# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:15:48 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-benzyl-5-nitro-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc2[nH]c(Cc3ccccc3)nc2c1
#
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
 EJY  EJY  2-benzyl-5-nitro-1H-benzimidazole  ligand  30  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EJY
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
 EJY  C4   C  CR6    0   0.241   3.3575   0.0160  -0.1298
 EJY  C5   C  CR16   0  -0.294   3.0759  -0.5881   1.1047
 EJY  C6   C  CR16   0  -0.296   1.8084  -1.0566   1.3776
 EJY  C7   C  CR56   0   0.376   0.8481  -0.8988   0.3845
 EJY  C10  C  CR5    0   0.472  -0.9223  -0.8400  -0.9182
 EJY  C13  C  CR16   0  -0.320  -4.0997  -0.9564   0.4793
 EJY  C15  C  CR16   0  -0.266  -5.0191   1.1334   1.2394
 EJY  C17  C  CR16   0  -0.278  -3.3540   1.1033  -0.4983
 EJY  C20  C  CR16   0  -0.365   2.4072   0.1758  -1.1267
 EJY  O1   O  O      0  -0.387   5.5272   0.3705   0.5012
 EJY  N2   N  N      1   0.329   4.7027   0.4957  -0.3759
 EJY  O3   O  O     -1  -0.387   4.9431   1.0028  -1.4486
 EJY  N8   N  NR15   0  -0.691  -0.4673  -1.2319   0.3073
 EJY  C11  C  CH2    0  -0.634  -2.3395  -1.0454  -1.3266
 EJY  C12  C  CR6    0   0.114  -3.2911  -0.2871  -0.4325
 EJY  C14  C  CR16   0  -0.238  -4.9603  -0.2507   1.3123
 EJY  C16  C  CR16   0  -0.240  -4.2130   1.8094   0.3303
 EJY  N18  N  N      0  -0.463   0.0039  -0.2736  -1.6384
 EJY  C19  C  CR56   0   0.153   1.1322  -0.2933  -0.8542
 EJY  H1   H  HCR6   0   0.295   3.8493  -0.6934   1.8504
 EJY  H2   H  HCR6   0   0.286   1.5821  -1.5256   2.3251
 EJY  H3   H  HCR6   0   0.256  -4.0624  -2.0380   0.5370
 EJY  H4   H  HCR6   0   0.258  -5.6907   1.6855   1.8840
 EJY  H5   H  HCR6   0   0.254  -2.7284   1.6370  -1.2047
 EJY  H6   H  HCR6   0   0.296   2.6367   0.6410  -2.0746
 EJY  H7   H  HNR5   0   0.426  -1.0104  -1.6897   1.0237
 EJY  H8   H  HCH2   0   0.294  -2.4382  -0.7196  -2.3622
 EJY  H9   H  HCH2   0   0.294  -2.5723  -2.1129  -1.3013
 EJY  H10  H  HCR6   0   0.258  -5.5848  -0.7863   2.0157
 EJY  H11  H  HCR6   0   0.258  -4.2566   2.8890   0.2650

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
 EJY  C17  C16  aromatic  1.387  0.020  1.387
 EJY  C17  C12  aromatic  1.393  0.020  1.393
 EJY  C11  C12  single    1.510  0.020  1.510
 EJY  C11  C10  single    1.489  0.020  1.489
 EJY  C16  C15  aromatic  1.390  0.020  1.390
 EJY  N8   C10  aromatic  1.365  0.020  1.365
 EJY  N8   C7   aromatic  1.359  0.020  1.359
 EJY  C12  C13  aromatic  1.390  0.020  1.390
 EJY  C15  C14  aromatic  1.387  0.020  1.387
 EJY  C13  C14  aromatic  1.390  0.020  1.390
 EJY  C10  N18  aromatic  1.303  0.020  1.303
 EJY  C6   C7   aromatic  1.390  0.020  1.390
 EJY  C6   C5   aromatic  1.379  0.020  1.379
 EJY  C7   C19  aromatic  1.408  0.020  1.408
 EJY  N18  C19  aromatic  1.374  0.020  1.374
