# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 09:45:53 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N~2~-(5-chloro-2-methoxyphenyl)-N-[trans-4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)cyclohexyl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cl)cc1NCC(=O)N[C@H]2CC[C@@H](CC2)N3C(=O)Nc4ccccc34
#
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
 K4E  K4E  N~2~-(5-chloro-2-methoxyphenyl)-N-[trans-4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)cyclohexyl]glycinamide  ligand  55  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K4E
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
 K4E  N1   N   NH1   0  -0.683  -3.9076   0.6219   0.1533
 K4E  C1   C   CR6   0   0.300  -5.1812   0.1850  -0.0966
 K4E  C2   C   CR16  0  -0.316  -5.4836  -1.1515  -0.3423
 K4E  C3   C   CR6   0  -0.050  -6.8029  -1.5429  -0.5487
 K4E  C4   C   CR16  0  -0.250  -7.8395  -0.6389  -0.5289
 K4E  C5   C   CR16  0  -0.390  -7.5434   0.7055  -0.2909
 K4E  C6   C   CR6   0   0.325  -6.2450   1.1215  -0.0736
 K4E  O1   O   O2    0  -0.476  -5.8707   2.3958   0.1671
 K4E  C7   C   CH3   0  -0.434  -6.8648   3.3997   0.1719
 K4E  CL1  CL  CL    0  -0.146  -7.1306  -3.2249  -0.8446
 K4E  C8   C   CH2   0  -0.411  -2.7778  -0.2269  -0.0818
 K4E  C9   C   C     0   0.539  -1.4913   0.5705   0.0627
 K4E  O2   O   O     0  -0.492  -1.4791   1.7886  -0.0457
 K4E  N2   N   NH1   0  -0.641  -0.4060  -0.1793   0.2855
 K4E  C10  C   CH1   0  -0.063   0.9554   0.3205   0.3090
 K4E  C11  C   CH2   0  -0.448   1.7425  -0.3793   1.4131
 K4E  C12  C   CH2   0  -0.444   3.1924   0.0906   1.4467
 K4E  C13  C   CH2   0  -0.437   1.6344   0.1339  -1.0479
 K4E  C14  C   CH2   0  -0.441   3.0859   0.6005  -1.0232
 K4E  C15  C   CH1   0  -0.075   3.8548  -0.1128   0.0858
 K4E  N3   N   NR5   0  -0.608   5.2663   0.2402   0.0977
 K4E  C16  C   CR5   0   0.663   5.7656   1.4951   0.3737
 K4E  O3   O   O     0  -0.505   5.1314   2.5022   0.6378
 K4E  N4   N   NR15  0  -0.749   7.1294   1.3836   0.2882
 K4E  C17  C   CR56  0   0.314   7.4972   0.0993  -0.0388
 K4E  C18  C   CR56  0   0.328   6.3095  -0.6307  -0.1623
 K4E  C19  C   CR16  0  -0.322   6.3338  -1.9733  -0.4938
 K4E  C20  C   CR16  0  -0.270   7.5780  -2.5666  -0.6962
 K4E  C21  C   CR16  0  -0.280   8.7563  -1.8375  -0.5704
 K4E  C22  C   CR16  0  -0.309   8.7327  -0.4853  -0.2371
 K4E  H1   H   HNH1  0   0.382  -3.7327   1.6034  -0.0009
 K4E  H2   H   HCR6  0   0.288  -4.6990  -1.8945  -0.3702
 K4E  H3   H   HCR6  0   0.271  -8.8618  -0.9486  -0.6926
 K4E  H4   H   HCR6  0   0.286  -8.3599   1.4144  -0.2787
 K4E  H5   H   HCH3  0   0.229  -7.3726   3.4725  -0.7934
 K4E  H6   H   HCH3  0   0.229  -7.6123   3.2274   0.9508
 K4E  H7   H   HCH3  0   0.261  -6.3566   4.3391   0.3735
