# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 01:56:20 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N-(1H-benzimidazol-1-yl)-2-phenylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1ccccc1)Nn2cnc3ccccc23
#
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
 41L  41L  N-(1H-benzimidazol-1-yl)-2-phenylacetamide  ligand  32  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_41L
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
 41L  C1   C  CR6   0   0.148  -3.0820   0.6837   0.1621
 41L  C2   C  CH2   0  -0.695  -1.7947   1.1965   0.7360
 41L  C3   C  C     0   0.570  -0.6326   0.2736   0.4382
 41L  N4   N  NC1   0  -0.525   0.4202   0.4363   1.2917
 41L  N5   N  NR5   0  -0.378   1.5752  -0.2371   1.0818
 41L  O6   O  O     0  -0.433  -0.6068  -0.5260  -0.4689
 41L  C7   C  CR16  0  -0.303  -3.4864   1.0514  -1.1173
 41L  C8   C  CR16  0  -0.242  -4.6696   0.5617  -1.6541
 41L  C9   C  CR16  0  -0.267  -5.4625  -0.3068  -0.9157
 41L  C10  C  CR16  0  -0.242  -5.0661  -0.6793   0.3624
 41L  C11  C  CR16  0  -0.293  -3.8834  -0.1859   0.8963
 41L  C12  C  CR56  0   0.372   2.6052   0.1422   0.2532
 41L  C13  C  CR56  0   0.116   3.5150  -0.9203   0.3281
 41L  N14  N  N     0  -0.453   3.0318  -1.9065   1.1653
 41L  C15  C  CR15  0   0.125   1.8858  -1.4677   1.5816
 41L  C16  C  CR16  0  -0.297   2.8197   1.2752  -0.5177
 41L  C17  C  CR16  0  -0.274   4.0047   1.3136  -1.2322
 41L  C18  C  CR16  0  -0.269   4.9326   0.2624  -1.1722
 41L  C19  C  CR16  0  -0.320   4.7038  -0.8609  -0.3974
 41L  H2   H  HCH2  0   0.313  -1.5448   2.1727   0.3094
 41L  H2A  H  HCH2  0   0.295  -1.8803   1.3496   1.8142
 41L  HN4  H  HNC1  0   0.433   0.4221   1.1370   2.0185
 41L  H7   H  HCR6  0   0.252  -2.8750   1.7315  -1.6983
 41L  H8   H  HCR6  0   0.256  -4.9713   0.8600  -2.6498
 41L  H9   H  HCR6  0   0.256  -6.3856  -0.6889  -1.3317
 41L  H10  H  HCR6  0   0.257  -5.6789  -1.3541   0.9460
 41L  H11  H  HCR6  0   0.252  -3.5839  -0.4783   1.8960
 41L  H15  H  HCR5  0   0.300   1.2134  -1.9768   2.2569
 41L  H16  H  HCR6  0   0.271   2.1031   2.0850  -0.5615
 41L  H17  H  HCR6  0   0.260   4.2216   2.1741  -1.8513
 41L  H18  H  HCR6  0   0.257   5.8466   0.3353  -1.7469
 41L  H19  H  HCR6  0   0.260   5.4213  -1.6699  -0.3534

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
 41L  C7   C1   aromatic  1.391  0.020  1.391
 41L  C1   C11  aromatic  1.392  0.020  1.392
 41L  C1   C2   single    1.500  0.020  1.500
 41L  C2   C3   single    1.514  0.020  1.514
 41L  C2   H2   single    0.970  0.020  1.090
 41L  C2   H2A  single    0.970  0.020  1.090
 41L  N4   C3   single    1.365  0.020  1.365
 41L  C3   O6   double    1.210  0.020  1.210
 41L  N4   N5   single    1.353  0.020  1.353
 41L  N4   HN4  single    0.860  0.020  1.020
 41L  N5   C15  aromatic  1.364  0.020  1.364
 41L  N5   C12  aromatic  1.375  0.020  1.375
 41L  C8   C7   aromatic  1.389  0.020  1.389
 41L  C7   H7   single    0.930  0.020  1.080
