# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 10:00:44 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 4-cyano-N-(2-cyclohexen-1-yl-4-piperidin-4-yl-phenyl)-1H-imidazole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc(cc1C2=CCCCC2)C3CCNCC3)c4[nH]cc(n4)C#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
 KRJ  KRJ  4-cyano-N-(2-cyclohexen-1-yl-4-piperidin-4-yl-phenyl)-1H-imidazole-2-carboxamide  ligand  53  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 OK
;

data_comp_KRJ
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
 KRJ  N01   N  NS    0  -0.243  -6.8539   1.5704  -0.3497
 KRJ  C02   C  CSP   0   0.001  -6.1302   0.6770  -0.2744
 KRJ  C03   C  CR5   0   0.099  -5.2421  -0.4229  -0.1859
 KRJ  C04   C  CR15  0  -0.002  -5.5732  -1.7583  -0.1229
 KRJ  N05   N  NR15  0  -0.592  -4.3941  -2.4009  -0.0509
 KRJ  C06   C  CR5   0   0.365  -3.4099  -1.4732  -0.0709
 KRJ  N07   N  N     0  -0.428  -3.8918  -0.2626  -0.1520
 KRJ  C08   C  C     0   0.497  -1.9754  -1.8391  -0.0087
 KRJ  O09   O  O     0  -0.457  -1.6360  -3.0070   0.0744
 KRJ  N10   N  NH1   0  -0.755  -1.1820  -0.7554  -0.0575
 KRJ  C11   C  CR6   0   0.305   0.2117  -0.6522  -0.0233
 KRJ  C12   C  CR16  0  -0.292   1.0649  -1.7531   0.0605
 KRJ  C13   C  CR16  0  -0.328   2.4365  -1.5659   0.1040
 KRJ  C14   C  CR6   0   0.216   3.0049  -0.2951   0.0763
 KRJ  C15   C  CR16  0  -0.390   2.1392   0.7895   0.0011
 KRJ  C16   C  CR6   0   0.036   0.7580   0.6409  -0.0629
 KRJ  C17   C  C     0  -0.017  -0.1139   1.8415  -0.1376
 KRJ  C18   C  C1    0  -0.257  -0.8118   2.1199  -1.2425
 KRJ  C19   C  CH2   0  -0.462  -1.7789   3.2580  -1.3546
 KRJ  C20   C  CH2   0  -0.447  -2.1541   3.8171   0.0118
 KRJ  C21   C  CH2   0  -0.443  -0.9054   4.0203   0.8594
 KRJ  C22   C  CH2   0  -0.479  -0.1884   2.6969   1.1002
 KRJ  C23   C  CH1   0  -0.341   4.4971  -0.0948   0.1068
 KRJ  C24   C  CH2   0  -0.421   5.1797  -0.6690  -1.1393
 KRJ  C25   C  CH2   0  -0.317   6.6914  -0.4629  -1.0712
 KRJ  N26   N  NH1   0  -0.575   7.3050  -0.9849   0.1395
 KRJ  C27   C  CH2   0  -0.318   6.6604  -0.4681   1.3363
 KRJ  C28   C  CH2   0  -0.422   5.1473  -0.6766   1.3657
 KRJ  HN05  H  HNR5  0   0.443  -4.2676  -3.4023   0.0034
 KRJ  H04   H  HCR5  0   0.328  -6.5239  -2.2633  -0.1252
 KRJ  HN10  H  HNH1  0   0.432  -1.6706   0.1293  -0.1462
 KRJ  H12   H  HCR6  0   0.276   0.6693  -2.7556   0.0916
 KRJ  H13   H  HCR6  0   0.248   3.0709  -2.4425   0.1605
 KRJ  H15   H  HCR6  0   0.245   2.5481   1.7942  -0.0214
 KRJ  H18   H  H     0   0.248  -0.6938   1.4834  -2.1152
 KRJ  H19   H  HCH2  0   0.237  -1.3454   4.0461  -1.9811
