# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 07:00:38 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 5-[(4-{cis-4-[3-(trifluoromethyl)phenyl]cyclohexyl}piperazin-1-yl)methyl]pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(c1)[C@@H]2CC[C@@H](CC2)N3CCN(CC3)CC4=CNC(=O)C=C4
#
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
 5GK  5GK  5-[(4-{cis-4-[3-(trifluoromethyl)phenyl]cyclohexyl}piperazin-1-yl)methyl]pyridin-2(1H)-one  ligand  58  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5GK
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
 5GK  C01  C  CR6   0   0.524  86.3253  117.8552  83.2665
 5GK  N01  N  NR16  0  -0.655  86.9877  117.0866  84.2020
 5GK  O01  O  O     0  -0.522  86.0863  117.4122  82.1437
 5GK  C02  C  CR16  0  -0.460  85.9684  119.1606  83.7534
 5GK  N02  N  NT    0  -0.422  87.4367  118.0684  88.2407
 5GK  C03  C  CR16  0  -0.145  86.2772  119.5546  85.0186
 5GK  N03  N  NT    0  -0.410  87.0392  116.6745  90.7622
 5GK  C04  C  CR16  0   0.038  87.3022  117.4753  85.4592
 5GK  C05  C  CR6   0  -0.075  86.9690  118.7086  85.9214
 5GK  C06  C  CH2   0  -0.302  87.3502  119.1650  87.3052
 5GK  C07  C  CH2   0  -0.288  86.1281  117.5613  88.6186
 5GK  C08  C  CH2   0  -0.333  86.2763  116.3732  89.5606
 5GK  C09  C  CH2   0  -0.338  88.3313  117.1861  90.3316
 5GK  C10  C  CH2   0  -0.285  88.2341  118.3960  89.4108
 5GK  C11  C  CH1   0  -0.065  86.3331  117.4906  91.7542
 5GK  C12  C  CH2   0  -0.471  85.0558  116.7922  92.2348
 5GK  C13  C  CH2   0  -0.400  85.3533  115.4712  92.9345
 5GK  C14  C  CH1   0  -0.342  86.2862  115.6847  94.1320
 5GK  C15  C  CR6   0   0.226  86.6232  114.3974  94.8377
 5GK  C16  C  CR16  0  -0.313  87.2600  113.3539  94.1700
 5GK  C17  C  CR16  0  -0.224  87.5908  112.1796  94.8306
 5GK  C18  C  CR16  0  -0.292  87.2932  112.0249  96.1749
 5GK  C19  C  CR6   0  -0.170  86.6573  113.0594  96.8523
 5GK  C20  C  CT    0   1.051  86.3485  112.8735  98.3039
 5GK  C21  C  CR16  0  -0.390  86.3257  114.2334  96.1879
 5GK  C22  C  CH2   0  -0.400  87.5543  116.4350  93.7060
 5GK  C23  C  CH2   0  -0.477  87.2010  117.7347  92.9928
 5GK  F01  F  F     0  -0.302  85.7238  113.9231  98.8451
 5GK  F02  F  F     0  -0.316  85.5650  111.8037  98.5113
 5GK  F03  F  F     0  -0.316  87.4621  112.6687  99.0247
 5GK  H1   H  HNR6  0   0.419  87.2541  116.1546  83.9143
 5GK  H2   H  HCR6  0   0.270  85.4358  119.8187  83.0804
 5GK  H4   H  HCR6  0   0.268  85.9819  120.5444  85.3490
 5GK  H6   H  HCR6  0   0.299  87.8198  116.7480  86.0684
 5GK  H7   H  HCH2  0   0.253  88.3289  119.6541  87.2636
 5GK  H8   H  HCH2  0   0.211  86.6422  119.9439  87.6368
 5GK  H9   H  HCH2  0   0.198  85.5128  118.3487  89.0885
 5GK  H10  H  HCH2  0   0.238  85.5915  117.2387  87.7232
 5GK  H11  H  HCH2  0   0.242  85.2938  115.9771  89.8134
 5GK  H12  H  HCH2  0   0.229  86.7990  115.5745  89.0231
 5GK  H13  H  HCH2  0   0.229  88.8384  116.3845  89.7842
 5GK  H14  H  HCH2  0   0.244  88.9673  117.4207  91.1847
 5GK  H15  H  HCH2  0   0.236  89.2384  118.6779  89.0837
 5GK  H16  H  HCH2  0   0.193  87.8264  119.2624  89.9593
 5GK  H17  H  HCH1  0   0.214  86.0419  118.4734  91.3498
 5GK  H18  H  HCH2  0   0.229  84.5558  117.4711  92.9327
 5GK  H19  H  HCH2  0   0.238  84.3427  116.6386  91.4226