 41L  C8   C9   aromatic  1.389  0.020  1.389
 41L  C8   H8   single    0.930  0.020  1.080
 41L  C9   C10  aromatic  1.389  0.020  1.389
 41L  C9   H9   single    0.930  0.020  1.080
 41L  C10  C11  aromatic  1.388  0.020  1.388
 41L  C10  H10  single    0.930  0.020  1.080
 41L  C11  H11  single    0.930  0.020  1.080
 41L  C12  C16  aromatic  1.387  0.020  1.387
 41L  C12  C13  aromatic  1.401  0.020  1.401
 41L  N14  C13  aromatic  1.381  0.020  1.381
 41L  C13  C19  aromatic  1.394  0.020  1.394
 41L  C15  N14  aromatic  1.296  0.020  1.296
 41L  C15  H15  single    0.930  0.020  1.080
 41L  C16  C17  aromatic  1.384  0.020  1.384
 41L  C16  H16  single    0.930  0.020  1.080
 41L  C17  C18  aromatic  1.403  0.020  1.403
 41L  C17  H17  single    0.930  0.020  1.080
 41L  C18  C19  aromatic  1.384  0.020  1.384
 41L  C18  H18  single    0.930  0.020  1.080
 41L  C19  H19  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
 41L  C11  C1   C7   118.88  3.000
 41L  C11  C1   C2   120.39  3.000
 41L  C7   C1   C2   120.73  3.000
 41L  H2A  C2   H2   106.12  3.000
 41L  H2A  C2   C3   109.87  3.000
 41L  H2   C2   C3   106.97  3.000
 41L  H2A  C2   C1   111.00  3.000
 41L  H2   C2   C1   110.60  3.000
 41L  C3   C2   C1   112.04  3.000
 41L  O6   C3   N4   122.09  3.000
 41L  O6   C3   C2   124.55  3.000
 41L  N4   C3   C2   113.36  3.000
 41L  HN4  N4   N5   117.09  3.000
 41L  HN4  N4   C3   122.29  3.000
 41L  N5   N4   C3   120.13  3.000
 41L  C15  N5   C12  107.40  3.000
 41L  C12  N5   N4   126.54  3.000
 41L  C15  N5   N4   125.90  3.000
 41L  H7   C7   C8   119.66  3.000
 41L  H7   C7   C1   119.68  3.000
 41L  C8   C7   C1   120.66  3.000
 41L  H8   C8   C9   120.16  3.000
 41L  H8   C8   C7   119.74  3.000
 41L  C9   C8   C7   120.10  3.000
 41L  H9   C9   C10  120.16  3.000
 41L  H9   C9   C8   120.23  3.000
 41L  C10  C9   C8   119.61  3.000
 41L  H10  C10  C11  119.78  3.000
 41L  H10  C10  C9   120.11  3.000
 41L  C11  C10  C9   120.11  3.000
 41L  H11  C11  C10  119.62  3.000
 41L  H11  C11  C1   119.74  3.000
 41L  C10  C11  C1   120.64  3.000
 41L  C16  C12  C13  123.28  3.000
 41L  C13  C12  N5   104.18  3.000
 41L  C16  C12  N5   132.53  3.000
 41L  C19  C13  N14  130.12  3.000
 41L  C19  C13  C12  119.59  3.000
 41L  N14  C13  C12  110.29  3.000
 41L  C15  N14  C13  105.22  3.000
 41L  H15  C15  N14  126.28  3.000
 41L  H15  C15  N5   120.82  3.000
 41L  N14  C15  N5   112.90  3.000
 41L  H16  C16  C17  121.68  3.000
 41L  H16  C16  C12  122.09  3.000
 41L  C17  C16  C12  116.23  3.000
 41L  H17  C17  C18  119.18  3.000
 41L  H17  C17  C16  119.27  3.000
 41L  C18  C17  C16  121.54  3.000
 41L  H18  C18  C19  119.46  3.000
 41L  H18  C18  C17  119.03  3.000
 41L  C19  C18  C17  121.51  3.000
 41L  H19  C19  C18  121.33  3.000
 41L  H19  C19  C13  120.82  3.000
 41L  C18  C19  C13  117.84  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
 41L  CONST_01  C9   C8   C7   C1      0.00   0.0  0
 41L  CONST_02  C9   C10  C11  C1      0.00   0.0  0