 K4E  H8   H   HCH2  0   0.264  -2.7725  -1.0705   0.6151
 K4E  H9   H   HCH2  0   0.266  -2.7790  -0.6635  -1.0927
 K4E  H10  H   HNH1  0   0.401  -0.5239  -1.1806   0.3324
 K4E  H11  H   HCH1  0   0.249   0.9063   1.3876   0.5377
 K4E  H12  H   HCH2  0   0.252   1.2721  -0.1893   2.3796
 K4E  H13  H   HCH2  0   0.226   1.7098  -1.4630   1.2508
 K4E  H14  H   HCH2  0   0.240   3.2303   1.1462   1.7245
 K4E  H15  H   HCH2  0   0.248   3.7428  -0.4627   2.2105
 K4E  H16  H   HCH2  0   0.224   1.5920  -0.9258  -1.3233
 K4E  H17  H   HCH2  0   0.248   1.0826   0.6805  -1.8155
 K4E  H18  H   HCH2  0   0.247   3.5549   0.3952  -1.9877
 K4E  H19  H   HCH2  0   0.238   3.1271   1.6807  -0.8675
 K4E  H20  H   HCH1  0   0.257   3.8241  -1.1842  -0.1316
 K4E  H21  H   HNR5  0   0.417   7.7547   2.1564   0.4513
 K4E  H22  H   HCR6  0   0.271   5.4262  -2.5531  -0.5969
 K4E  H23  H   HCR6  0   0.256   7.6239  -3.6158  -0.9560
 K4E  H24  H   HCR6  0   0.256   9.7077  -2.3254  -0.7347
 K4E  H25  H   HCR6  0   0.268   9.6465   0.0853  -0.1362

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
 K4E  C13  C14  single    1.525  0.020  1.525
 K4E  C13  C10  single    1.529  0.020  1.529
 K4E  C14  C15  single    1.526  0.020  1.526
 K4E  O3   C16  double    1.219  0.020  1.219
 K4E  O2   C9   double    1.223  0.020  1.223
 K4E  C8   C9   single    1.520  0.020  1.520
 K4E  C8   N1   single    1.433  0.020  1.433
 K4E  C9   N2   single    1.338  0.020  1.338
 K4E  N1   C1   single    1.369  0.020  1.369
 K4E  C7   O1   single    1.413  0.020  1.413
 K4E  C10  N2   single    1.450  0.020  1.450
 K4E  C10  C11  single    1.526  0.020  1.526
 K4E  O1   C6   single    1.350  0.020  1.350
 K4E  C16  N4   single    1.371  0.020  1.371
 K4E  C16  N3   single    1.378  0.020  1.378
 K4E  N4   C17  single    1.375  0.020  1.375
 K4E  C15  N3   single    1.455  0.020  1.455
 K4E  C15  C12  single    1.527  0.020  1.527
 K4E  N3   C18  single    1.384  0.020  1.384
 K4E  C1   C6   aromatic  1.418  0.020  1.418
 K4E  C1   C2   aromatic  1.392  0.020  1.392
 K4E  C17  C18  aromatic  1.400  0.020  1.400
 K4E  C17  C22  aromatic  1.381  0.020  1.381
 K4E  C6   C5   aromatic  1.381  0.020  1.381
 K4E  C18  C19  aromatic  1.383  0.020  1.383
 K4E  C11  C12  single    1.524  0.020  1.524
 K4E  C22  C21  aromatic  1.393  0.020  1.393
 K4E  C19  C20  aromatic  1.393  0.020  1.393
 K4E  C2   C3   aromatic  1.392  0.020  1.392
 K4E  C21  C20  aromatic  1.391  0.020  1.391
 K4E  C5   C4   aromatic  1.397  0.020  1.397
 K4E  C3   C4   aromatic  1.375  0.020  1.375
 K4E  C3   CL1  single    1.739  0.020  1.739
 K4E  N1   H1   single    0.890  0.020  1.040
 K4E  C2   H2   single    0.930  0.020  1.080
 K4E  C4   H3   single    0.930  0.020  1.080
