# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 13:38:23 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]amino}-2-phenylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(C#N)c(N[C@@H](C(N)=O)c2ccccc2)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
 96I  96I  "(2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]amino}-2-phenylacetamide"
  ligand  55  30  .  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_96I
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
 96I  C01  C  CH3   0  -0.659  -45.5549   -6.9113  31.5365
 96I  C03  C  CR6   0   0.327  -46.0763   -9.0475  30.3410
 96I  C04  C  CR6   0  -0.209  -45.2113   -9.2738  29.2763
 96I  C05  C  CSP   0  -0.015  -44.8284   -8.2339  28.3995
 96I  C07  C  CR6   0   0.579  -44.6657  -10.5785  29.1106
 96I  C10  C  C     0   0.535  -43.9857  -13.2430  27.6119
 96I  C13  C  CR6   0   0.094  -41.9250  -12.0028  27.0721
 96I  C14  C  CR16  0  -0.290  -42.1229  -11.5230  25.7787
 96I  C15  C  CR16  0  -0.235  -41.0651  -11.4657  24.8832
 96I  C16  C  CR16  0  -0.260  -39.8020  -11.8985  25.2655
 96I  C20  C  CR6   0   0.597  -45.9649  -11.4385  30.8095
 96I  C02  C  CH2   0  -0.548  -46.5517   -7.6591  30.6492
 96I  C09  C  CH1   0  -0.232  -43.0705  -12.0944  28.0543
 96I  C17  C  CR16  0  -0.236  -39.6013  -12.3850  26.5496
 96I  C18  C  CR16  0  -0.311  -40.6585  -12.4352  27.4484
 96I  C22  C  CH2   0  -0.336  -45.7635  -13.8365  31.1989
 96I  C23  C  CH2   0  -0.457  -46.5811  -14.6911  30.2304
 96I  C24  C  CH1   0  -0.050  -48.0833  -14.4319  30.4022
 96I  C26  C  CH2   0  -0.486  -48.3440  -13.9936  31.8368
 96I  C27  C  CH2   0  -0.312  -47.6965  -12.6329  32.0996
 96I  C28  C  CR6   0  -0.242  -46.4292  -10.1286  31.1526
 96I  C29  C  CSP   0   0.012  -47.0945   -9.8545  32.3720
 96I  N06  N  NS    0  -0.251  -44.4895   -7.4132  27.6604
 96I  N08  N  NH1   0  -0.696  -43.7468  -10.8210  28.1557
 96I  N19  N  N     0  -0.533  -45.0540  -11.5968  29.8486
 96I  N21  N  NT    0  -0.483  -46.3995  -12.5455  31.4272
 96I  N30  N  NS    0  -0.261  -47.5918   -9.5833  33.3792
 96I  O12  O  O     0  -0.477  -43.6896  -14.3889  27.9069
 96I  H1   H  HCH3  0   0.247  -45.9340   -5.9162  31.7652
 96I  H2   H  HCH3  0   0.239  -45.3907   -7.4322  32.4795
 96I  H3   H  HCH3  0   0.238  -44.5906   -6.7977  31.0414
 96I  H4   H  HCR6  0   0.263  -43.1034  -11.1896  25.4593
 96I  H5   H  HCR6  0   0.260  -41.2293  -11.0874  23.8828
 96I  H6   H  HCR6  0   0.259  -38.9779  -11.8557  24.5653
 96I  H7   H  HCH2  0   0.274  -46.6965   -7.1091  29.7180
 96I  H8   H  HCH2  0   0.271  -47.5255   -7.6972  31.1373
 96I  H9   H  HCH1  0   0.300  -42.6747  -12.3891  29.0300
 96I  H10  H  HCR6  0   0.260  -38.6198  -12.7223  26.8564
 96I  H11  H  HCR6  0   0.258  -40.4945  -12.8078  28.4522
 96I  H12  H  HCH2  0   0.263  -45.6957  -14.3301  32.1706
 96I  H13  H  HCH2  0   0.276  -44.7485  -13.6907  30.8445
 96I  H14  H  HCH2  0   0.233  -46.3741  -15.7433  30.4399
 96I  H15  H  HCH2  0   0.245  -46.2797  -14.5003  29.1994
