# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 11:19:06 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: ~{N}-(2-azanyl-3~{H}-benzimidazol-5-yl)-2-(3-chlorophenyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]c2cc(NC(=O)Cc3cccc(Cl)c3)ccc2n1
#
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
 7ZG  7ZG  ~{N}-(2-azanyl-3~{H}-benzimidazol-5-yl)-2-(3-chlorophenyl)ethanamide  ligand  34  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7ZG
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
 7ZG  N1   N   NR15  0  -0.725   4.4028  -1.4223  -0.6674
 7ZG  N3   N   N     0  -0.520   5.6463  -0.2717   0.7836
 7ZG  C4   C   CR56  0   0.378   3.5922  -0.4120  -0.2081
 7ZG  C5   C   CR56  0   0.145   4.3947   0.2955   0.7010
 7ZG  C6   C   C     0   0.554  -0.5714   0.9514  -0.7339
 7ZG  C7   C   CR16  0  -0.399   2.2818  -0.0804  -0.5067
 7ZG  C13  C   CH2   0  -0.691  -1.8404   1.7916  -0.7264
 7ZG  C15  C   CR16  0  -0.252  -3.6499   0.5335   0.4580
 7ZG  C17  C   CR6   0  -0.021  -4.7762  -0.2735   0.4411
 7ZG  C20  C   CR16  0  -0.294  -3.6365   0.5129  -1.9414
 7ZG  C21  C   CR16  0  -0.229  -5.3481  -0.6953  -0.7485
 7ZG  C2   C   CR5   0   0.603   5.6065  -1.2885  -0.0402
 7ZG  C9   C   CR6   0   0.348   1.7555   1.0286   0.1563
 7ZG  O10  O   O     0  -0.466  -0.5020  -0.0987  -1.3480
 7ZG  N11  N   NH2   0  -0.849   6.6087  -2.1804  -0.2356
 7ZG  C12  C   CR16  0  -0.335   3.8525   1.4001   1.3463
 7ZG  C14  C   CR6   0   0.139  -3.0717   0.9344  -0.7423
 7ZG  C16  C   CR16  0  -0.365   2.5424   1.7519   1.0677
 7ZG  C19  C   CR16  0  -0.248  -4.7662  -0.2922  -1.9421
 7ZG  H1   H   HNR5  0   0.417   4.1472  -2.1523  -1.3132
 7ZG  H3   H   HCR6  0   0.285   1.7042  -0.6551  -1.2121
 7ZG  H4   H   HCH2  0   0.286  -1.8581   2.4669   0.1304
 7ZG  H5   H   HCH2  0   0.306  -1.8105   2.4237  -1.6190
 7ZG  H6   H   HCR6  0   0.276  -3.2236   0.8519   1.4010
 7ZG  H7   H   HCR6  0   0.258  -3.1986   0.8240  -2.8811
 7ZG  H8   H   HCR6  0   0.279  -6.2298  -1.3215  -0.7468
 7ZG  H9   H   HNH1  0   0.416   0.2359   2.3590   0.4489
 7ZG  H10  H   HNH2  0   0.398   6.6413  -2.6517  -1.1252
 7ZG  H11  H   HNH2  0   0.397   7.5134  -1.8799   0.0889
 7ZG  H12  H   HCR6  0   0.252   4.4350   1.9757   2.0539
 7ZG  H13  H   HCR6  0   0.262   2.1109   2.6099   1.5700
 7ZG  H14  H   HCR6  0   0.268  -5.2037  -0.6087  -2.8797
 7ZG  N8   N   NH1   0  -0.742   0.4454   1.4979  -0.0323
 7ZG  CL1  CL  CL    0  -0.131  -5.4873  -0.7617   1.9468

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
 7ZG  CL1  C17  single    1.735  0.020  1.735
 7ZG  C21  C17  aromatic  1.386  0.020  1.386
 7ZG  C21  C19  aromatic  1.388  0.020  1.388
 7ZG  C17  C15  aromatic  1.386  0.020  1.386
 7ZG  C19  C20  aromatic  1.387  0.020  1.387
 7ZG  C15  C14  aromatic  1.391  0.020  1.391
 7ZG  C20  C14  aromatic  1.391  0.020  1.391
 7ZG  C14  C13  single    1.500  0.020  1.500
 7ZG  C13  C6   single    1.522  0.020  1.522
 7ZG  N8   C6   single    1.351  0.020  1.351
 7ZG  N8   C9   single    1.404  0.020  1.404
 7ZG  C6   O10  double    1.218  0.020  1.218
 7ZG  C16  C9   aromatic  1.405  0.020  1.405
 7ZG  C16  C12  aromatic  1.385  0.020  1.385
 7ZG  C9   C7   aromatic  1.395  0.020  1.395
