# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 03:31:20 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(C#N)c(S[C@@H](C(N)=O)c2ccc(cc2)C(F)(F)F)nc(N3CCC(N)CC3)c1C#N
#
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
 C79  C79  "(2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl)phenyl]acetamide"
  ligand  57  34  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_C79
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
 C79  C01  C  CH3   0  -0.659  -45.0861   -7.0988  31.5153
 C79  C02  C  CH2   0  -0.550  -46.2308   -7.6510  30.6630
 C79  C03  C  CR6   0   0.342  -45.9225   -9.0301  30.1644
 C79  C04  C  CR6   0  -0.220  -46.2882  -10.1639  30.8877
 C79  C05  C  CSP   0   0.010  -46.7951   -9.9814  32.1997
 C79  C07  C  CR6   0   0.603  -45.9898  -11.4642  30.3707
 C79  C09  C  CH2   0  -0.319  -45.9144  -13.8977  30.5373
 C79  C10  C  CH2   0  -0.447  -46.8466  -14.6639  29.6124
 C79  C11  C  CH1   0  -0.105  -48.2277  -14.8348  30.2392
 C79  C12  C  CH2   0  -0.434  -48.7499  -13.4677  30.6665
 C79  C13  C  CH2   0  -0.326  -47.7718  -12.7036  31.5541
 C79  C16  C  CR6   0   0.123  -44.7495  -10.5181  28.6857
 C79  C18  C  CH1   0  -0.589  -43.2307  -12.4799  27.4373
 C79  C19  C  CR6   0   0.149  -41.9598  -12.6551  26.6436
 C79  C20  C  CR16  0  -0.288  -40.7577  -12.8763  27.3059
 C79  C21  C  CR16  0  -0.251  -39.5755  -12.9985  26.5962
 C79  C22  C  CR6   0  -0.202  -39.5858  -12.8927  25.2102
 C79  C23  C  CT    0   1.052  -38.3049  -13.0565  24.4543
 C79  C27  C  CR16  0  -0.262  -40.7829  -12.6796  24.5398
 C79  C28  C  CR16  0  -0.251  -41.9631  -12.5594  25.2561
 C79  C29  C  C     0   0.567  -44.3146  -13.4412  26.9454
 C79  C32  C  CR6   0  -0.102  -45.1715   -9.2117  29.0019
 C79  C33  C  CSP   0  -0.030  -44.7618   -8.1170  28.2023
 C79  F24  F  F     0  -0.309  -37.2776  -12.4651  25.0771
 C79  F25  F  F     0  -0.313  -37.9786  -14.3508  24.3168
 C79  F26  F  F     0  -0.303  -38.3670  -12.5406  23.2234
 C79  N06  N  NS    0  -0.243  -47.1501   -9.8030  33.2837
 C79  N08  N  NT    0  -0.476  -46.4742  -12.5957  30.8934
 C79  N15  N  N     0  -0.488  -45.1544  -11.5776  29.3273
 C79  N30  N  NH2   0  -0.797  -45.2874  -12.9415  26.1818
 C79  N34  N  NS    0  -0.235  -44.4205   -7.2412  27.5327
 C79  O31  O  O     0  -0.466  -44.2044  -14.6194  27.2385
 C79  S17  S  S2    0   0.122  -43.6110  -10.7020  27.3622
 C79  H1   H  HCH3  0   0.250  -45.3322   -6.0955  31.8600
 C79  H2   H  HCH3  0   0.241  -44.9066   -7.7203  32.3919
 C79  H3   H  HCH3  0   0.240  -44.1587   -7.0411  30.9462
 C79  H4   H  HCH2  0   0.278  -46.4084   -6.9881  29.8147
 C79  H5   H  HCH2  0   0.276  -47.1543   -7.6596  31.2422
 C79  H6   H  HCH2  0   0.255  -45.7790  -14.4488  31.4702
 C79  H7   H  HCH2  0   0.277  -44.9374  -13.7639  30.0848
 C79  H8   H  HCH2  0   0.241  -46.4061  -15.6382  29.3855
 C79  H9   H  HCH2  0   0.235  -46.9397  -14.1295  28.6635
 C79  H10  H  HCH1  0   0.223  -48.9069  -15.2309  29.4710
 C79  H11  H  HCH2  0   0.237  -48.9624  -12.8704  29.7756
 C79  H12  H  HCH2  0   0.248  -49.6955  -13.5700  31.2064