 96I  H16  H  HCH1  0   0.205  -48.3587  -13.5889  29.7482
 96I  H17  H  HCH2  0   0.258  -49.4146  -13.8947  32.0290
 96I  H18  H  HCH2  0   0.238  -47.9699  -14.7536  32.5274
 96I  H19  H  HCH2  0   0.260  -48.3504  -11.8616  31.6920
 96I  H20  H  HCH2  0   0.262  -47.6003  -12.4591  33.1731
 96I  H21  H  HNH1  0   0.421  -43.3297  -10.0361  27.6785
 96I  H22  H  HNH2  0   0.405  -45.6562  -13.6192  26.5080
 96I  H23  H  HNH2  0   0.412  -45.2640  -11.9487  26.6543
 96I  H24  H  HNH2  0   0.342  -49.8290  -15.4115  30.0717
 96I  H25  H  HNH2  0   0.343  -48.6146  -15.9402  29.1519
 96I  N25  N  NH2   0  -0.800  -48.8407  -15.6343  30.0913
 96I  N11  N  NH2   0  -0.798  -45.0316  -12.9074  26.8510

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
 96I  C15  C16  aromatic  1.389  0.020  1.389
 96I  C15  C14  aromatic  1.387  0.020  1.387
 96I  C16  C17  aromatic  1.388  0.020  1.388
 96I  C14  C13  aromatic  1.394  0.020  1.394
 96I  C17  C18  aromatic  1.389  0.020  1.389
 96I  N11  C10  single    1.336  0.020  1.336
 96I  C13  C18  aromatic  1.390  0.020  1.390
 96I  C13  C09  single    1.512  0.020  1.512
 96I  O12  C10  double    1.220  0.020  1.220
 96I  C10  C09  single    1.534  0.020  1.534
 96I  C09  N08  single    1.445  0.020  1.445
 96I  N06  C05  triple    1.155  0.020  1.155
 96I  N08  C07  single    1.347  0.020  1.347
 96I  C05  C04  single    1.413  0.020  1.413
 96I  C07  C04  aromatic  1.424  0.020  1.424
 96I  C07  N19  aromatic  1.316  0.020  1.316
 96I  C04  C03  aromatic  1.390  0.020  1.390
 96I  N19  C20  aromatic  1.333  0.020  1.333
 96I  C23  C24  single    1.534  0.020  1.534
 96I  C23  C22  single    1.529  0.020  1.529
 96I  C24  N25  single    1.455  0.020  1.455
 96I  C24  C26  single    1.523  0.020  1.523
 96I  C03  C02  single    1.500  0.020  1.500
 96I  C03  C28  aromatic  1.397  0.020  1.397
 96I  C02  C01  single    1.530  0.020  1.530
 96I  C20  C28  aromatic  1.432  0.020  1.432
 96I  C20  N21  single    1.340  0.020  1.340
 96I  C28  C29  single    1.416  0.020  1.416
 96I  C22  N21  single    1.457  0.020  1.457
 96I  C26  C27  single    1.530  0.020  1.530
 96I  N21  C27  single    1.464  0.020  1.464
 96I  C29  N30  triple    1.156  0.020  1.156
 96I  C01  H1   single    0.970  0.020  1.090
 96I  C01  H2   single    0.970  0.020  1.090
 96I  C01  H3   single    0.970  0.020  1.090
 96I  C14  H4   single    0.930  0.020  1.080
 96I  C15  H5   single    0.930  0.020  1.080
 96I  C16  H6   single    0.930  0.020  1.080
 96I  C02  H7   single    0.970  0.020  1.090
 96I  C02  H8   single    0.970  0.020  1.090
 96I  C09  H9   single    0.970  0.020  1.090
 96I  C17  H10  single    0.930  0.020  1.080
 96I  C18  H11  single    0.930  0.020  1.080
 96I  C22  H12  single    0.970  0.020  1.090
 96I  C22  H13  single    0.970  0.020  1.090
 96I  C23  H14  single    0.970  0.020  1.090
 96I  C23  H15  single    0.970  0.020  1.090
 96I  C24  H16  single    0.970  0.020  1.090
 96I  C26  H17  single    0.970  0.020  1.090
