# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:33:37 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 1-[(1H-benzimidazol-2-yl)methyl]-4-[(2,4-dichlorophenyl)methyl]-1,3-dihydro-2H-imidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CC2=CN(Cc3[nH]c4ccccc4n3)C(=O)N2)c(Cl)c1
#
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
 JFA  JFA  1-[(1H-benzimidazol-2-yl)methyl]-4-[(2,4-dichlorophenyl)methyl]-1,3-dihydro-2H-imidazol-2-one  ligand  39  25  .  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_JFA
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
 JFA  C1   C   CR16  0  -0.183  -4.9262  -1.4799   1.2694
 JFA  C2   C   CR16  0  -0.352  -3.7085  -0.9663   1.6872
 JFA  C3   C   CR6   0   0.235  -3.1136   0.1279   1.0670
 JFA  C4   C   CH2   0  -0.639  -1.7703   0.6285   1.5326
 JFA  C5   C   CR5   0   0.339  -0.6658   0.1781   0.6431
 JFA  C6   C   CR15  0  -0.140   0.1672   0.8728  -0.1490
 JFA  N1   N   NR15  0  -0.697   3.9485  -0.8582  -0.5389
 JFA  N2   N   N     0  -0.470   4.1506   1.3274  -0.8765
 JFA  N3   N   NR15  0  -0.712  -0.3425  -1.1616   0.4791
 JFA  C8   C   CR5   0   0.450   3.3984   0.2756  -1.0438
 JFA  C16  C   CR6   0  -0.106  -3.7966   0.7001  -0.0041
 JFA  C17  C   CR16  0  -0.150  -5.0176   0.2153  -0.4445
 JFA  C    C   CR6   0  -0.066  -5.5695  -0.8790   0.2012
 JFA  CL   CL  CL    0  -0.115  -7.0933  -1.4942  -0.3395
 JFA  C15  C   CR5   0   0.677   0.6915  -1.3117  -0.3947
 JFA  O    O   O     0  -0.544   1.2556  -2.3453  -0.7469
 JFA  N    N   NR5   0  -0.488   0.9890  -0.0385  -0.7967
 JFA  C14  C   CR56  0   0.132   5.2685   0.8666  -0.2197
 JFA  C9   C   CR56  0   0.336   5.1556  -0.5162   0.0067
 JFA  C13  C   CR16  0  -0.333   6.4039   1.5516   0.2130
 JFA  C12  C   CR16  0  -0.273   7.3888   0.8279   0.8602
 JFA  C11  C   CR16  0  -0.280   7.2584  -0.5529   1.0783
 JFA  C10  C   CR16  0  -0.318   6.1408  -1.2517   0.6568
 JFA  H1   H   HCR6  0   0.287  -5.3637  -2.3304   1.7733
 JFA  H2   H   HCR6  0   0.274  -3.2069  -1.4299   2.5280
 JFA  H3   H   HCH2  0   0.289  -1.7555   1.7176   1.5811
 JFA  H4   H   HCH2  0   0.292  -1.5959   0.2718   2.5507
 JFA  H5   H   HCR5  0   0.301   0.2293   1.9321  -0.3294
 JFA  H6   H   HCH2  0   0.298   1.8825   1.2594  -2.1340
 JFA  H7   H   HCH2  0   0.299   2.0496  -0.4422  -2.5344
 JFA  H10  H   HNR5  0   0.412  -0.7655  -1.9346   0.9678
 JFA  H11  H   HCR6  0   0.301  -5.5279   0.6851  -1.2738
 JFA  H12  H   HCR6  0   0.254   6.5078   2.6159   0.0450
 JFA  H13  H   HCR6  0   0.252   8.2805   1.3326   1.2083
 JFA  H14  H   HCR6  0   0.256   8.0526  -1.0825   1.5880
 JFA  H15  H   HCR6  0   0.285   6.0412  -2.3157   0.8253
 JFA  C7   C   CH2   0  -0.429   2.0618   0.2738  -1.7105
 JFA  CL1  CL  CL    0  -0.103  -3.1312   2.0716  -0.8236