 EJY  C5   C4   aromatic  1.403  0.020  1.403
 EJY  C19  C20  aromatic  1.386  0.020  1.386
 EJY  C4   C20  aromatic  1.386  0.020  1.386
 EJY  C4   N2   single    1.449  0.020  1.449
 EJY  N2   O3   single    1.211  0.020  1.211
 EJY  N2   O1   double    1.210  0.020  1.210
 EJY  C5   H1   single    0.930  0.020  1.080
 EJY  C6   H2   single    0.930  0.020  1.080
 EJY  C13  H3   single    0.930  0.020  1.080
 EJY  C15  H4   single    0.930  0.020  1.080
 EJY  C17  H5   single    0.930  0.020  1.080
 EJY  C20  H6   single    0.930  0.020  1.080
 EJY  N8   H7   single    0.860  0.020  1.020
 EJY  C11  H8   single    0.970  0.020  1.090
 EJY  C11  H9   single    0.970  0.020  1.090
 EJY  C14  H10  single    0.930  0.020  1.080
 EJY  C16  H11  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
 EJY  N2   C4   C20  118.42  3.000
 EJY  N2   C4   C5   118.57  3.000
 EJY  C20  C4   C5   123.01  3.000
 EJY  H1   C5   C6   119.26  3.000
 EJY  H1   C5   C4   120.40  3.000
 EJY  C6   C5   C4   120.33  3.000
 EJY  H2   C6   C7   122.05  3.000
 EJY  H2   C6   C5   120.89  3.000
 EJY  C7   C6   C5   117.07  3.000
 EJY  C19  C7   N8   104.52  3.000
 EJY  C19  C7   C6   122.54  3.000
 EJY  N8   C7   C6   132.94  3.000
 EJY  N18  C10  C11  125.80  3.000
 EJY  N18  C10  N8   112.60  3.000
 EJY  C11  C10  N8   121.60  3.000
 EJY  H3   C13  C14  119.73  3.000
 EJY  H3   C13  C12  119.70  3.000
 EJY  C14  C13  C12  120.57  3.000
 EJY  H4   C15  C16  120.08  3.000
 EJY  H4   C15  C14  120.26  3.000
 EJY  C16  C15  C14  119.66  3.000
 EJY  H5   C17  C16  119.75  3.000
 EJY  H5   C17  C12  119.73  3.000
 EJY  C16  C17  C12  120.52  3.000
 EJY  H6   C20  C19  120.91  3.000
 EJY  H6   C20  C4   122.33  3.000
 EJY  C19  C20  C4   116.76  3.000
 EJY  O3   N2   O1   123.38  3.000
 EJY  O1   N2   C4   118.36  3.000
 EJY  O3   N2   C4   118.26  3.000
 EJY  H7   N8   C10  126.06  3.000
 EJY  H7   N8   C7   126.29  3.000
 EJY  C10  N8   C7   107.66  3.000
 EJY  H9   C11  H8   107.14  3.000
 EJY  H9   C11  C12  110.03  3.000
 EJY  H8   C11  C12  110.82  3.000
 EJY  H9   C11  C10  109.33  3.000
 EJY  H8   C11  C10  107.79  3.000
 EJY  C12  C11  C10  111.60  3.000
 EJY  C11  C12  C17  120.10  3.000
 EJY  C11  C12  C13  120.87  3.000
 EJY  C17  C12  C13  119.02  3.000
 EJY  H10  C14  C15  120.22  3.000
 EJY  H10  C14  C13  119.70  3.000
 EJY  C15  C14  C13  120.08  3.000
 EJY  H11  C16  C17  119.78  3.000
 EJY  H11  C16  C15  120.07  3.000
 EJY  C17  C16  C15  120.15  3.000
 EJY  C19  N18  C10  105.19  3.000
 EJY  N18  C19  C20  129.68  3.000
 EJY  C20  C19  C7   120.29  3.000
 EJY  N18  C19  C7   110.03  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
 EJY  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 EJY  CONST_02  C7   C19  C20  C4     0.00   0.0  0
 EJY  CONST_03  N18  C19  C20  C4   180.00   0.0  0
 EJY  CONST_04  N8   C7   C6   C5   180.00   0.0  0