 41L  CONST_03  C13  N14  C15  N5      0.00   0.0  0
 41L  CONST_04  C17  C16  C12  N5    180.00   0.0  0
 41L  CONST_05  N14  C13  C12  N5      0.00   0.0  0
 41L  CONST_06  C19  C13  C12  N5    180.00   0.0  0
 41L  CONST_07  C10  C11  C1   C7      0.00   0.0  0
 41L  CONST_08  C10  C9   C8   C7      0.00   0.0  0
 41L  CONST_09  C11  C1   C7   C8      0.00   0.0  0
 41L  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 41L  CONST_11  N14  C15  N5   C12     0.00   0.0  0
 41L  CONST_12  C18  C17  C16  C12     0.00   0.0  0
 41L  CONST_13  C15  N14  C13  C12     0.00   0.0  0
 41L  CONST_14  C18  C19  C13  C12     0.00   0.0  0
 41L  CONST_15  C15  N5   C12  C13     0.00   0.0  0
 41L  CONST_16  C17  C16  C12  C13     0.00   0.0  0
 41L  CONST_17  C17  C18  C19  C13     0.00   0.0  0
 41L  CONST_18  C16  C12  C13  N14   180.00   0.0  0
 41L  CONST_19  C18  C19  C13  N14   180.00   0.0  0
 41L  CONST_20  C16  C12  N5   C15   180.00   0.0  0
 41L  CONST_21  C19  C13  N14  C15   180.00   0.0  0
 41L  CONST_22  C19  C13  C12  C16     0.00   0.0  0
 41L  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 41L  CONST_24  C8   C7   C1   C2    180.00   0.0  0
 41L  CONST_25  C10  C11  C1   C2    180.00   0.0  0
 41L  CONST_26  N14  C15  N5   N4    180.00   0.0  0
 41L  CONST_27  C16  C12  N5   N4      0.00   0.0  0
 41L  CONST_28  C13  C12  N5   N4    180.00   0.0  0
 41L  CONST_29  H8   C8   C7   C1    180.00   0.0  0
 41L  CONST_30  H10  C10  C11  C1    180.00   0.0  0
 41L  CONST_31  H16  C16  C12  N5      0.00   0.0  0
 41L  CONST_32  H11  C11  C1   C7    180.00   0.0  0
 41L  CONST_33  H9   C9   C8   C7    180.00   0.0  0
 41L  CONST_34  H7   C7   C8   C9    180.00   0.0  0
 41L  CONST_35  H15  C15  N5   C12   180.00   0.0  0
 41L  CONST_36  H17  C17  C16  C12   180.00   0.0  0
 41L  CONST_37  H19  C19  C13  C12   180.00   0.0  0
 41L  CONST_38  H18  C18  C19  C13   180.00   0.0  0
 41L  CONST_42  N5   N4   C3   C2    180.00   0.0  0
 41L  CONST_43  O6   C3   N4   N5      0.00   0.0  0
 41L  Var_01    C7   C1   C2   C3    -90.84  30.0  2
 41L  Var_02    N4   C3   C2   C1   -158.77  30.0  3

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
 41L  plan-1  C1   0.020
 41L  plan-1  C2   0.020
 41L  plan-1  C7   0.020
 41L  plan-1  C8   0.020
 41L  plan-1  C9   0.020
 41L  plan-1  C10  0.020
 41L  plan-1  C11  0.020
 41L  plan-1  H7   0.020
 41L  plan-1  H8   0.020
 41L  plan-1  H9   0.020
 41L  plan-1  H10  0.020
 41L  plan-1  H11  0.020
 41L  plan-2  N4   0.020
 41L  plan-2  N5   0.020
 41L  plan-2  C12  0.020
 41L  plan-2  C13  0.020
 41L  plan-2  N14  0.020
 41L  plan-2  C15  0.020
 41L  plan-2  C16  0.020
 41L  plan-2  C17  0.020
 41L  plan-2  C18  0.020
 41L  plan-2  C19  0.020
 41L  plan-2  H15  0.020
 41L  plan-2  H16  0.020
 41L  plan-2  H17  0.020
 41L  plan-2  H18  0.020
 41L  plan-2  H19  0.020
 41L  plan-3  C2   0.020
 41L  plan-3  C3   0.020
 41L  plan-3  N4   0.020
 41L  plan-3  N5   0.020
 41L  plan-3  O6   0.020
 41L  plan-3  HN4  0.020