 C79  H13  H  HCH2  0   0.273  -48.1905  -11.7241  31.7564
 C79  H14  H  HCH2  0   0.256  -47.6393  -13.2063  32.5136
 C79  H15  H  HCH1  0   0.353  -43.0430  -12.7293  28.4823
 C79  H16  H  HCR6  0   0.273  -40.7409  -12.9499  28.3859
 C79  H17  H  HCR6  0   0.279  -38.6537  -13.1698  27.1365
 C79  H18  H  HCR6  0   0.277  -40.8141  -12.5994  23.4618
 C79  H19  H  HCR6  0   0.272  -42.8871  -12.3881  24.7177
 C79  H20  H  HNH2  0   0.345  -49.0535  -15.8479  31.7981
 C79  H21  H  HNH2  0   0.345  -47.8100  -16.6228  31.1140
 C79  H23  H  HNH2  0   0.410  -46.0008  -13.5514  25.8150
 C79  H24  H  HNH2  0   0.414  -45.3492  -11.9626  25.9552
 C79  N14  N  NH2   0  -0.796  -48.1323  -15.7069  31.4020

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
 C79  F26  C23  single    1.336  0.020  1.336
 C79  F25  C23  single    1.342  0.020  1.342
 C79  C23  F24  single    1.339  0.020  1.339
 C79  C23  C22  single    1.496  0.020  1.496
 C79  C27  C22  aromatic  1.389  0.020  1.389
 C79  C27  C28  aromatic  1.386  0.020  1.386
 C79  C22  C21  aromatic  1.390  0.020  1.390
 C79  C28  C19  aromatic  1.391  0.020  1.391
 C79  C21  C20  aromatic  1.384  0.020  1.384
 C79  N30  C29  single    1.334  0.020  1.334
 C79  C19  C20  aromatic  1.390  0.020  1.390
 C79  C19  C18  single    1.509  0.020  1.509
 C79  C29  O31  double    1.219  0.020  1.219
 C79  C29  C18  single    1.530  0.020  1.530
 C79  C18  S17  single    1.820  0.020  1.820
 C79  S17  C16  single    1.755  0.020  1.755
 C79  N34  C33  triple    1.154  0.020  1.154
 C79  C33  C32  single    1.416  0.020  1.416
 C79  C16  C32  aromatic  1.409  0.020  1.409
 C79  C16  N15  aromatic  1.303  0.020  1.303
 C79  C32  C03  aromatic  1.396  0.020  1.396
 C79  N15  C07  aromatic  1.341  0.020  1.341
 C79  C10  C11  single    1.526  0.020  1.526
 C79  C10  C09  single    1.520  0.020  1.520
 C79  C11  C12  single    1.525  0.020  1.525
 C79  C11  N14  single    1.457  0.020  1.457
 C79  C03  C02  single    1.499  0.020  1.499
 C79  C03  C04  aromatic  1.394  0.020  1.394
 C79  C12  C13  single    1.526  0.020  1.526
 C79  C07  C04  aromatic  1.431  0.020  1.431
 C79  C07  N08  single    1.337  0.020  1.337
 C79  C02  C01  single    1.530  0.020  1.530
 C79  C09  N08  single    1.461  0.020  1.461
 C79  C04  C05  single    1.418  0.020  1.418
 C79  N08  C13  single    1.460  0.020  1.460
 C79  C05  N06  triple    1.155  0.020  1.155
 C79  C01  H1   single    0.970  0.020  1.090
 C79  C01  H2   single    0.970  0.020  1.090
 C79  C01  H3   single    0.970  0.020  1.090
 C79  C02  H4   single    0.970  0.020  1.090
 C79  C02  H5   single    0.970  0.020  1.090
 C79  C09  H6   single    0.970  0.020  1.090
 C79  C09  H7   single    0.970  0.020  1.090
 C79  C10  H8   single    0.970  0.020  1.090
 C79  C10  H9   single    0.970  0.020  1.090
 C79  C11  H10  single    0.970  0.020  1.090
 C79  C12  H11  single    0.970  0.020  1.090
 C79  C12  H12  single    0.970  0.020  1.090
 C79  C13  H13  single    0.970  0.020  1.090
 C79  C13  H14  single    0.970  0.020  1.090