 EJY  CONST_05  C19  C7   C6   C5     0.00   0.0  0
 EJY  CONST_06  C19  C20  C4   C5     0.00   0.0  0
 EJY  CONST_07  C10  N8   C7   C6   180.00   0.0  0
 EJY  CONST_08  N18  C19  C7   C6   180.00   0.0  0
 EJY  CONST_09  C20  C19  C7   C6     0.00   0.0  0
 EJY  CONST_10  C20  C4   C5   C6     0.00   0.0  0
 EJY  CONST_11  N18  C10  N8   C7     0.00   0.0  0
 EJY  CONST_12  C10  N18  C19  C7     0.00   0.0  0
 EJY  CONST_13  C19  C7   N8   C10    0.00   0.0  0
 EJY  CONST_14  C20  C19  N18  C10  180.00   0.0  0
 EJY  CONST_15  C16  C17  C12  C13    0.00   0.0  0
 EJY  CONST_16  C16  C15  C14  C13    0.00   0.0  0
 EJY  CONST_17  C12  C17  C16  C15    0.00   0.0  0
 EJY  CONST_18  C12  C13  C14  C15    0.00   0.0  0
 EJY  CONST_19  C14  C15  C16  C17    0.00   0.0  0
 EJY  CONST_20  C14  C13  C12  C17    0.00   0.0  0
 EJY  CONST_21  N8   C7   C19  C20  180.00   0.0  0
 EJY  CONST_22  C19  N18  C10  N8     0.00   0.0  0
 EJY  CONST_23  N18  C19  C7   N8     0.00   0.0  0
 EJY  CONST_24  N2   C4   C5   C6   180.00   0.0  0
 EJY  CONST_25  C11  C10  N8   C7   180.00   0.0  0
 EJY  CONST_26  C19  C20  C4   N2   180.00   0.0  0
 EJY  CONST_27  C16  C17  C12  C11  180.00   0.0  0
 EJY  CONST_28  C14  C13  C12  C11  180.00   0.0  0
 EJY  CONST_29  C19  N18  C10  C11  180.00   0.0  0
 EJY  CONST_30  H2   C6   C5   C4   180.00   0.0  0
 EJY  CONST_31  H6   C20  C4   C5   180.00   0.0  0
 EJY  CONST_32  H7   N8   C7   C6     0.00   0.0  0
 EJY  CONST_33  H1   C5   C6   C7   180.00   0.0  0
 EJY  CONST_34  H5   C17  C12  C13  180.00   0.0  0
 EJY  CONST_35  H4   C15  C14  C13  180.00   0.0  0
 EJY  CONST_36  H3   C13  C14  C15  180.00   0.0  0
 EJY  CONST_37  H11  C16  C17  C12  180.00   0.0  0
 EJY  CONST_38  H10  C14  C13  C12  180.00   0.0  0
 EJY  CONST_39  O3   N2   C4   C5   180.00   0.0  0
 EJY  CONST_40  O1   N2   C4   C5     0.00   0.0  0
 EJY  CONST_41  O3   N2   C4   C20    0.00   0.0  0
 EJY  CONST_42  O1   N2   C4   C20  180.00   0.0  0
 EJY  Var_01    C17  C12  C11  C10   70.66  30.0  2
 EJY  Var_02    C12  C11  C10  N8    62.12  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
 EJY  plan-1  C13  0.020
 EJY  plan-1  C15  0.020
 EJY  plan-1  C17  0.020
 EJY  plan-1  C11  0.020
 EJY  plan-1  C12  0.020
 EJY  plan-1  C14  0.020
 EJY  plan-1  C16  0.020
 EJY  plan-1  H3   0.020
 EJY  plan-1  H4   0.020
 EJY  plan-1  H5   0.020
 EJY  plan-1  H10  0.020
 EJY  plan-1  H11  0.020
 EJY  plan-2  C4   0.020
 EJY  plan-2  C5   0.020
 EJY  plan-2  C6   0.020
 EJY  plan-2  C7   0.020
 EJY  plan-2  C10  0.020
 EJY  plan-2  C20  0.020
 EJY  plan-2  N2   0.020
 EJY  plan-2  N8   0.020
 EJY  plan-2  C11  0.020
 EJY  plan-2  N18  0.020
 EJY  plan-2  C19  0.020
 EJY  plan-2  H1   0.020
 EJY  plan-2  H2   0.020
 EJY  plan-2  H6   0.020
 EJY  plan-2  H7   0.020
 EJY  plan-3  C4   0.020
 EJY  plan-3  O1   0.020
 EJY  plan-3  N2   0.020
 EJY  plan-3  O3   0.020