 JFA  H8   H   HNR5  0   0.428   3.5219  -1.7738  -0.5638

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
 JFA  C4   C3   single    1.507  0.020  1.507
 JFA  C4   C5   single    1.488  0.020  1.488
 JFA  CL1  C16  single    1.731  0.020  1.731
 JFA  C16  C3   aromatic  1.393  0.020  1.393
 JFA  C16  C17  aromatic  1.386  0.020  1.386
 JFA  C3   C2   aromatic  1.391  0.020  1.391
 JFA  C17  C    aromatic  1.385  0.020  1.385
 JFA  C2   C1   aromatic  1.386  0.020  1.386
 JFA  C    C1   aromatic  1.384  0.020  1.384
 JFA  C    CL   single    1.730  0.020  1.730
 JFA  C5   N3   single    1.388  0.020  1.388
 JFA  C5   C6   double    1.343  0.020  1.343
 JFA  N3   C15  single    1.362  0.020  1.362
 JFA  C6   N    single    1.388  0.020  1.388
 JFA  C15  O    double    1.229  0.020  1.229
 JFA  C15  N    single    1.368  0.020  1.368
 JFA  N    C7   single    1.443  0.020  1.443
 JFA  C7   C8   single    1.494  0.020  1.494
 JFA  C8   N2   aromatic  1.304  0.020  1.304
 JFA  C8   N1   aromatic  1.358  0.020  1.358
 JFA  N2   C14  aromatic  1.376  0.020  1.376
 JFA  N1   C9   aromatic  1.368  0.020  1.368
 JFA  C14  C9   aromatic  1.406  0.020  1.406
 JFA  C14  C13  aromatic  1.395  0.020  1.395
 JFA  C9   C10  aromatic  1.391  0.020  1.391
 JFA  C13  C12  aromatic  1.383  0.020  1.383
 JFA  C10  C11  aromatic  1.384  0.020  1.384
 JFA  C12  C11  aromatic  1.404  0.020  1.404
 JFA  C1   H1   single    0.930  0.020  1.080
 JFA  C2   H2   single    0.930  0.020  1.080
 JFA  C4   H3   single    0.970  0.020  1.090
 JFA  C4   H4   single    0.970  0.020  1.090
 JFA  C6   H5   single    0.930  0.020  1.080
 JFA  C7   H6   single    0.970  0.020  1.090
 JFA  C7   H7   single    0.970  0.020  1.090
 JFA  N1   H8   single    0.860  0.020  1.020
 JFA  N3   H10  single    0.860  0.020  1.020
 JFA  C17  H11  single    0.930  0.020  1.080
 JFA  C13  H12  single    0.930  0.020  1.080
 JFA  C12  H13  single    0.930  0.020  1.080
 JFA  C11  H14  single    0.930  0.020  1.080
 JFA  C10  H15  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
 JFA  H1   C1   C    120.87  3.000
 JFA  H1   C1   C2   120.43  3.000
 JFA  C    C1   C2   118.69  3.000
 JFA  H2   C2   C3   118.99  3.000
 JFA  H2   C2   C1   118.83  3.000
 JFA  C3   C2   C1   122.19  3.000
 JFA  C16  C3   C4   122.54  3.000
 JFA  C16  C3   C2   117.13  3.000
 JFA  C4   C3   C2   120.30  3.000
 JFA  H4   C4   H3   106.40  3.000
 JFA  H4   C4   C5   109.86  3.000
 JFA  H3   C4   C5   108.60  3.000
 JFA  H4   C4   C3   108.75  3.000
 JFA  H3   C4   C3   110.96  3.000
 JFA  C5   C4   C3   112.11  3.000
 JFA  N3   C5   C6   106.57  3.000
 JFA  C6   C5   C4   131.02  3.000
 JFA  N3   C5   C4   122.40  3.000
 JFA  H5   C6   N    122.27  3.000
 JFA  H5   C6   C5   130.07  3.000