 C79  C18  H15  single    0.970  0.020  1.090
 C79  C20  H16  single    0.930  0.020  1.080
 C79  C21  H17  single    0.930  0.020  1.080
 C79  C27  H18  single    0.930  0.020  1.080
 C79  C28  H19  single    0.930  0.020  1.080
 C79  N14  H20  single    0.890  0.020  1.040
 C79  N14  H21  single    0.890  0.020  1.040
 C79  N30  H23  single    0.860  0.020  1.020
 C79  N30  H24  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
 C79  H3   C01  H2   108.07  3.000
 C79  H3   C01  H1   107.98  3.000
 C79  H2   C01  H1   107.95  3.000
 C79  H3   C01  C02  111.40  3.000
 C79  H2   C01  C02  111.44  3.000
 C79  H1   C01  C02  109.86  3.000
 C79  H5   C02  H4   106.26  3.000
 C79  H5   C02  C03  110.11  3.000
 C79  H4   C02  C03  109.50  3.000
 C79  H5   C02  C01  109.92  3.000
 C79  H4   C02  C01  109.61  3.000
 C79  C03  C02  C01  111.31  3.000
 C79  C32  C03  C04  117.87  3.000
 C79  C04  C03  C02  121.46  3.000
 C79  C32  C03  C02  120.50  3.000
 C79  C07  C04  C05  121.72  3.000
 C79  C05  C04  C03  117.98  3.000
 C79  C07  C04  C03  119.81  3.000
 C79  N06  C05  C04  180.00  3.000
 C79  N15  C07  N08  117.26  3.000
 C79  N08  C07  C04  123.52  3.000
 C79  N15  C07  C04  119.19  3.000
 C79  H7   C09  H6   107.88  3.000
 C79  H7   C09  N08  109.67  3.000
 C79  H6   C09  N08  106.80  3.000
 C79  H7   C09  C10  111.13  3.000
 C79  H6   C09  C10  109.97  3.000
 C79  N08  C09  C10  111.25  3.000
 C79  H9   C10  H8   106.85  3.000
 C79  H9   C10  C11  109.52  3.000
 C79  H8   C10  C11  110.50  3.000
 C79  H9   C10  C09  109.51  3.000
 C79  H8   C10  C09  109.17  3.000
 C79  C11  C10  C09  111.19  3.000
 C79  H10  C11  N14  112.49  3.000
 C79  H10  C11  C12  107.90  3.000
 C79  N14  C11  C12  109.61  3.000
 C79  H10  C11  C10  108.20  3.000
 C79  N14  C11  C10  109.60  3.000
 C79  C12  C11  C10  108.95  3.000
 C79  H12  C12  H11  106.58  3.000
 C79  H12  C12  C13  108.30  3.000
 C79  H11  C12  C13  108.96  3.000
 C79  H12  C12  C11  110.52  3.000
 C79  H11  C12  C11  109.15  3.000
 C79  C13  C12  C11  113.11  3.000
 C79  H14  C13  H13  107.40  3.000
 C79  H14  C13  N08  108.91  3.000
 C79  H13  C13  N08  111.15  3.000
 C79  H14  C13  C12  111.01  3.000
 C79  H13  C13  C12  108.26  3.000
 C79  N08  C13  C12  110.09  3.000
 C79  S17  C16  N15  119.18  3.000
 C79  N15  C16  C32  123.39  3.000
 C79  S17  C16  C32  117.43  3.000
 C79  H15  C18  S17  107.39  3.000
 C79  H15  C18  C29  106.64  3.000
 C79  S17  C18  C29  116.91  3.000
 C79  H15  C18  C19  109.43  3.000
 C79  S17  C18  C19  105.54  3.000
 C79  C29  C18  C19  110.77  3.000
 C79  C28  C19  C20  119.23  3.000
 C79  C20  C19  C18  119.75  3.000
 C79  C28  C19  C18  120.99  3.000
 C79  H16  C20  C21  119.49  3.000
 C79  H16  C20  C19  119.97  3.000
 C79  C21  C20  C19  120.55  3.000
 C79  H17  C21  C22  121.07  3.000
 C79  H17  C21  C20  119.05  3.000
 C79  C22  C21  C20  119.88  3.000
 C79  C27  C22  C23  120.72  3.000
 C79  C27  C22  C21  119.97  3.000
 C79  C23  C22  C21  119.28  3.000
 C79  F26  C23  F25  106.82  3.000
 C79  F25  C23  F24  106.69  3.000
 C79  F26  C23  F24  107.08  3.000