 96I  C26  H18  single    0.970  0.020  1.090
 96I  C27  H19  single    0.970  0.020  1.090
 96I  C27  H20  single    0.970  0.020  1.090
 96I  N08  H21  single    0.860  0.020  1.020
 96I  N11  H22  single    0.860  0.020  1.020
 96I  N11  H23  single    0.860  0.020  1.020
 96I  N25  H24  single    0.890  0.020  1.040
 96I  N25  H25  single    0.890  0.020  1.040

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
 96I  H3   C01  H2   108.04  3.000
 96I  H3   C01  H1   107.95  3.000
 96I  H2   C01  H1   107.90  3.000
 96I  H3   C01  C02  111.35  3.000
 96I  H2   C01  C02  111.50  3.000
 96I  H1   C01  C02  109.97  3.000
 96I  C28  C03  C02  121.12  3.000
 96I  C28  C03  C04  118.43  3.000
 96I  C02  C03  C04  120.36  3.000
 96I  C07  C04  C05  119.89  3.000
 96I  C07  C04  C03  118.47  3.000
 96I  C05  C04  C03  121.60  3.000
 96I  N06  C05  C04  180.00  3.000
 96I  N19  C07  N08  117.35  3.000
 96I  N19  C07  C04  122.05  3.000
 96I  N08  C07  C04  120.58  3.000
 96I  O12  C10  N11  124.31  3.000
 96I  O12  C10  C09  119.27  3.000
 96I  N11  C10  C09  116.31  3.000
 96I  C18  C13  C09  119.71  3.000
 96I  C09  C13  C14  121.08  3.000
 96I  C18  C13  C14  119.19  3.000
 96I  H4   C14  C15  119.14  3.000
 96I  H4   C14  C13  120.53  3.000
 96I  C15  C14  C13  120.33  3.000
 96I  H5   C15  C16  120.10  3.000
 96I  H5   C15  C14  119.70  3.000
 96I  C16  C15  C14  120.20  3.000
 96I  H6   C16  C17  120.16  3.000
 96I  H6   C16  C15  120.14  3.000
 96I  C17  C16  C15  119.71  3.000
 96I  N21  C20  N19  117.10  3.000
 96I  N21  C20  C28  122.70  3.000
 96I  N19  C20  C28  120.19  3.000
 96I  H8   C02  H7   106.33  3.000
 96I  H8   C02  C03  110.05  3.000
 96I  H7   C02  C03  109.47  3.000
 96I  H8   C02  C01  109.85  3.000
 96I  H7   C02  C01  109.58  3.000
 96I  C03  C02  C01  111.42  3.000
 96I  H9   C09  N08  110.14  3.000
 96I  H9   C09  C13  108.77  3.000
 96I  N08  C09  C13  110.29  3.000
 96I  H9   C09  C10  105.75  3.000
 96I  N08  C09  C10  113.63  3.000
 96I  C13  C09  C10  108.06  3.000
 96I  H10  C17  C18  119.72  3.000
 96I  H10  C17  C16  120.18  3.000
 96I  C18  C17  C16  120.10  3.000
 96I  H11  C18  C17  119.80  3.000
 96I  H11  C18  C13  119.73  3.000
 96I  C17  C18  C13  120.47  3.000
 96I  H13  C22  H12  107.05  3.000
 96I  H13  C22  N21  109.90  3.000
 96I  H12  C22  N21  106.75  3.000
 96I  H13  C22  C23  111.63  3.000
 96I  H12  C22  C23  110.14  3.000
 96I  N21  C22  C23  111.17  3.000
 96I  H15  C23  H14  107.29  3.000
 96I  H15  C23  C24  110.30  3.000
 96I  H14  C23  C24  109.07  3.000
 96I  H15  C23  C22  110.68  3.000
 96I  H14  C23  C22  108.39  3.000
 96I  C24  C23  C22  111.00  3.000
 96I  H16  C24  N25  112.05  3.000
 96I  H16  C24  C26  107.22  3.000
 96I  N25  C24  C26  110.50  3.000
 96I  H16  C24  C23  107.91  3.000
 96I  C26  C24  C23  108.77  3.000
 96I  N25  C24  C23  110.26  3.000
 96I  H18  C26  H17  106.70  3.000
 96I  H18  C26  C27  111.42  3.000
 96I  H17  C26  C27  107.71  3.000
 96I  H18  C26  C24  109.67  3.000
