# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:47:27 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-[(cis-4-aminocyclohexyl)amino]-3-(1H-benzimidazol-2-yl)pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC[C@H](CC1)NC2=C(C(=O)NC=C2)c3[nH]c4ccccc4n3
#
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
 66P  66P  4-[(cis-4-aminocyclohexyl)amino]-3-(1H-benzimidazol-2-yl)pyridin-2(1H)-one  ligand  45  24  .  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_66P
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
 66P  C2   C  CR6   0   0.494  -1.0480  -1.5633  -0.2604
 66P  C3   C  CR16  0  -0.461  -1.9410  -2.6795  -0.2342
 66P  N4   N  N     0  -0.592   0.9856   0.5619  -0.2455
 66P  C5   C  CH1   0  -0.112  -2.8776   0.0317  -0.8103
 66P  C7   C  CH2   0  -0.460  -2.4264   2.5318  -0.7303
 66P  C9   C  CH2   0  -0.436  -3.2498   1.3603   1.3156
 66P  C10  C  CH2   0  -0.441  -3.7072   0.1781   0.4692
 66P  C11  C  CR5   0   0.579   1.2837  -0.7080  -0.0278
 66P  C12  C  CR56  0   0.309   3.2197   0.3469   0.0757
 66P  C13  C  CR56  0   0.196   2.1712   1.2447  -0.1881
 66P  C15  C  CR16  0  -0.272   3.7568   3.0200  -0.2397
 66P  C    C  CR6   0   0.539   0.8095  -3.1212   0.2567
 66P  C1   C  CR6   0  -0.393   0.3290  -1.7967  -0.0082
 66P  N1   N  NH1   0  -0.704  -1.5022  -0.3420  -0.5302
 66P  C8   C  CH1   0  -0.051  -3.2816   2.6633   0.5242
 66P  N2   N  NH2   0  -0.804  -2.7878   3.7556   1.3503
 66P  C6   C  CH2   0  -0.457  -2.8702   1.3484  -1.5869
 66P  C4   C  CR16  0   0.051  -1.4529  -3.9128   0.0178
 66P  N    N  NR16  0  -0.672  -0.1429  -4.1199   0.2512
 66P  C14  C  CR16  0  -0.341   2.4405   2.6029  -0.3480
 66P  C16  C  CR16  0  -0.282   4.7920   2.1115   0.0226
 66P  C17  C  CR16  0  -0.321   4.5418   0.7578   0.1859
 66P  N3   N  NR15  0  -0.725   2.6189  -0.8770   0.1713
 66P  H1   H  HCR6  0   0.289  -2.9977  -2.5616  -0.4121
 66P  H3   H  HCH1  0   0.261  -3.3294  -0.7341  -1.4468
 66P  H4   H  HCH2  0   0.240  -2.4866   3.4483  -1.3244
 66P  H5   H  HCH2  0   0.218  -1.3755   2.4344  -0.4324
 66P  H6   H  HCH2  0   0.233  -3.8906   1.4441   2.1983
 66P  H7   H  HCH2  0   0.214  -2.2323   1.1923   1.6853
 66P  H8   H  HCH2  0   0.228  -4.7541   0.3128   0.1792
 66P  H9   H  HCH2  0   0.241  -3.6686  -0.7431   1.0558
 66P  H10  H  HCR6  0   0.249   3.9939   4.0691  -0.3602
 66P  H12  H  HNH1  0   0.438  -0.7918   0.3914  -0.5141
 66P  H13  H  HCH1  0   0.187  -4.3229   2.8253   0.1960
 66P  H14  H  HNH2  0   0.340  -2.8356   4.6217   0.8267
 66P  H15  H  HNH2  0   0.340  -3.4084   3.8835   2.1408
 66P  H17  H  HCH2  0   0.247  -2.2328   1.2542  -2.4692
 66P  H18  H  HCH2  0   0.241  -3.8836   1.5276  -1.9562
 66P  H19  H  HCR6  0   0.316  -2.0847  -4.7880   0.0457
 66P  H20  H  HCR6  0   0.250   1.6429   3.3068  -0.5500
 66P  H21  H  HCR6  0   0.252   5.8088   2.4744   0.0988
 66P  H22  H  HCR6  0   0.262   5.3418   0.0573   0.3875
 66P  H2   H  HNR6  0   0.421   0.1820  -5.0576   0.4381
 66P  H11  H  HNR5  0   0.420   3.0314  -1.7802   0.3617
 66P  O    O  O     0  -0.531   1.9853  -3.4346   0.4844

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
 66P  C16  C15  aromatic  1.402  0.020  1.402
 66P  C16  C17  aromatic  1.386  0.020  1.386
 66P  C15  C14  aromatic  1.385  0.020  1.385
 66P  C17  C12  aromatic  1.389  0.020  1.389
 66P  C14  C13  aromatic  1.394  0.020  1.394
 66P  C12  C13  aromatic  1.405  0.020  1.405
 66P  C12  N3   aromatic  1.367  0.020  1.367
 66P  C13  N4   aromatic  1.369  0.020  1.369
 66P  N3   C11  aromatic  1.360  0.020  1.360
 66P  N4   C11  aromatic  1.322  0.020  1.322