 KRJ  H19A  H  HCH2  0   0.242  -2.6708   2.9172  -1.8874
 KRJ  H20   H  HCH2  0   0.234  -2.6995   4.7559  -0.1026
 KRJ  H20A  H  HCH2  0   0.220  -2.8292   3.1178   0.5155
 KRJ  H21   H  HCH2  0   0.222  -0.2308   4.7115   0.3445
 KRJ  H21A  H  HCH2  0   0.235  -1.1550   4.4829   1.8163
 KRJ  H22   H  HCH2  0   0.243  -0.6885   2.1278   1.8927
 KRJ  H22A  H  HCH2  0   0.249   0.8255   2.8780   1.4703
 KRJ  H23   H  HCH1  0   0.234   4.6831   0.9867   0.1134
 KRJ  H24   H  HCH2  0   0.217   4.9636  -1.7401  -1.2217
 KRJ  H24A  H  HCH2  0   0.231   4.7765  -0.1974  -2.0397
 KRJ  H25   H  HCH2  0   0.235   7.1738  -0.9240  -1.9358
 KRJ  H25A  H  HCH2  0   0.215   6.9101   0.6093  -1.1291
 KRJ  HN26  H  HNH1  0   0.337   7.2222  -1.9956   0.1362
 KRJ  H27   H  HCH2  0   0.235   7.1213  -0.9319   2.2110
 KRJ  H27A  H  HCH2  0   0.215   6.8762   0.6042   1.4035
 KRJ  H28   H  HCH2  0   0.232   4.7211  -0.2113   2.2586
 KRJ  H28A  H  HCH2  0   0.216   4.9343  -1.7489   1.4377

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
 KRJ  N01   C02   triple    1.152  0.020  1.152
 KRJ  C02   C03   single    1.417  0.020  1.417
 KRJ  C03   N07   aromatic  1.360  0.020  1.360
 KRJ  C03   C04   aromatic  1.377  0.020  1.377
 KRJ  H04   C04   single    0.930  0.020  1.080
 KRJ  C04   N05   aromatic  1.345  0.020  1.345
 KRJ  C06   N05   aromatic  1.353  0.020  1.353
 KRJ  N05   HN05  single    0.860  0.020  1.020
 KRJ  N07   C06   aromatic  1.305  0.020  1.305
 KRJ  C06   C08   single    1.482  0.020  1.482
 KRJ  N10   C08   single    1.344  0.020  1.344
 KRJ  C08   O09   double    1.219  0.020  1.219
 KRJ  HN10  N10   single    0.860  0.020  1.020
 KRJ  N10   C11   single    1.398  0.020  1.398
 KRJ  C16   C11   aromatic  1.404  0.020  1.404
 KRJ  C11   C12   aromatic  1.395  0.020  1.395
 KRJ  C12   H12   single    0.930  0.020  1.080
 KRJ  C12   C13   aromatic  1.385  0.020  1.385
 KRJ  C14   C13   aromatic  1.392  0.020  1.392
 KRJ  C13   H13   single    0.930  0.020  1.080
 KRJ  C15   C14   aromatic  1.390  0.020  1.390
 KRJ  C14   C23   single    1.506  0.020  1.506
 KRJ  C16   C15   aromatic  1.391  0.020  1.391
 KRJ  H15   C15   single    0.930  0.020  1.080
 KRJ  C17   C16   single    1.486  0.020  1.486
 KRJ  C22   C17   single    1.506  0.020  1.506
 KRJ  C18   C17   double    1.336  0.020  1.336
 KRJ  C19   C18   single    1.498  0.020  1.498
 KRJ  C18   H18   single    0.930  0.020  1.080
 KRJ  C20   C19   single    1.523  0.020  1.523
 KRJ  H19A  C19   single    0.970  0.020  1.090
 KRJ  H19   C19   single    0.970  0.020  1.090
 KRJ  H20A  C20   single    0.970  0.020  1.090
 KRJ  C20   H20   single    0.970  0.020  1.090