 96I  H17  C26  C24  111.08  3.000
 96I  C27  C26  C24  110.21  3.000
 96I  H20  C27  H19  107.93  3.000
 96I  H20  C27  N21  111.36  3.000
 96I  H19  C27  N21  108.51  3.000
 96I  H20  C27  C26  110.35  3.000
 96I  H19  C27  C26  108.13  3.000
 96I  N21  C27  C26  110.44  3.000
 96I  C29  C28  C20  122.41  3.000
 96I  C29  C28  C03  117.99  3.000
 96I  C20  C28  C03  119.13  3.000
 96I  N30  C29  C28  180.00  3.000
 96I  H21  N08  C09  117.31  3.000
 96I  H21  N08  C07  118.50  3.000
 96I  C09  N08  C07  121.83  3.000
 96I  C20  N19  C07  120.91  3.000
 96I  C27  N21  C22  113.95  3.000
 96I  C27  N21  C20  123.26  3.000
 96I  C22  N21  C20  121.20  3.000
 96I  H25  N25  H24  105.43  3.000
 96I  H25  N25  C24  109.35  3.000
 96I  H24  N25  C24  109.28  3.000
 96I  H23  N11  H22  117.62  3.000
 96I  H23  N11  C10  122.11  3.000
 96I  H22  N11  C10  120.13  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
 96I  CONST_01  N19  C07  C04  C03     0.00   0.0  0
 96I  CONST_02  N19  C20  C28  C03     0.00   0.0  0
 96I  CONST_03  C20  N19  C07  C04     0.00   0.0  0
 96I  CONST_04  C20  C28  C03  C04     0.00   0.0  0
 96I  CONST_05  C28  C03  C04  C07     0.00   0.0  0
 96I  CONST_06  C28  C20  N19  C07     0.00   0.0  0
 96I  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 96I  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 96I  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 96I  CONST_10  C17  C18  C13  C14     0.00   0.0  0
 96I  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 96I  CONST_12  C18  C13  C14  C15     0.00   0.0  0
 96I  CONST_13  N21  C20  C28  C03   180.00   0.0  0
 96I  CONST_14  N21  C20  N19  C07   180.00   0.0  0
 96I  CONST_15  N08  C07  C04  C03   180.00   0.0  0
 96I  CONST_16  C29  C28  C03  C04   180.00   0.0  0
 96I  CONST_17  N19  C07  C04  C05   180.00   0.0  0
 96I  CONST_18  C28  C03  C04  C05   180.00   0.0  0
 96I  CONST_19  C02  C03  C04  C07   180.00   0.0  0
 96I  CONST_20  C09  C13  C14  C15   180.00   0.0  0
 96I  CONST_21  N08  C07  N19  C20   180.00   0.0  0
 96I  CONST_22  C02  C03  C28  C20   180.00   0.0  0
 96I  CONST_23  C17  C18  C13  C09   180.00   0.0  0
 96I  CONST_26  H5   C15  C14  C13   180.00   0.0  0
 96I  CONST_27  H10  C17  C18  C13   180.00   0.0  0
 96I  CONST_28  H6   C16  C15  C14   180.00   0.0  0
 96I  CONST_29  H11  C18  C13  C14   180.00   0.0  0
 96I  CONST_30  H10  C17  C16  C15   180.00   0.0  0
 96I  CONST_31  H4   C14  C15  C16   180.00   0.0  0
 96I  CONST_32  H11  C18  C17  C16   180.00   0.0  0
 96I  CONST_33  H5   C15  C16  C17   180.00   0.0  0
 96I  CONST_34  H6   C16  C17  C18   180.00   0.0  0
 96I  CONST_35  H4   C14  C13  C18   180.00   0.0  0
 96I  CONST_36  C09  N08  C07  C04   180.00   0.0  0
 96I  CONST_37  N19  C07  N08  C09     0.00   0.0  0
 96I  CONST_38  H21  N08  C07  C04     0.00   0.0  0
 96I  CONST_39  H21  N08  C07  N19   180.00   0.0  0
 96I  CONST_40  H22  N11  C10  C09   180.00   0.0  0
 96I  CONST_41  H23  N11  C10  C09     0.00   0.0  0