 K4E  C5   H4   single    0.930  0.020  1.080
 K4E  C7   H5   single    0.970  0.020  1.090
 K4E  C7   H6   single    0.970  0.020  1.090
 K4E  C7   H7   single    0.970  0.020  1.090
 K4E  C8   H8   single    0.970  0.020  1.090
 K4E  C8   H9   single    0.970  0.020  1.090
 K4E  N2   H10  single    0.860  0.020  1.020
 K4E  C10  H11  single    0.970  0.020  1.090
 K4E  C11  H12  single    0.970  0.020  1.090
 K4E  C11  H13  single    0.970  0.020  1.090
 K4E  C12  H14  single    0.970  0.020  1.090
 K4E  C12  H15  single    0.970  0.020  1.090
 K4E  C13  H16  single    0.970  0.020  1.090
 K4E  C13  H17  single    0.970  0.020  1.090
 K4E  C14  H18  single    0.970  0.020  1.090
 K4E  C14  H19  single    0.970  0.020  1.090
 K4E  C15  H20  single    0.970  0.020  1.090
 K4E  N4   H21  single    0.860  0.020  1.020
 K4E  C19  H22  single    0.930  0.020  1.080
 K4E  C20  H23  single    0.930  0.020  1.080
 K4E  C21  H24  single    0.930  0.020  1.080
 K4E  C22  H25  single    0.930  0.020  1.080

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
 K4E  H1   N1   C8   114.50  3.000
 K4E  H1   N1   C1   116.34  3.000
 K4E  C8   N1   C1   120.97  3.000
 K4E  C6   C1   C2   118.30  3.000
 K4E  C2   C1   N1   122.72  3.000
 K4E  C6   C1   N1   118.96  3.000
 K4E  H2   C2   C3   119.41  3.000
 K4E  H2   C2   C1   120.45  3.000
 K4E  C3   C2   C1   120.14  3.000
 K4E  CL1  C3   C4   119.74  3.000
 K4E  CL1  C3   C2   118.42  3.000
 K4E  C4   C3   C2   121.84  3.000
 K4E  H3   C4   C5   120.13  3.000
 K4E  H3   C4   C3   121.50  3.000
 K4E  C5   C4   C3   118.37  3.000
 K4E  H4   C5   C6   120.72  3.000
 K4E  H4   C5   C4   118.21  3.000
 K4E  C6   C5   C4   121.07  3.000
 K4E  O1   C6   C5   124.99  3.000
 K4E  C5   C6   C1   120.28  3.000
 K4E  O1   C6   C1   114.74  3.000
 K4E  C7   O1   C6   118.44  3.000
 K4E  H7   C7   H6   108.89  3.000
 K4E  H7   C7   H5   108.87  3.000
 K4E  H6   C7   H5   108.78  3.000
 K4E  H7   C7   O1   106.61  3.000
 K4E  H6   C7   O1   111.81  3.000
 K4E  H5   C7   O1   111.79  3.000
 K4E  H9   C8   H8   106.20  3.000
 K4E  H9   C8   C9   107.22  3.000
 K4E  H8   C8   C9   109.86  3.000
 K4E  H9   C8   N1   112.62  3.000
 K4E  H8   C8   N1   110.86  3.000
 K4E  C9   C8   N1   109.94  3.000
 K4E  N2   C9   O2   124.39  3.000
 K4E  N2   C9   C8   114.10  3.000
 K4E  O2   C9   C8   121.50  3.000
 K4E  H10  N2   C10  116.79  3.000
 K4E  H10  N2   C9   117.97  3.000
 K4E  C10  N2   C9   124.82  3.000
 K4E  H11  C10  C13  108.96  3.000
 K4E  H11  C10  C11  108.64  3.000
 K4E  C13  C10  C11  110.92  3.000
 K4E  H11  C10  N2   107.33  3.000
 K4E  C11  C10  N2   109.75  3.000
 K4E  C13  C10  N2   111.13  3.000
 K4E  H13  C11  H12  106.87  3.000
 K4E  H13  C11  C12  109.66  3.000