 KRJ  C20   C21   single    1.523  0.020  1.523
 KRJ  H21A  C21   single    0.970  0.020  1.090
 KRJ  H21   C21   single    0.970  0.020  1.090
 KRJ  C21   C22   single    1.524  0.020  1.524
 KRJ  C22   H22A  single    0.970  0.020  1.090
 KRJ  C22   H22   single    0.970  0.020  1.090
 KRJ  C28   C23   single    1.532  0.020  1.532
 KRJ  C23   C24   single    1.532  0.020  1.532
 KRJ  C23   H23   single    0.970  0.020  1.090
 KRJ  H24   C24   single    0.970  0.020  1.090
 KRJ  C24   C25   single    1.527  0.020  1.527
 KRJ  C24   H24A  single    0.970  0.020  1.090
 KRJ  H25A  C25   single    0.970  0.020  1.090
 KRJ  C25   H25   single    0.970  0.020  1.090
 KRJ  C25   N26   single    1.454  0.020  1.454
 KRJ  C27   N26   single    1.454  0.020  1.454
 KRJ  N26   HN26  single    0.890  0.020  1.040
 KRJ  H27   C27   single    0.970  0.020  1.090
 KRJ  C28   C27   single    1.528  0.020  1.528
 KRJ  C27   H27A  single    0.970  0.020  1.090
 KRJ  H28   C28   single    0.970  0.020  1.090
 KRJ  C28   H28A  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
 KRJ  C03   C02  N01  180.00  3.000
 KRJ  N07   C03  C04  110.59  3.000
 KRJ  C04   C03  C02  127.23  3.000
 KRJ  N07   C03  C02  122.18  3.000
 KRJ  H04   C04  N05  123.39  3.000
 KRJ  N05   C04  C03  104.77  3.000
 KRJ  H04   C04  C03  131.84  3.000
 KRJ  HN05  N05  C06  126.10  3.000
 KRJ  HN05  N05  C04  125.87  3.000
 KRJ  C06   N05  C04  108.02  3.000
 KRJ  C08   C06  N07  126.08  3.000
 KRJ  C08   C06  N05  122.30  3.000
 KRJ  N07   C06  N05  111.61  3.000
 KRJ  C06   N07  C03  104.99  3.000
 KRJ  N10   C08  O09  127.64  3.000
 KRJ  O09   C08  C06  120.60  3.000
 KRJ  N10   C08  C06  111.77  3.000
 KRJ  HN10  N10  C11  114.71  3.000
 KRJ  C11   N10  C08  130.33  3.000
 KRJ  HN10  N10  C08  114.96  3.000
 KRJ  C16   C11  C12  119.36  3.000
 KRJ  C12   C11  N10  123.56  3.000
 KRJ  C16   C11  N10  117.07  3.000
 KRJ  H12   C12  C13  119.22  3.000
 KRJ  C13   C12  C11  120.05  3.000
 KRJ  H12   C12  C11  120.73  3.000
 KRJ  H13   C13  C14  120.02  3.000
 KRJ  H13   C13  C12  118.17  3.000
 KRJ  C14   C13  C12  121.80  3.000
 KRJ  C23   C14  C15  120.97  3.000
 KRJ  C23   C14  C13  121.70  3.000
 KRJ  C15   C14  C13  117.33  3.000
 KRJ  H15   C15  C16  118.18  3.000
 KRJ  H15   C15  C14  119.28  3.000
 KRJ  C16   C15  C14  122.53  3.000
 KRJ  C17   C16  C15  119.92  3.000
 KRJ  C17   C16  C11  121.15  3.000
 KRJ  C15   C16  C11  118.91  3.000
 KRJ  C22   C17  C18  122.37  3.000
 KRJ  C18   C17  C16  121.09  3.000
 KRJ  C22   C17  C16  116.52  3.000
 KRJ  H18   C18  C19  117.07  3.000
 KRJ  H18   C18  C17  119.04  3.000
 KRJ  C19   C18  C17  123.88  3.000