 7ZG  C12  C5   aromatic  1.389  0.020  1.389
 7ZG  C7   C4   aromatic  1.384  0.020  1.384
 7ZG  C5   C4   aromatic  1.404  0.020  1.404
 7ZG  C5   N3   aromatic  1.377  0.020  1.377
 7ZG  C4   N1   aromatic  1.374  0.020  1.374
 7ZG  N3   C2   aromatic  1.309  0.020  1.309
 7ZG  N1   C2   aromatic  1.364  0.020  1.364
 7ZG  C2   N11  single    1.356  0.020  1.356
 7ZG  N1   H1   single    0.860  0.020  1.020
 7ZG  C7   H3   single    0.930  0.020  1.080
 7ZG  C13  H4   single    0.970  0.020  1.090
 7ZG  C13  H5   single    0.970  0.020  1.090
 7ZG  C15  H6   single    0.930  0.020  1.080
 7ZG  C20  H7   single    0.930  0.020  1.080
 7ZG  C21  H8   single    0.930  0.020  1.080
 7ZG  N8   H9   single    0.860  0.020  1.020
 7ZG  N11  H10  single    0.890  0.020  1.040
 7ZG  N11  H11  single    0.890  0.020  1.040
 7ZG  C12  H12  single    0.930  0.020  1.080
 7ZG  C16  H13  single    0.930  0.020  1.080
 7ZG  C19  H14  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
 7ZG  H1   N1   C2   126.14  3.000
 7ZG  H1   N1   C4   126.66  3.000
 7ZG  C2   N1   C4   107.14  3.000
 7ZG  C2   N3   C5   104.75  3.000
 7ZG  C7   C4   C5   124.06  3.000
 7ZG  C5   C4   N1   104.46  3.000
 7ZG  C7   C4   N1   131.48  3.000
 7ZG  C12  C5   C4   118.58  3.000
 7ZG  C4   C5   N3   110.54  3.000
 7ZG  C12  C5   N3   130.88  3.000
 7ZG  O10  C6   N8   124.58  3.000
 7ZG  O10  C6   C13  121.72  3.000
 7ZG  N8   C6   C13  113.68  3.000
 7ZG  H3   C7   C9   122.19  3.000
 7ZG  H3   C7   C4   121.38  3.000
 7ZG  C9   C7   C4   116.43  3.000
 7ZG  H5   C13  H4   106.47  3.000
 7ZG  H5   C13  C14  110.11  3.000
 7ZG  H4   C13  C14  110.40  3.000
 7ZG  H5   C13  C6   106.99  3.000
 7ZG  H4   C13  C6   111.04  3.000
 7ZG  C14  C13  C6   111.64  3.000
 7ZG  H6   C15  C14  120.19  3.000
 7ZG  H6   C15  C17  120.13  3.000
 7ZG  C14  C15  C17  119.68  3.000
 7ZG  CL1  C17  C21  119.35  3.000
 7ZG  C21  C17  C15  121.54  3.000
 7ZG  CL1  C17  C15  119.10  3.000
 7ZG  H7   C20  C19  119.72  3.000
 7ZG  H7   C20  C14  119.81  3.000
 7ZG  C19  C20  C14  120.47  3.000
 7ZG  H8   C21  C19  120.76  3.000
 7ZG  H8   C21  C17  120.75  3.000
 7ZG  C19  C21  C17  118.49  3.000
 7ZG  N11  C2   N3   125.39  3.000
 7ZG  N11  C2   N1   121.44  3.000
 7ZG  N3   C2   N1   113.10  3.000
 7ZG  C16  C9   N8   115.96  3.000
 7ZG  C16  C9   C7   120.42  3.000
 7ZG  N8   C9   C7   123.63  3.000
 7ZG  H11  N11  H10  113.27  3.000
 7ZG  H11  N11  C2   114.92  3.000
 7ZG  H10  N11  C2   117.32  3.000
 7ZG  H12  C12  C16  120.37  3.000
 7ZG  H12  C12  C5   121.10  3.000
 7ZG  C16  C12  C5   118.53  3.000
 7ZG  C20  C14  C15  119.19  3.000
 7ZG  C20  C14  C13  121.03  3.000
 7ZG  C15  C14  C13  119.77  3.000
 7ZG  H13  C16  C12  118.98  3.000
 7ZG  H13  C16  C9   119.03  3.000
 7ZG  C12  C16  C9   121.99  3.000
 7ZG  H14  C19  C21  119.39  3.000
 7ZG  H14  C19  C20  119.97  3.000
 7ZG  C21  C19  C20  120.64  3.000
 7ZG  H9   N8   C9   114.52  3.000
 7ZG  H9   N8   C6   115.91  3.000
 7ZG  C9   N8   C6   129.55  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
 7ZG  CONST_01  C9   C7   C4   N1    180.00   0.0  0
 7ZG  CONST_02  C12  C5   C4   N1    180.00   0.0  0
 7ZG  CONST_03  N3   C5   C4   N1      0.00   0.0  0
 7ZG  CONST_04  C5   N3   C2   N1      0.00   0.0  0