 K4E  H12  C11  C12  109.67  3.000
 K4E  H13  C11  C10  109.32  3.000
 K4E  H12  C11  C10  109.79  3.000
 K4E  C12  C11  C10  111.42  3.000
 K4E  H15  C12  H14  107.11  3.000
 K4E  H15  C12  C15  109.70  3.000
 K4E  H14  C12  C15  109.90  3.000
 K4E  H15  C12  C11  109.79  3.000
 K4E  H14  C12  C11  109.67  3.000
 K4E  C15  C12  C11  110.60  3.000
 K4E  H17  C13  H16  106.73  3.000
 K4E  H17  C13  C14  109.83  3.000
 K4E  H16  C13  C14  109.69  3.000
 K4E  H17  C13  C10  109.78  3.000
 K4E  H16  C13  C10  108.90  3.000
 K4E  C14  C13  C10  111.78  3.000
 K4E  H19  C14  H18  107.19  3.000
 K4E  H19  C14  C15  109.85  3.000
 K4E  H18  C14  C15  109.73  3.000
 K4E  H19  C14  C13  109.93  3.000
 K4E  H18  C14  C13  109.70  3.000
 K4E  C15  C14  C13  110.38  3.000
 K4E  H20  C15  N3   105.46  3.000
 K4E  H20  C15  C14  107.41  3.000
 K4E  N3   C15  C14  112.41  3.000
 K4E  H20  C15  C12  107.19  3.000
 K4E  N3   C15  C12  112.41  3.000
 K4E  C14  C15  C12  111.51  3.000
 K4E  C18  N3   C16  109.73  3.000
 K4E  C18  N3   C15  125.25  3.000
 K4E  C16  N3   C15  125.02  3.000
 K4E  N4   C16  O3   126.73  3.000
 K4E  N4   C16  N3   105.89  3.000
 K4E  O3   C16  N3   127.38  3.000
 K4E  H21  N4   C17  126.07  3.000
 K4E  H21  N4   C16  123.02  3.000
 K4E  C17  N4   C16  110.90  3.000
 K4E  C22  C17  C18  121.71  3.000
 K4E  C22  C17  N4   131.96  3.000
 K4E  C18  C17  N4   106.33  3.000
 K4E  C19  C18  C17  120.84  3.000
 K4E  C19  C18  N3   132.01  3.000
 K4E  C17  C18  N3   107.15  3.000
 K4E  H22  C19  C20  120.47  3.000
 K4E  H22  C19  C18  121.89  3.000
 K4E  C20  C19  C18  117.64  3.000
 K4E  H23  C20  C21  119.61  3.000
 K4E  H23  C20  C19  119.06  3.000
 K4E  C21  C20  C19  121.33  3.000
 K4E  H24  C21  C22  119.29  3.000
 K4E  H24  C21  C20  119.65  3.000
 K4E  C22  C21  C20  121.06  3.000
 K4E  H25  C22  C21  121.33  3.000
 K4E  H25  C22  C17  121.26  3.000
 K4E  C21  C22  C17  117.42  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
 K4E  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 K4E  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 K4E  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 K4E  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 K4E  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 K4E  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 K4E  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 K4E  CONST_08  C20  C21  C22  C17    0.00   0.0  0
 K4E  CONST_09  C21  C22  C17  C18    0.00   0.0  0
 K4E  CONST_10  C21  C20  C19  C18    0.00   0.0  0
 K4E  CONST_11  C22  C17  C18  C19    0.00   0.0  0
 K4E  CONST_12  C22  C21  C20  C19    0.00   0.0  0
 K4E  CONST_13  N4   C16  N3   C15  180.00   0.0  0
 K4E  CONST_14  C17  C18  N3   C15  180.00   0.0  0
 K4E  CONST_15  C17  N4   C16  N3     0.00   0.0  0