 96I  CONST_42  H22  N11  C10  O12     0.00   0.0  0
 96I  CONST_43  H23  N11  C10  O12   180.00   0.0  0
 96I  Var_01    C23  C22  N21  C20  -101.29  30.0  1
 96I  Var_02    C26  C27  N21  C20   140.14  30.0  1
 96I  Var_03    N19  C20  N21  C22     8.87  30.0  3
 96I  Var_04    C28  C20  N21  C22  -170.53  30.0  3
 96I  Var_05    C26  C27  N21  C22   -25.63  30.0  1
 96I  Var_06    C27  N21  C22  C23    64.80  30.0  1
 96I  Var_07    N21  C22  C23  C24   -33.73  30.0  1
 96I  Var_08    N21  C27  C26  C24   -38.51  30.0  1
 96I  Var_09    N19  C20  N21  C27  -155.90  30.0  3
 96I  Var_10    C28  C20  N21  C27    24.70  30.0  3
 96I  Var_11    H12  C22  N21  C20   138.57  30.0  1
 96I  Var_12    H13  C22  N21  C20    22.80  30.0  1
 96I  Var_13    H19  C27  N21  C20    21.77  30.0  1
 96I  Var_14    H20  C27  N21  C20   -96.89  30.0  1
 96I  Var_15    H19  C27  N21  C22  -144.00  30.0  1
 96I  Var_16    H20  C27  N21  C22    97.34  30.0  1
 96I  Var_17    H12  C22  C23  C24    84.38  30.0  1
 96I  Var_18    H13  C22  C23  C24  -156.84  30.0  1
 96I  Var_19    H19  C27  C26  C24    80.09  30.0  1
 96I  Var_20    H20  C27  C26  C24  -162.07  30.0  1
 96I  Var_21    H12  C22  N21  C27   -55.34  30.0  1
 96I  Var_22    H13  C22  N21  C27  -171.10  30.0  1
 96I  Var_23    H14  C23  C22  N21  -153.50  30.0  1
 96I  Var_24    H15  C23  C22  N21    89.10  30.0  1
 96I  Var_25    H17  C26  C27  N21  -159.83  30.0  1
 96I  Var_26    H18  C26  C27  N21    83.47  30.0  1
 96I  Var_27    C04  C03  C02  C01   -85.27  30.0  2
 96I  Var_28    C28  C03  C02  C01    91.23  30.0  2
 96I  Var_29    H7   C02  C03  C04    36.09  30.0  2
 96I  Var_30    H8   C02  C03  C04   152.62  30.0  2
 96I  Var_31    H7   C02  C03  C28  -147.40  30.0  2
 96I  Var_32    H8   C02  C03  C28   -30.88  30.0  2
 96I  Var_33    H1   C01  C02  C03  -178.63  30.0  3
 96I  Var_34    H2   C01  C02  C03   -58.99  30.0  3
 96I  Var_35    H3   C01  C02  C03    61.76  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
 96I  chir_01  C09  C13  C10  N08  positiv
 96I  chir_02  C24  C23  N25  C26  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
 96I  plan-1  C03  0.020
 96I  plan-1  C04  0.020
 96I  plan-1  C05  0.020
 96I  plan-1  C07  0.020
 96I  plan-1  C20  0.020
 96I  plan-1  C02  0.020
 96I  plan-1  C28  0.020
 96I  plan-1  C29  0.020
 96I  plan-1  N06  0.020
 96I  plan-1  N08  0.020
 96I  plan-1  N19  0.020
 96I  plan-1  N21  0.020
 96I  plan-1  N30  0.020
 96I  plan-2  C13  0.020
 96I  plan-2  C14  0.020
 96I  plan-2  C15  0.020
 96I  plan-2  C16  0.020
 96I  plan-2  C09  0.020
 96I  plan-2  C17  0.020
 96I  plan-2  C18  0.020
 96I  plan-2  H4   0.020
 96I  plan-2  H5   0.020
 96I  plan-2  H6   0.020
 96I  plan-2  H10  0.020
 96I  plan-2  H11  0.020
 96I  plan-3  C10  0.020
 96I  plan-3  C09  0.020
 96I  plan-3  O12  0.020
 96I  plan-3  H22  0.020
 96I  plan-3  H23  0.020
 96I  plan-3  N11  0.020
 96I  plan-4  C07  0.020
 96I  plan-4  C09  0.020
 96I  plan-4  N08  0.020
 96I  plan-4  H21  0.020