 7ZG  CONST_05  C16  C12  C5   N3    180.00   0.0  0
 7ZG  CONST_06  C7   C4   C5   N3    180.00   0.0  0
 7ZG  CONST_07  C4   N1   C2   N3      0.00   0.0  0
 7ZG  CONST_08  C16  C9   C7   C4      0.00   0.0  0
 7ZG  CONST_09  C16  C12  C5   C4      0.00   0.0  0
 7ZG  CONST_10  C2   N3   C5   C4      0.00   0.0  0
 7ZG  CONST_11  C9   C16  C12  C5      0.00   0.0  0
 7ZG  CONST_12  C9   C7   C4   C5      0.00   0.0  0
 7ZG  CONST_13  C2   N1   C4   C5      0.00   0.0  0
 7ZG  CONST_14  C12  C16  C9   C7      0.00   0.0  0
 7ZG  CONST_15  C12  C5   C4   C7      0.00   0.0  0
 7ZG  CONST_16  C2   N1   C4   C7    180.00   0.0  0
 7ZG  CONST_17  C19  C21  C17  C15     0.00   0.0  0
 7ZG  CONST_18  C19  C20  C14  C15     0.00   0.0  0
 7ZG  CONST_19  C20  C19  C21  C17     0.00   0.0  0
 7ZG  CONST_20  C20  C14  C15  C17     0.00   0.0  0
 7ZG  CONST_21  C14  C15  C17  C21     0.00   0.0  0
 7ZG  CONST_22  C14  C20  C19  C21     0.00   0.0  0
 7ZG  CONST_23  C12  C5   N3   C2    180.00   0.0  0
 7ZG  CONST_24  N8   C9   C7   C4    180.00   0.0  0
 7ZG  CONST_25  N11  C2   N1   C4    180.00   0.0  0
 7ZG  CONST_26  N11  C2   N3   C5    180.00   0.0  0
 7ZG  CONST_27  C17  C15  C14  C13   180.00   0.0  0
 7ZG  CONST_28  C19  C20  C14  C13   180.00   0.0  0
 7ZG  CONST_29  C12  C16  C9   N8    180.00   0.0  0
 7ZG  CONST_30  CL1  C17  C15  C14   180.00   0.0  0
 7ZG  CONST_31  C19  C21  C17  CL1   180.00   0.0  0
 7ZG  CONST_32  H3   C7   C4   N1      0.00   0.0  0
 7ZG  CONST_33  H12  C12  C5   N3      0.00   0.0  0
 7ZG  CONST_34  H1   N1   C2   N3    180.00   0.0  0
 7ZG  CONST_35  H13  C16  C12  C5    180.00   0.0  0
 7ZG  CONST_36  H8   C21  C17  C15   180.00   0.0  0
 7ZG  CONST_37  H7   C20  C14  C15   180.00   0.0  0
 7ZG  CONST_38  H14  C19  C21  C17   180.00   0.0  0
 7ZG  CONST_39  H6   C15  C14  C20   180.00   0.0  0
 7ZG  CONST_40  C16  C9   N8   C6    180.00   0.0  0
 7ZG  CONST_41  C7   C9   N8   C6      0.00   0.0  0
 7ZG  CONST_43  H11  N11  C2   N1    180.00   0.0  0
 7ZG  CONST_44  H9   N8   C9   C7    180.00   0.0  0
 7ZG  CONST_45  C9   N8   C6   C13   180.00   0.0  0
 7ZG  CONST_46  O10  C6   N8   C9      0.00   0.0  0
 7ZG  Var_01    C15  C14  C13  C6     90.60  30.0  2
 7ZG  Var_02    C14  C13  C6   N8   -146.06  30.0  2

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
 7ZG  plan-1  C13  0.020
 7ZG  plan-1  C15  0.020
 7ZG  plan-1  C17  0.020
 7ZG  plan-1  C20  0.020
 7ZG  plan-1  C21  0.020
 7ZG  plan-1  C14  0.020
 7ZG  plan-1  C19  0.020
 7ZG  plan-1  H6   0.020
 7ZG  plan-1  H7   0.020
 7ZG  plan-1  H8   0.020
 7ZG  plan-1  H14  0.020
 7ZG  plan-1  CL1  0.020
 7ZG  plan-2  N1   0.020
 7ZG  plan-2  N3   0.020
 7ZG  plan-2  C4   0.020
 7ZG  plan-2  C5   0.020
 7ZG  plan-2  C7   0.020
 7ZG  plan-2  C2   0.020
 7ZG  plan-2  C9   0.020
 7ZG  plan-2  N11  0.020
 7ZG  plan-2  C12  0.020
 7ZG  plan-2  C16  0.020
 7ZG  plan-2  H1   0.020
 7ZG  plan-2  H3   0.020
 7ZG  plan-2  H12  0.020
 7ZG  plan-2  H13  0.020
 7ZG  plan-2  N8   0.020
 7ZG  plan-3  C6   0.020
 7ZG  plan-3  C13  0.020
 7ZG  plan-3  C9   0.020
 7ZG  plan-3  O10  0.020
 7ZG  plan-3  H9   0.020
 7ZG  plan-3  N8   0.020
 7ZG  plan-4  C2   0.020
 7ZG  plan-4  N11  0.020
 7ZG  plan-4  H10  0.020
 7ZG  plan-4  H11  0.020