 JFA  N    C6   C5   107.63  3.000
 JFA  H8   N1   C9   127.51  3.000
 JFA  H8   N1   C8   125.21  3.000
 JFA  C9   N1   C8   107.28  3.000
 JFA  C14  N2   C8   105.06  3.000
 JFA  H10  N3   C15  123.04  3.000
 JFA  H10  N3   C5   125.83  3.000
 JFA  C15  N3   C5   111.04  3.000
 JFA  N2   C8   N1   113.09  3.000
 JFA  N1   C8   C7   121.84  3.000
 JFA  N2   C8   C7   125.06  3.000
 JFA  C17  C16  CL1  117.75  3.000
 JFA  C17  C16  C3   122.19  3.000
 JFA  CL1  C16  C3   120.07  3.000
 JFA  H11  C17  C    120.84  3.000
 JFA  H11  C17  C16  120.51  3.000
 JFA  C    C17  C16  118.64  3.000
 JFA  CL   C    C17  119.09  3.000
 JFA  CL   C    C1   119.75  3.000
 JFA  C17  C    C1   121.16  3.000
 JFA  N    C15  O    126.78  3.000
 JFA  N    C15  N3   104.54  3.000
 JFA  O    C15  N3   128.68  3.000
 JFA  C15  N    C7   123.30  3.000
 JFA  C7   N    C6   126.42  3.000
 JFA  C15  N    C6   110.20  3.000
 JFA  C13  C14  C9   119.90  3.000
 JFA  C13  C14  N2   130.16  3.000
 JFA  C9   C14  N2   109.94  3.000
 JFA  C10  C9   C14  122.59  3.000
 JFA  C10  C9   N1   132.78  3.000
 JFA  C14  C9   N1   104.63  3.000
 JFA  H12  C13  C12  121.25  3.000
 JFA  H12  C13  C14  120.86  3.000
 JFA  C12  C13  C14  117.89  3.000
 JFA  H13  C12  C11  119.03  3.000
 JFA  H13  C12  C13  119.56  3.000
 JFA  C11  C12  C13  121.42  3.000
 JFA  H14  C11  C10  119.28  3.000
 JFA  H14  C11  C12  119.10  3.000
 JFA  C10  C11  C12  121.62  3.000
 JFA  H15  C10  C11  121.57  3.000
 JFA  H15  C10  C9   121.85  3.000
 JFA  C11  C10  C9   116.58  3.000
 JFA  H7   C7   H6   107.37  3.000
 JFA  H7   C7   N    109.13  3.000
 JFA  H6   C7   N    108.67  3.000
 JFA  H7   C7   C8   110.35  3.000
 JFA  H6   C7   C8   108.67  3.000
 JFA  N    C7   C8   112.50  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
 JFA  CONST_01  C16  C3   C2   C1     0.00   0.0  0
 JFA  CONST_02  C16  C17  C    C1     0.00   0.0  0
 JFA  CONST_03  C17  C16  C3   C2     0.00   0.0  0
 JFA  CONST_04  C17  C    C1   C2     0.00   0.0  0
 JFA  CONST_05  C    C17  C16  C3     0.00   0.0  0
 JFA  CONST_06  C    C1   C2   C3     0.00   0.0  0
 JFA  CONST_07  C14  N2   C8   N1     0.00   0.0  0
 JFA  CONST_08  N2   C14  C9   N1     0.00   0.0  0
 JFA  CONST_09  C13  C14  C9   N1   180.00   0.0  0
 JFA  CONST_10  C11  C10  C9   N1   180.00   0.0  0
 JFA  CONST_11  C9   N1   C8   N2     0.00   0.0  0
 JFA  CONST_12  C10  C9   C14  N2   180.00   0.0  0
 JFA  CONST_13  C12  C13  C14  N2   180.00   0.0  0
 JFA  CONST_14  C9   C14  N2   C8     0.00   0.0  0
 JFA  CONST_15  C13  C14  N2   C8   180.00   0.0  0
 JFA  CONST_16  C14  C9   N1   C8     0.00   0.0  0
 JFA  CONST_17  C10  C9   N1   C8   180.00   0.0  0
 JFA  CONST_18  C11  C10  C9   C14    0.00   0.0  0
 JFA  CONST_19  C11  C12  C13  C14    0.00   0.0  0