 KRJ  H19A  C19  H19  105.56  3.000
 KRJ  H19   C19  C20  110.25  3.000
 KRJ  H19A  C19  C20  110.52  3.000
 KRJ  H19   C19  C18  109.50  3.000
 KRJ  H19A  C19  C18  109.05  3.000
 KRJ  C20   C19  C18  111.77  3.000
 KRJ  H20A  C20  H20  106.82  3.000
 KRJ  H20   C20  C21  110.68  3.000
 KRJ  H20A  C20  C21  109.56  3.000
 KRJ  C21   C20  C19  110.26  3.000
 KRJ  H20   C20  C19  110.16  3.000
 KRJ  H20A  C20  C19  109.28  3.000
 KRJ  H21A  C21  H21  106.60  3.000
 KRJ  H21   C21  C22  109.43  3.000
 KRJ  H21A  C21  C22  109.70  3.000
 KRJ  C22   C21  C20  110.96  3.000
 KRJ  H21   C21  C20  109.13  3.000
 KRJ  H21A  C21  C20  110.91  3.000
 KRJ  H22A  C22  H22  105.31  3.000
 KRJ  H22   C22  C21  110.50  3.000
 KRJ  H22A  C22  C21  110.21  3.000
 KRJ  H22   C22  C17  108.77  3.000
 KRJ  H22A  C22  C17  109.03  3.000
 KRJ  C21   C22  C17  112.73  3.000
 KRJ  H23   C23  C28  107.31  3.000
 KRJ  H23   C23  C24  107.38  3.000
 KRJ  C28   C23  C24  109.69  3.000
 KRJ  H23   C23  C14  107.40  3.000
 KRJ  C24   C23  C14  112.03  3.000
 KRJ  C28   C23  C14  112.75  3.000
 KRJ  H24A  C24  H24  106.67  3.000
 KRJ  H24A  C24  C25  110.09  3.000
 KRJ  H24   C24  C25  109.30  3.000
 KRJ  H24A  C24  C23  110.11  3.000
 KRJ  C25   C24  C23  110.74  3.000
 KRJ  H24   C24  C23  109.85  3.000
 KRJ  H25A  C25  H25  106.44  3.000
 KRJ  H25   C25  N26  108.74  3.000
 KRJ  H25A  C25  N26  108.12  3.000
 KRJ  N26   C25  C24  113.97  3.000
 KRJ  H25   C25  C24  110.18  3.000
 KRJ  H25A  C25  C24  109.10  3.000
 KRJ  HN26  N26  C27  108.71  3.000
 KRJ  HN26  N26  C25  108.70  3.000
 KRJ  C27   N26  C25  111.75  3.000
 KRJ  H27A  C27  H27  106.46  3.000
 KRJ  H27A  C27  C28  109.11  3.000
 KRJ  H27   C27  C28  110.16  3.000
 KRJ  H27A  C27  N26  108.11  3.000
 KRJ  C28   C27  N26  113.98  3.000
 KRJ  H27   C27  N26  108.74  3.000
 KRJ  H28A  C28  H28  106.68  3.000
 KRJ  H28A  C28  C27  109.11  3.000
 KRJ  H28   C28  C27  110.10  3.000
 KRJ  H28A  C28  C23  110.08  3.000
 KRJ  H28   C28  C23  110.12  3.000
 KRJ  C27   C28  C23  110.66  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
 KRJ  CONST_01  N05   C06  N07  C03    0.00   0.0  0
 KRJ  CONST_02  C06   N05  C04  C03    0.00   0.0  0
 KRJ  CONST_03  C06   N07  C03  C04    0.00   0.0  0
 KRJ  CONST_04  N07   C06  N05  C04    0.00   0.0  0
 KRJ  CONST_05  N07   C03  C04  N05    0.00   0.0  0
 KRJ  CONST_06  C14   C15  C16  C11    0.00   0.0  0
 KRJ  CONST_07  C14   C13  C12  C11    0.00   0.0  0
 KRJ  CONST_08  C15   C16  C11  C12    0.00   0.0  0
 KRJ  CONST_09  C15   C14  C13  C12    0.00   0.0  0
 KRJ  CONST_10  C16   C11  C12  C13    0.00   0.0  0