 66P  C11  C1   single    1.448  0.020  1.448
 66P  O    C    double    1.238  0.020  1.238
 66P  C1   C    single    1.434  0.020  1.434
 66P  C1   C2   double    1.419  0.020  1.419
 66P  C    N    single    1.380  0.020  1.380
 66P  C10  C9   single    1.524  0.020  1.524
 66P  C10  C5   single    1.532  0.020  1.532
 66P  C9   C8   single    1.525  0.020  1.525
 66P  N1   C2   single    1.331  0.020  1.331
 66P  N1   C5   single    1.453  0.020  1.453
 66P  C2   C3   single    1.430  0.020  1.430
 66P  N    C4   single    1.347  0.020  1.347
 66P  C5   C6   single    1.529  0.020  1.529
 66P  C3   C4   double    1.350  0.020  1.350
 66P  C8   N2   single    1.456  0.020  1.456
 66P  C8   C7   single    1.524  0.020  1.524
 66P  C6   C7   single    1.527  0.020  1.527
 66P  C3   H1   single    0.930  0.020  1.080
 66P  C5   H3   single    0.970  0.020  1.090
 66P  C7   H4   single    0.970  0.020  1.090
 66P  C7   H5   single    0.970  0.020  1.090
 66P  C9   H6   single    0.970  0.020  1.090
 66P  C9   H7   single    0.970  0.020  1.090
 66P  C10  H8   single    0.970  0.020  1.090
 66P  C10  H9   single    0.970  0.020  1.090
 66P  C15  H10  single    0.930  0.020  1.080
 66P  N1   H12  single    0.860  0.020  1.020
 66P  C8   H13  single    0.970  0.020  1.090
 66P  N2   H14  single    0.890  0.020  1.040
 66P  N2   H15  single    0.890  0.020  1.040
 66P  C6   H17  single    0.970  0.020  1.090
 66P  C6   H18  single    0.970  0.020  1.090
 66P  C4   H19  single    0.930  0.020  1.080
 66P  C14  H20  single    0.930  0.020  1.080
 66P  C16  H21  single    0.930  0.020  1.080
 66P  C17  H22  single    0.930  0.020  1.080
 66P  N    H2   single    0.860  0.020  1.020
 66P  N3   H11  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
 66P  N1   C2   C1   121.21  3.000
 66P  N1   C2   C3   120.46  3.000
 66P  C1   C2   C3   118.32  3.000
 66P  H1   C3   C4   119.02  3.000
 66P  H1   C3   C2   121.59  3.000
 66P  C4   C3   C2   119.39  3.000
 66P  C13  N4   C11  106.06  3.000
 66P  H3   C5   C6   108.03  3.000
 66P  H3   C5   N1   108.86  3.000
 66P  C6   C5   N1   108.36  3.000
 66P  H3   C5   C10  109.23  3.000
 66P  C6   C5   C10  110.16  3.000
 66P  N1   C5   C10  112.11  3.000
 66P  H5   C7   H4   105.95  3.000
 66P  H5   C7   C6   111.23  3.000
 66P  H4   C7   C6   109.18  3.000
 66P  H5   C7   C8   108.78  3.000
 66P  H4   C7   C8   110.12  3.000
 66P  C6   C7   C8   111.44  3.000
 66P  H7   C9   H6   106.47  3.000
 66P  H7   C9   C8   109.00  3.000
 66P  H6   C9   C8   109.94  3.000
 66P  H7   C9   C10  110.32  3.000
 66P  H6   C9   C10  109.38  3.000
 66P  C8   C9   C10  111.61  3.000
 66P  H9   C10  H8   106.25  3.000
 66P  H9   C10  C9   110.19  3.000
 66P  H8   C10  C9   109.80  3.000
 66P  H9   C10  C5   110.40  3.000
 66P  H8   C10  C5   107.96  3.000
 66P  C9   C10  C5   112.05  3.000
 66P  N3   C11  C1   123.48  3.000
 66P  C1   C11  N4   125.13  3.000
 66P  N3   C11  N4   111.38  3.000
 66P  N3   C12  C17  132.67  3.000
 66P  N3   C12  C13  104.91  3.000
 66P  C17  C12  C13  122.42  3.000
 66P  C14  C13  C12  119.99  3.000
 66P  C12  C13  N4   109.59  3.000
 66P  C14  C13  N4   130.42  3.000
 66P  H10  C15  C16  119.16  3.000
 66P  H10  C15  C14  119.43  3.000
 66P  C16  C15  C14  121.42  3.000
 66P  N    C    C1   115.89  3.000
 66P  N    C    O    118.23  3.000
 66P  C1   C    O    125.88  3.000
 66P  C    C1   C11  118.43  3.000
 66P  C    C1   C2   120.66  3.000
 66P  C11  C1   C2   120.90  3.000
 66P  H12  N1   C5   118.49  3.000
 66P  H12  N1   C2   114.73  3.000
 66P  C5   N1   C2   126.76  3.000
 66P  H13  C8   N2   112.25  3.000
 66P  H13  C8   C9   107.42  3.000