 C79  F24  C23  C22  111.92  3.000
 C79  F25  C23  C22  111.44  3.000
 C79  F26  C23  C22  112.54  3.000
 C79  H18  C27  C28  118.96  3.000
 C79  H18  C27  C22  121.17  3.000
 C79  C28  C27  C22  119.87  3.000
 C79  H19  C28  C27  118.91  3.000
 C79  H19  C28  C19  120.59  3.000
 C79  C27  C28  C19  120.51  3.000
 C79  O31  C29  N30  124.45  3.000
 C79  O31  C29  C18  117.77  3.000
 C79  N30  C29  C18  117.73  3.000
 C79  C33  C32  C16  120.22  3.000
 C79  C16  C32  C03  117.96  3.000
 C79  C33  C32  C03  121.69  3.000
 C79  N34  C33  C32  180.00  3.000
 C79  C13  N08  C09  112.63  3.000
 C79  C13  N08  C07  124.15  3.000
 C79  C09  N08  C07  121.33  3.000
 C79  C16  N15  C07  120.51  3.000
 C79  H24  N30  H23  117.59  3.000
 C79  H24  N30  C29  122.55  3.000
 C79  H23  N30  C29  119.86  3.000
 C79  C18  S17  C16  101.94  3.000
 C79  H21  N14  H20  105.95  3.000
 C79  H21  N14  C11  109.59  3.000
 C79  H20  N14  C11  109.63  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
 C79  CONST_01  N15  C16  C32  C03     0.00   0.0  0
 C79  CONST_02  N15  C07  C04  C03     0.00   0.0  0
 C79  CONST_03  C16  C32  C03  C04     0.00   0.0  0
 C79  CONST_04  C16  N15  C07  C04     0.00   0.0  0
 C79  CONST_05  C32  C16  N15  C07     0.00   0.0  0
 C79  CONST_06  C32  C03  C04  C07     0.00   0.0  0
 C79  CONST_07  C22  C27  C28  C19     0.00   0.0  0
 C79  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 C79  CONST_09  C27  C22  C21  C20     0.00   0.0  0
 C79  CONST_10  C27  C28  C19  C20     0.00   0.0  0
 C79  CONST_11  C28  C27  C22  C21     0.00   0.0  0
 C79  CONST_12  C28  C19  C20  C21     0.00   0.0  0
 C79  CONST_13  N08  C07  C04  C03   180.00   0.0  0
 C79  CONST_14  N08  C07  N15  C16   180.00   0.0  0
 C79  CONST_15  C16  C32  C03  C02   180.00   0.0  0
 C79  CONST_16  C07  C04  C03  C02   180.00   0.0  0
 C79  CONST_17  S17  C16  C32  C03   180.00   0.0  0
 C79  CONST_18  C33  C32  C03  C04   180.00   0.0  0
 C79  CONST_19  C32  C03  C04  C05   180.00   0.0  0
 C79  CONST_22  S17  C16  N15  C07   180.00   0.0  0
 C79  CONST_23  C27  C28  C19  C18   180.00   0.0  0
 C79  CONST_24  C21  C20  C19  C18   180.00   0.0  0
 C79  CONST_25  C23  C22  C21  C20   180.00   0.0  0
 C79  CONST_26  C28  C27  C22  C23   180.00   0.0  0
 C79  CONST_27  N15  C16  C32  C33   180.00   0.0  0
 C79  CONST_28  H18  C27  C28  C19   180.00   0.0  0
 C79  CONST_29  H17  C21  C20  C19   180.00   0.0  0
 C79  CONST_30  H19  C28  C19  C20   180.00   0.0  0
 C79  CONST_31  H18  C27  C22  C21   180.00   0.0  0
 C79  CONST_32  H19  C28  C27  C22   180.00   0.0  0
 C79  CONST_33  H16  C20  C21  C22   180.00   0.0  0
 C79  CONST_34  H17  C21  C22  C27   180.00   0.0  0
 C79  CONST_35  H16  C20  C19  C28   180.00   0.0  0
 C79  CONST_36  H23  N30  C29  C18   180.00   0.0  0
 C79  CONST_37  H24  N30  C29  C18     0.00   0.0  0
 C79  CONST_38  H23  N30  C29  O31     0.00   0.0  0
 C79  CONST_39  H24  N30  C29  O31   180.00   0.0  0
 C79  Var_01    C09  N08  C07  C04  -165.86  30.0  2
 C79  Var_02    C13  N08  C07  C04    30.96  30.0  2
 C79  Var_03    C10  C09  N08  C07  -106.22  30.0  1