 5GK  H20  H  HCH2  0   0.230  84.4224  115.0096  93.2738
 5GK  H21  H  HCH2  0   0.225  85.8112  114.7779  92.2243
 5GK  H22  H  HCH1  0   0.233  85.7534  116.3257  94.8452
 5GK  H23  H  HCR6  0   0.255  87.5078  113.4557  93.1203
 5GK  H24  H  HCR6  0   0.265  88.0863  111.3799  94.2963
 5GK  H25  H  HCR6  0   0.272  87.5605  111.1050  96.6795
 5GK  H26  H  HCR6  0   0.262  85.8320  115.0425  96.7112
 5GK  H27  H  HCH2  0   0.226  88.1539  115.7996  93.0478
 5GK  H28  H  HCH2  0   0.231  88.1667  116.6479  94.5862
 5GK  H29  H  HCH2  0   0.238  88.1030  118.2990  92.7501
 5GK  H30  H  HCH2  0   0.231  86.6317  118.3768  93.6727

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
 5GK  O01  C01  double    1.230  0.020  1.230
 5GK  C01  N01  single    1.380  0.020  1.380
 5GK  C01  C02  single    1.438  0.020  1.438
 5GK  N01  C04  single    1.353  0.020  1.353
 5GK  C02  C03  double    1.361  0.020  1.361
 5GK  C04  C05  double    1.359  0.020  1.359
 5GK  C03  C05  single    1.417  0.020  1.417
 5GK  C05  C06  single    1.506  0.020  1.506
 5GK  C06  N02  single    1.444  0.020  1.444
 5GK  N02  C07  single    1.453  0.020  1.453
 5GK  N02  C10  single    1.453  0.020  1.453
 5GK  C07  C08  single    1.523  0.020  1.523
 5GK  C10  C09  single    1.524  0.020  1.524
 5GK  C08  N03  single    1.455  0.020  1.455
 5GK  C09  N03  single    1.455  0.020  1.455
 5GK  N03  C11  single    1.466  0.020  1.466
 5GK  C11  C12  single    1.533  0.020  1.533
 5GK  C11  C23  single    1.532  0.020  1.532
 5GK  C12  C13  single    1.524  0.020  1.524
 5GK  C23  C22  single    1.524  0.020  1.524
 5GK  C13  C14  single    1.533  0.020  1.533
 5GK  C16  C17  aromatic  1.387  0.020  1.387
 5GK  C16  C15  aromatic  1.393  0.020  1.393
 5GK  C22  C14  single    1.534  0.020  1.534
 5GK  C17  C18  aromatic  1.385  0.020  1.385
 5GK  C14  C15  single    1.506  0.020  1.506
 5GK  C15  C21  aromatic  1.392  0.020  1.392
 5GK  C18  C19  aromatic  1.391  0.020  1.391
 5GK  C21  C19  aromatic  1.389  0.020  1.389
 5GK  C19  C20  single    1.496  0.020  1.496
 5GK  C20  F02  single    1.342  0.020  1.342
 5GK  C20  F03  single    1.342  0.020  1.342
 5GK  C20  F01  single    1.336  0.020  1.336
 5GK  N01  H1   single    0.860  0.020  1.020
 5GK  C02  H2   single    0.930  0.020  1.080
 5GK  C03  H4   single    0.930  0.020  1.080
 5GK  C04  H6   single    0.930  0.020  1.080
 5GK  C06  H7   single    0.970  0.020  1.090
 5GK  C06  H8   single    0.970  0.020  1.090
 5GK  C07  H9   single    0.970  0.020  1.090
 5GK  C07  H10  single    0.970  0.020  1.090
 5GK  C08  H11  single    0.970  0.020  1.090
 5GK  C08  H12  single    0.970  0.020  1.090
 5GK  C09  H13  single    0.970  0.020  1.090
 5GK  C09  H14  single    0.970  0.020  1.090
 5GK  C10  H15  single    0.970  0.020  1.090
 5GK  C10  H16  single    0.970  0.020  1.090
 5GK  C11  H17  single    0.970  0.020  1.090
 5GK  C12  H18  single    0.970  0.020  1.090
 5GK  C12  H19  single    0.970  0.020  1.090
 5GK  C13  H20  single    0.970  0.020  1.090
 5GK  C13  H21  single    0.970  0.020  1.090
 5GK  C14  H22  single    0.970  0.020  1.090
 5GK  C16  H23  single    0.930  0.020  1.080
 5GK  C17  H24  single    0.930  0.020  1.080
 5GK  C18  H25  single    0.930  0.020  1.080