 KRJ  CONST_11  C16   C15  C14  C13    0.00   0.0  0
 KRJ  CONST_12  C17   C16  C11  C12  180.00   0.0  0
 KRJ  CONST_13  C23   C14  C13  C12  180.00   0.0  0
 KRJ  CONST_14  C17   C16  C15  C14  180.00   0.0  0
 KRJ  CONST_15  C23   C14  C15  C16  180.00   0.0  0
 KRJ  CONST_16  C06   N07  C03  C02  180.00   0.0  0
 KRJ  CONST_17  N05   C04  C03  C02  180.00   0.0  0
 KRJ  CONST_18  C08   C06  N07  C03  180.00   0.0  0
 KRJ  CONST_19  C08   C06  N05  C04  180.00   0.0  0
 KRJ  CONST_20  C15   C16  C11  N10  180.00   0.0  0
 KRJ  CONST_21  C17   C16  C11  N10    0.00   0.0  0
 KRJ  CONST_22  C13   C12  C11  N10  180.00   0.0  0
 KRJ  CONST_23  HN05  N05  C04  C03  180.00   0.0  0
 KRJ  CONST_24  H04   C04  N05  C06  180.00   0.0  0
 KRJ  CONST_25  H15   C15  C16  C11  180.00   0.0  0
 KRJ  CONST_26  H13   C13  C12  C11  180.00   0.0  0
 KRJ  CONST_27  H12   C12  C13  C14  180.00   0.0  0
 KRJ  CONST_28  C11   N10  C08  C06  180.00   0.0  0
 KRJ  CONST_29  C16   C11  N10  C08  180.00   0.0  0
 KRJ  CONST_30  C12   C11  N10  C08    0.00   0.0  0
 KRJ  CONST_31  HN10  N10  C11  C12  180.00   0.0  0
 KRJ  CONST_32  C11   N10  C08  O09    0.00   0.0  0
 KRJ  Var_01    C22   C17  C16  C11  109.01  30.0  1
 KRJ  Var_02    C21   C22  C17  C16  170.14  30.0  1
 KRJ  Var_03    C19   C18  C17  C16  175.68  30.0  1
 KRJ  Var_04    C20   C21  C22  C17   42.90  30.0  1
 KRJ  Var_05    C20   C19  C18  C17  -15.39  30.0  1
 KRJ  Var_06    C21   C20  C19  C18   46.64  30.0  1
 KRJ  Var_07    C22   C21  C20  C19  -61.59  30.0  1
 KRJ  Var_08    N26   C27  C28  C23  -54.49  30.0  1
 KRJ  Var_09    N26   C25  C24  C23   54.32  30.0  1
 KRJ  Var_10    C27   N26  C25  C24  -53.51  30.0  1
 KRJ  Var_11    C28   C27  N26  C25   53.61  30.0  1
 KRJ  Var_12    N10   C08  C06  N05  179.32  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
 KRJ  chir_01  C23  C14  C28  C24  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
 KRJ  plan-1  N01   0.020
 KRJ  plan-1  C02   0.020
 KRJ  plan-1  C03   0.020
 KRJ  plan-1  C04   0.020
 KRJ  plan-1  N05   0.020
 KRJ  plan-1  C06   0.020
 KRJ  plan-1  N07   0.020
 KRJ  plan-1  C08   0.020
 KRJ  plan-1  HN05  0.020
 KRJ  plan-1  H04   0.020
 KRJ  plan-2  N10   0.020
 KRJ  plan-2  C11   0.020
 KRJ  plan-2  C12   0.020
 KRJ  plan-2  C13   0.020
 KRJ  plan-2  C14   0.020
 KRJ  plan-2  C15   0.020
 KRJ  plan-2  C16   0.020
 KRJ  plan-2  C17   0.020
 KRJ  plan-2  C23   0.020
 KRJ  plan-2  H12   0.020
 KRJ  plan-2  H13   0.020
 KRJ  plan-2  H15   0.020
 KRJ  plan-3  C06   0.020
 KRJ  plan-3  C08   0.020
 KRJ  plan-3  O09   0.020
 KRJ  plan-3  N10   0.020
 KRJ  plan-3  C11   0.020
 KRJ  plan-3  HN10  0.020