 C79  Var_04    C12  C13  N08  C07   107.66  30.0  1
 C79  Var_05    N15  C07  N08  C09    12.40  30.0  2
 C79  Var_06    C12  C13  N08  C09   -56.81  30.0  1
 C79  Var_07    C13  N08  C09  C10    58.75  30.0  1
 C79  Var_08    N08  C09  C10  C11   -56.64  30.0  1
 C79  Var_09    N08  C13  C12  C11    54.65  30.0  1
 C79  Var_10    N15  C07  N08  C13  -150.78  30.0  2
 C79  Var_11    H6   C09  N08  C07   133.78  30.0  1
 C79  Var_12    H7   C09  N08  C07    17.13  30.0  1
 C79  Var_13    H13  C13  N08  C07   -12.29  30.0  1
 C79  Var_14    H14  C13  N08  C07  -130.42  30.0  1
 C79  Var_15    H13  C13  N08  C09  -176.76  30.0  1
 C79  Var_16    H14  C13  N08  C09    65.11  30.0  1
 C79  Var_17    H6   C09  C10  C11    61.47  30.0  1
 C79  Var_18    H7   C09  C10  C11  -179.15  30.0  1
 C79  Var_19    H13  C13  C12  C11   176.34  30.0  1
 C79  Var_20    H14  C13  C12  C11   -66.02  30.0  1
 C79  Var_21    H6   C09  N08  C13   -61.26  30.0  1
 C79  Var_22    H7   C09  N08  C13  -177.90  30.0  1
 C79  Var_23    H8   C10  C09  N08  -178.81  30.0  1
 C79  Var_24    H9   C10  C09  N08    64.53  30.0  1
 C79  Var_25    H11  C12  C13  N08   -66.93  30.0  1
 C79  Var_26    H12  C12  C13  N08   177.51  30.0  1
 C79  Var_27    C32  C03  C02  C01   -84.56  30.0  2
 C79  Var_28    C04  C03  C02  C01    90.79  30.0  2
 C79  Var_29    C32  C16  S17  C18   174.30  30.0  2
 C79  Var_30    N15  C16  S17  C18    -5.30  30.0  2
 C79  Var_31    F26  C23  C22  C21  -160.81  30.0  2
 C79  Var_32    F25  C23  C22  C21    79.22  30.0  2
 C79  Var_33    F24  C23  C22  C21   -40.16  30.0  2
 C79  Var_34    F26  C23  C22  C27    21.24  30.0  2
 C79  Var_35    F25  C23  C22  C27   -98.73  30.0  2
 C79  Var_36    F24  C23  C22  C27   141.89  30.0  2
 C79  Var_37    H4   C02  C03  C04  -147.85  30.0  2
 C79  Var_38    H5   C02  C03  C04   -31.36  30.0  2
 C79  Var_39    H4   C02  C03  C32    36.80  30.0  2
 C79  Var_40    H5   C02  C03  C32   153.29  30.0  2
 C79  Var_41    H1   C01  C02  C03   179.68  30.0  3
 C79  Var_42    H2   C01  C02  C03   -60.72  30.0  3
 C79  Var_43    H3   C01  C02  C03    60.07  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
 C79  chir_01  C11  C10  C12  N14  positiv
 C79  chir_02  C18  C19  C29  S17  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
 C79  plan-1  C02  0.020
 C79  plan-1  C03  0.020
 C79  plan-1  C04  0.020
 C79  plan-1  C05  0.020
 C79  plan-1  C07  0.020
 C79  plan-1  C16  0.020
 C79  plan-1  C32  0.020
 C79  plan-1  C33  0.020
 C79  plan-1  N06  0.020
 C79  plan-1  N08  0.020
 C79  plan-1  N15  0.020
 C79  plan-1  N34  0.020
 C79  plan-1  S17  0.020
 C79  plan-2  C18  0.020
 C79  plan-2  C19  0.020
 C79  plan-2  C20  0.020
 C79  plan-2  C21  0.020
 C79  plan-2  C22  0.020
 C79  plan-2  C23  0.020
 C79  plan-2  C27  0.020
 C79  plan-2  C28  0.020
 C79  plan-2  H16  0.020
 C79  plan-2  H17  0.020
 C79  plan-2  H18  0.020
 C79  plan-2  H19  0.020
 C79  plan-3  C18  0.020
 C79  plan-3  C29  0.020
 C79  plan-3  N30  0.020
 C79  plan-3  O31  0.020
 C79  plan-3  H23  0.020
 C79  plan-3  H24  0.020