 JFA  CONST_20  C12  C13  C14  C9     0.00   0.0  0
 JFA  CONST_21  C12  C11  C10  C9     0.00   0.0  0
 JFA  CONST_22  C10  C9   C14  C13    0.00   0.0  0
 JFA  CONST_23  C10  C11  C12  C13    0.00   0.0  0
 JFA  CONST_24  N    C15  N3   C5     0.00   0.0  0
 JFA  CONST_25  C15  N    C6   C5     0.00   0.0  0
 JFA  CONST_26  C15  N3   C5   C6     0.00   0.0  0
 JFA  CONST_27  N3   C15  N    C6     0.00   0.0  0
 JFA  CONST_28  N    C6   C5   N3     0.00   0.0  0
 JFA  CONST_29  C4   C3   C2   C1   180.00   0.0  0
 JFA  CONST_30  CL1  C16  C3   C2   180.00   0.0  0
 JFA  CONST_31  CL   C    C1   C2   180.00   0.0  0
 JFA  CONST_32  C17  C16  C3   C4   180.00   0.0  0
 JFA  CONST_33  C14  N2   C8   C7   180.00   0.0  0
 JFA  CONST_34  C9   N1   C8   C7   180.00   0.0  0
 JFA  CONST_35  C    C17  C16  CL1  180.00   0.0  0
 JFA  CONST_36  CL   C    C17  C16  180.00   0.0  0
 JFA  CONST_37  O    C15  N3   C5   180.00   0.0  0
 JFA  CONST_38  C7   N    C6   C5   180.00   0.0  0
 JFA  CONST_39  O    C15  N    C6   180.00   0.0  0
 JFA  CONST_40  N3   C15  N    C7   180.00   0.0  0
 JFA  CONST_41  H11  C17  C    C1   180.00   0.0  0
 JFA  CONST_42  H1   C1   C2   C3   180.00   0.0  0
 JFA  CONST_43  H15  C10  C9   N1     0.00   0.0  0
 JFA  CONST_44  H8   N1   C8   N2   180.00   0.0  0
 JFA  CONST_45  H12  C13  C14  N2     0.00   0.0  0
 JFA  CONST_46  H2   C2   C3   C16  180.00   0.0  0
 JFA  CONST_47  H13  C12  C13  C14  180.00   0.0  0
 JFA  CONST_48  H14  C11  C10  C9   180.00   0.0  0
 JFA  CONST_49  H10  N3   C5   C6   180.00   0.0  0
 JFA  CONST_50  O    C15  N    C7     0.00   0.0  0
 JFA  Var_01    C5   C4   C3   C2   101.24  30.0  3
 JFA  Var_02    N3   C5   C4   C3   -63.33  30.0  3
 JFA  Var_03    C8   C7   N    C6    97.23  30.0  3
 JFA  Var_04    N    C7   C8   N1    66.19  30.0  1

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
 JFA  plan-1  C4   0.020
 JFA  plan-1  C5   0.020
 JFA  plan-1  C6   0.020
 JFA  plan-1  N3   0.020
 JFA  plan-1  C15  0.020
 JFA  plan-1  O    0.020
 JFA  plan-1  N    0.020
 JFA  plan-1  H5   0.020
 JFA  plan-1  H10  0.020
 JFA  plan-1  C7   0.020
 JFA  plan-2  C1   0.020
 JFA  plan-2  C2   0.020
 JFA  plan-2  C3   0.020
 JFA  plan-2  C4   0.020
 JFA  plan-2  C16  0.020
 JFA  plan-2  C17  0.020
 JFA  plan-2  C    0.020
 JFA  plan-2  CL   0.020
 JFA  plan-2  H1   0.020
 JFA  plan-2  H2   0.020
 JFA  plan-2  H11  0.020
 JFA  plan-2  CL1  0.020
 JFA  plan-3  N1   0.020
 JFA  plan-3  N2   0.020
 JFA  plan-3  C8   0.020
 JFA  plan-3  C14  0.020
 JFA  plan-3  C9   0.020
 JFA  plan-3  C13  0.020
 JFA  plan-3  C12  0.020
 JFA  plan-3  C11  0.020
 JFA  plan-3  C10  0.020
 JFA  plan-3  H12  0.020
 JFA  plan-3  H13  0.020
 JFA  plan-3  H14  0.020
 JFA  plan-3  H15  0.020
 JFA  plan-3  C7   0.020
 JFA  plan-3  H8   0.020