 5GK  C21  H26  single    0.930  0.020  1.080
 5GK  C22  H27  single    0.970  0.020  1.090
 5GK  C22  H28  single    0.970  0.020  1.090
 5GK  C23  H29  single    0.970  0.020  1.090
 5GK  C23  H30  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
 5GK  C02  C01  O01  125.98  3.000
 5GK  C02  C01  N01  113.28  3.000
 5GK  O01  C01  N01  120.74  3.000
 5GK  H1   N01  C04  117.90  3.000
 5GK  H1   N01  C01  116.55  3.000
 5GK  C04  N01  C01  125.55  3.000
 5GK  H2   C02  C03  120.94  3.000
 5GK  H2   C02  C01  117.64  3.000
 5GK  C03  C02  C01  121.42  3.000
 5GK  C10  N02  C07  111.30  3.000
 5GK  C10  N02  C06  112.54  3.000
 5GK  C07  N02  C06  112.30  3.000
 5GK  H4   C03  C05  118.92  3.000
 5GK  H4   C03  C02  119.06  3.000
 5GK  C05  C03  C02  122.02  3.000
 5GK  C11  N03  C09  115.61  3.000
 5GK  C11  N03  C08  114.94  3.000
 5GK  C09  N03  C08  107.10  3.000
 5GK  H6   C04  C05  122.46  3.000
 5GK  H6   C04  N01  116.21  3.000
 5GK  C05  C04  N01  121.33  3.000
 5GK  C06  C05  C04  121.70  3.000
 5GK  C06  C05  C03  121.86  3.000
 5GK  C04  C05  C03  116.41  3.000
 5GK  H8   C06  H7   105.64  3.000
 5GK  H8   C06  C05  109.11  3.000
 5GK  H7   C06  C05  109.07  3.000
 5GK  H8   C06  N02  112.32  3.000
 5GK  H7   C06  N02  108.08  3.000
 5GK  C05  C06  N02  112.35  3.000
 5GK  H10  C07  H9   106.60  3.000
 5GK  H10  C07  C08  108.91  3.000
 5GK  H9   C07  C08  110.32  3.000
 5GK  H10  C07  N02  109.40  3.000
 5GK  H9   C07  N02  111.32  3.000
 5GK  C08  C07  N02  110.20  3.000
 5GK  H12  C08  H11  106.21  3.000
 5GK  H12  C08  C07  108.16  3.000
 5GK  H11  C08  C07  109.84  3.000
 5GK  H12  C08  N03  107.83  3.000
 5GK  H11  C08  N03  110.89  3.000
 5GK  C07  C08  N03  113.59  3.000
 5GK  H14  C09  H13  106.18  3.000
 5GK  H14  C09  C10  109.84  3.000
 5GK  H13  C09  C10  107.98  3.000
 5GK  H14  C09  N03  111.25  3.000
 5GK  H13  C09  N03  107.56  3.000
 5GK  C10  C09  N03  113.67  3.000
 5GK  H16  C10  H15  106.60  3.000
 5GK  H16  C10  C09  110.29  3.000
 5GK  H15  C10  C09  109.09  3.000
 5GK  H16  C10  N02  111.98  3.000
 5GK  H15  C10  N02  108.74  3.000
 5GK  C09  C10  N02  110.03  3.000
 5GK  H17  C11  C23  107.72  3.000
 5GK  H17  C11  C12  107.53  3.000
 5GK  C23  C11  C12  106.93  3.000
 5GK  H17  C11  N03  112.05  3.000
 5GK  C23  C11  N03  111.28  3.000
 5GK  C12  C11  N03  111.09  3.000
 5GK  H19  C12  H18  105.26  3.000
 5GK  H19  C12  C13  110.31  3.000
 5GK  H18  C12  C13  109.51  3.000
 5GK  H19  C12  C11  112.03  3.000
 5GK  H18  C12  C11  107.33  3.000
 5GK  C13  C12  C11  112.09  3.000
 5GK  H21  C13  H20  106.89  3.000
 5GK  H21  C13  C14  109.94  3.000
 5GK  H20  C13  C14  109.55  3.000
 5GK  H21  C13  C12  109.46  3.000
 5GK  H20  C13  C12  110.01  3.000
 5GK  C14  C13  C12  110.90  3.000
 5GK  H22  C14  C22  107.24  3.000
 5GK  H22  C14  C15  107.66  3.000
 5GK  C22  C14  C15  111.30  3.000
 5GK  H22  C14  C13  107.08  3.000
 5GK  C15  C14  C13  112.53  3.000
 5GK  C22  C14  C13  110.75  3.000
 5GK  C21  C15  C16  118.31  3.000
 5GK  C21  C15  C14  120.48  3.000
 5GK  C16  C15  C14  121.19  3.000
 5GK  H23  C16  C17  119.10  3.000
 5GK  H23  C16  C15  119.91  3.000
 5GK  C17  C16  C15  120.99  3.000
 5GK  H24  C17  C18  119.67  3.000
 5GK  H24  C17  C16  119.98  3.000
