23  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
 KRX  plan-1  O2   0.020
 KRX  plan-1  C3   0.020
 KRX  plan-1  C4   0.020
 KRX  plan-1  C5   0.020
 KRX  plan-1  C6   0.020
 KRX  plan-1  C7   0.020
 KRX  plan-1  C8   0.020
 KRX  plan-1  C9   0.020
 KRX  plan-1  H4   0.020
 KRX  plan-1  H8   0.020
 KRX  plan-1  H5   0.020
 KRX  plan-1  H6   0.020
 KRX  plan-2  C7   0.020
 KRX  plan-2  C9   0.020
 KRX  plan-2  C10  0.020
 KRX  plan-2  C11  0.020
 KRX  plan-2  C12  0.020
 KRX  plan-2  C13  0.020
 KRX  plan-2  N14  0.020
 KRX  plan-2  C15  0.020
 KRX  plan-2  H10  0.020
 KRX  plan-2  H11  0.020
 KRX  plan-2  H13  0.020
 KRX  plan-3  C12  0.020
 KRX  plan-3  C15  0.020
 KRX  plan-3  O16  0.020
 KRX  plan-3  N17  0.020
 KRX  plan-3  C18  0.020
 KRX  plan-3  H17  0.020