 66P  N2   C8   C9   109.85  3.000
 66P  H13  C8   C7   107.30  3.000
 66P  N2   C8   C7   109.97  3.000
 66P  C9   C8   C7   109.99  3.000
 66P  H15  N2   H14  105.45  3.000
 66P  H15  N2   C8   109.26  3.000
 66P  H14  N2   C8   109.40  3.000
 66P  H18  C6   H17  106.39  3.000
 66P  H18  C6   C7   109.39  3.000
 66P  H17  C6   C7   110.51  3.000
 66P  H18  C6   C5   107.95  3.000
 66P  H17  C6   C5   109.80  3.000
 66P  C7   C6   C5   112.58  3.000
 66P  H19  C4   N    116.11  3.000
 66P  H19  C4   C3   122.25  3.000
 66P  N    C4   C3   121.64  3.000
 66P  H2   N    C4   119.20  3.000
 66P  H2   N    C    116.69  3.000
 66P  C4   N    C    124.11  3.000
 66P  H20  C14  C15  121.26  3.000
 66P  H20  C14  C13  120.83  3.000
 66P  C15  C14  C13  117.91  3.000
 66P  H21  C16  C17  119.26  3.000
 66P  H21  C16  C15  119.31  3.000
 66P  C17  C16  C15  121.43  3.000
 66P  H22  C17  C16  121.37  3.000
 66P  H22  C17  C12  121.80  3.000
 66P  C16  C17  C12  116.83  3.000
 66P  H11  N3   C12  129.33  3.000
 66P  H11  N3   C11  122.61  3.000
 66P  C12  N3   C11  108.06  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
 66P  CONST_01  C15  C14  C13  N4    180.00   0.0  0
 66P  CONST_02  C17  C12  C13  N4    180.00   0.0  0
 66P  CONST_03  N3   C12  C13  N4      0.00   0.0  0
 66P  CONST_04  C12  N3   C11  N4      0.00   0.0  0
 66P  CONST_05  C17  C12  N3   C11   180.00   0.0  0
 66P  CONST_06  C13  C12  N3   C11     0.00   0.0  0
 66P  CONST_07  C14  C13  N4   C11   180.00   0.0  0
 66P  CONST_08  C12  C13  N4   C11     0.00   0.0  0
 66P  CONST_09  C15  C16  C17  C12     0.00   0.0  0
 66P  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 66P  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 66P  CONST_12  C16  C17  C12  C13     0.00   0.0  0
 66P  CONST_13  N3   C11  N4   C13     0.00   0.0  0
 66P  CONST_14  C17  C16  C15  C14     0.00   0.0  0
 66P  CONST_15  C17  C12  C13  C14     0.00   0.0  0
 66P  CONST_16  N3   C12  C13  C14   180.00   0.0  0
 66P  CONST_17  N3   C12  C17  C16   180.00   0.0  0
 66P  CONST_18  C1   C11  N3   C12   180.00   0.0  0
 66P  CONST_19  C1   C11  N4   C13   180.00   0.0  0
 66P  CONST_20  C4   N    C    C1      0.00   0.0  0
 66P  CONST_21  C4   N    C    O     180.00   0.0  0
 66P  CONST_22  H20  C14  C13  N4      0.00   0.0  0
 66P  CONST_23  H11  N3   C11  N4    180.00   0.0  0
 66P  CONST_24  H21  C16  C17  C12   180.00   0.0  0
 66P  CONST_25  H10  C15  C14  C13   180.00   0.0  0
 66P  CONST_26  H22  C17  C12  C13   180.00   0.0  0
 66P  CONST_27  H2   N    C    C1    180.00   0.0  0
 66P  Var_01    N3   C11  C1   C2   -178.20  30.0  2
 66P  Var_02    C8   C9   C10  C5     56.24  30.0  1
 66P  Var_03    C8   C7   C6   C5    -55.49  30.0  1
 66P  Var_04    C5   N1   C2   C3      0.52  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
 66P  chir_01  C5  C10  N1  C6  positiv
 66P  chir_02  C8  N2   C7  C9  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
 66P  plan-1  C2   0.020
 66P  plan-1  C3   0.020
 66P  plan-1  C11  0.020
 66P  plan-1  C    0.020
 66P  plan-1  C1   0.020
 66P  plan-1  N1   0.020
 66P  plan-1  C4   0.020
 66P  plan-1  N    0.020
 66P  plan-1  H1   0.020
 66P  plan-1  H19  0.020
 66P  plan-1  H2   0.020
 66P  plan-1  O    0.020
 66P  plan-2  N4   0.020
 66P  plan-2  C11  0.020
 66P  plan-2  C12  0.020
 66P  plan-2  C13  0.020
 66P  plan-2  C15  0.020
 66P  plan-2  C1   0.020
 66P  plan-2  C14  0.020
 66P  plan-2  C16  0.020
 66P  plan-2  C17  0.020
 66P  plan-2  N3   0.020
 66P  plan-2  H10  0.020
 66P  plan-2  H20  0.020
 66P  plan-2  H21  0.020
 66P  plan-2  H22  0.020
 66P  plan-2  H11  0.020