 5GK  C18  C17  C16  120.35  3.000
 5GK  H25  C18  C19  121.19  3.000
 5GK  H25  C18  C17  119.61  3.000
 5GK  C19  C18  C17  119.20  3.000
 5GK  C21  C19  C20  121.33  3.000
 5GK  C20  C19  C18  118.34  3.000
 5GK  C21  C19  C18  120.33  3.000
 5GK  F03  C20  F02  106.24  3.000
 5GK  F03  C20  F01  106.87  3.000
 5GK  F02  C20  F01  106.90  3.000
 5GK  F01  C20  C19  113.08  3.000
 5GK  F03  C20  C19  111.64  3.000
 5GK  F02  C20  C19  111.69  3.000
 5GK  H26  C21  C19  120.62  3.000
 5GK  H26  C21  C15  118.56  3.000
 5GK  C19  C21  C15  120.82  3.000
 5GK  H28  C22  H27  106.89  3.000
 5GK  H28  C22  C23  109.91  3.000
 5GK  H27  C22  C23  109.93  3.000
 5GK  H28  C22  C14  109.56  3.000
 5GK  H27  C22  C14  109.64  3.000
 5GK  C23  C22  C14  110.83  3.000
 5GK  H30  C23  H29  105.35  3.000
 5GK  H30  C23  C22  109.27  3.000
 5GK  H29  C23  C22  110.70  3.000
 5GK  H30  C23  C11  107.51  3.000
 5GK  H29  C23  C11  111.77  3.000
 5GK  C22  C23  C11  111.95  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
 5GK  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 5GK  CONST_02  C18  C19  C21  C15    0.00   0.0  0
 5GK  CONST_03  C19  C18  C17  C16    0.00   0.0  0
 5GK  CONST_04  C19  C21  C15  C16    0.00   0.0  0
 5GK  CONST_05  C21  C15  C16  C17    0.00   0.0  0
 5GK  CONST_06  C21  C19  C18  C17    0.00   0.0  0
 5GK  CONST_07  C17  C16  C15  C14  180.00   0.0  0
 5GK  CONST_08  C19  C21  C15  C14  180.00   0.0  0
 5GK  CONST_09  C04  N01  C01  C02    0.00   0.0  0
 5GK  CONST_10  C20  C19  C21  C15  180.00   0.0  0
 5GK  CONST_11  C20  C19  C18  C17  180.00   0.0  0
 5GK  CONST_12  C04  N01  C01  O01  180.00   0.0  0
 5GK  CONST_13  H23  C16  C15  C14    0.00   0.0  0
 5GK  CONST_14  H26  C21  C15  C14    0.00   0.0  0
 5GK  CONST_15  H24  C17  C16  C15  180.00   0.0  0
 5GK  CONST_16  H25  C18  C17  C16  180.00   0.0  0
 5GK  CONST_17  H1   N01  C01  C02  180.00   0.0  0
 5GK  Var_01    N03  C08  C07  N02   57.05  30.0  1
 5GK  Var_02    N03  C09  C10  N02  -57.23  30.0  1
 5GK  Var_03    C09  C10  N02  C07   55.06  30.0  1
 5GK  Var_04    C09  N03  C08  C07  -56.10  30.0  1
 5GK  Var_05    C10  N02  C07  C08  -55.06  30.0  1
 5GK  Var_06    C10  C09  N03  C08   56.26  30.0  1
 5GK  Var_07    C14  C13  C12  C11   57.92  30.0  1
 5GK  Var_08    C14  C22  C23  C11  -58.36  30.0  1
 5GK  Var_09    C04  C05  C06  N02  -29.70  30.0  2
 5GK  Var_10    C07  N02  C06  C05  -73.78  30.0  3
 5GK  Var_11    F02  C20  C19  C18  -58.59  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
 5GK  chir_01  C11  N03  C12  C23  negativ
 5GK  chir_02  C14  C13  C22  C15  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
 5GK  plan-1  C01  0.020
 5GK  plan-1  N01  0.020
 5GK  plan-1  O01  0.020
 5GK  plan-1  C02  0.020
 5GK  plan-1  C03  0.020
 5GK  plan-1  C04  0.020
 5GK  plan-1  C05  0.020
 5GK  plan-1  C06  0.020
 5GK  plan-1  H1   0.020
 5GK  plan-1  H2   0.020
 5GK  plan-1  H4   0.020
 5GK  plan-1  H6   0.020
 5GK  plan-2  C14  0.020
 5GK  plan-2  C15  0.020
 5GK  plan-2  C16  0.020
 5GK  plan-2  C17  0.020
 5GK  plan-2  C18  0.020
 5GK  plan-2  C19  0.020
 5GK  plan-2  C20  0.020
 5GK  plan-2  C21  0.020
 5GK  plan-2  H23  0.020
 5GK  plan-2  H24  0.020
 5GK  plan-2  H25  0.020
 5GK  plan-2  H26  0.020