 K4E  CONST_16  N4   C17  C18  N3     0.00   0.0  0
 K4E  CONST_17  C18  C17  N4   C16    0.00   0.0  0
 K4E  CONST_18  C17  C18  N3   C16    0.00   0.0  0
 K4E  CONST_19  C18  N3   C16  N4     0.00   0.0  0
 K4E  CONST_20  C5   C6   C1   N1   180.00   0.0  0
 K4E  CONST_21  C3   C2   C1   N1   180.00   0.0  0
 K4E  CONST_22  CL1  C3   C2   C1   180.00   0.0  0
 K4E  CONST_23  O1   C6   C1   C2   180.00   0.0  0
 K4E  CONST_24  O1   C6   C5   C4   180.00   0.0  0
 K4E  CONST_25  CL1  C3   C4   C5   180.00   0.0  0
 K4E  CONST_26  O3   C16  N3   C15    0.00   0.0  0
 K4E  CONST_27  C17  N4   C16  O3   180.00   0.0  0
 K4E  CONST_28  C18  N3   C16  O3   180.00   0.0  0
 K4E  CONST_29  H4   C5   C6   C1   180.00   0.0  0
 K4E  CONST_30  H3   C4   C3   C2   180.00   0.0  0
 K4E  CONST_31  H2   C2   C3   C4   180.00   0.0  0
 K4E  CONST_32  H22  C19  C18  N3     0.00   0.0  0
 K4E  CONST_33  H25  C22  C17  N4     0.00   0.0  0
 K4E  CONST_34  H24  C21  C22  C17  180.00   0.0  0
 K4E  CONST_35  H23  C20  C19  C18  180.00   0.0  0
 K4E  CONST_36  H21  N4   C16  N3   180.00   0.0  0
 K4E  CONST_37  C8   N1   C1   C2     0.00   0.0  0
 K4E  CONST_38  C8   N1   C1   C6   180.00   0.0  0
 K4E  CONST_40  C10  N2   C9   C8   180.00   0.0  0
 K4E  CONST_41  C10  N2   C9   O2     0.00   0.0  0
 K4E  CONST_42  H10  N2   C9   C8     0.00   0.0  0
 K4E  Var_01    C15  C14  C13  C10   55.47  30.0  1
 K4E  Var_02    C15  C12  C11  C10  -55.91  30.0  1
 K4E  Var_03    C9   C8   N1   C1   170.97  30.0  1
 K4E  Var_04    H5   C7   O1   C6   -60.65  30.0  3
 K4E  Var_05    O2   C9   C8   N1   -21.49  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
 K4E  chir_01  C10  C13  N2   C11  negativ
 K4E  chir_02  C15  N3   C12  C14  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
 K4E  plan-1  N1   0.020
 K4E  plan-1  C1   0.020
 K4E  plan-1  C2   0.020
 K4E  plan-1  C3   0.020
 K4E  plan-1  C4   0.020
 K4E  plan-1  C5   0.020
 K4E  plan-1  C6   0.020
 K4E  plan-1  O1   0.020
 K4E  plan-1  CL1  0.020
 K4E  plan-1  H2   0.020
 K4E  plan-1  H3   0.020
 K4E  plan-1  H4   0.020
 K4E  plan-2  C15  0.020
 K4E  plan-2  N3   0.020
 K4E  plan-2  C16  0.020
 K4E  plan-2  O3   0.020
 K4E  plan-2  N4   0.020
 K4E  plan-2  C17  0.020
 K4E  plan-2  C18  0.020
 K4E  plan-2  C19  0.020
 K4E  plan-2  C20  0.020
 K4E  plan-2  C21  0.020
 K4E  plan-2  C22  0.020
 K4E  plan-2  H21  0.020
 K4E  plan-2  H22  0.020
 K4E  plan-2  H23  0.020
 K4E  plan-2  H24  0.020
 K4E  plan-2  H25  0.020
 K4E  plan-3  N1   0.020
 K4E  plan-3  C1   0.020
 K4E  plan-3  C8   0.020
 K4E  plan-3  H1   0.020
 K4E  plan-4  C8   0.020
 K4E  plan-4  C9   0.020
 K4E  plan-4  O2   0.020
 K4E  plan-4  N2   0.020
 K4E  plan-4  C10  0.020
 K4E  plan-4  H10  0.020

