# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:50:56 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 2-imidazol-1-yl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1c2ccccc2nc1n3ccnc3
#
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
 5JE  5JE  2-imidazol-1-yl-1H-benzimidazole  ligand  22  14  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5JE
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
 5JE  C1   C  CR5   0   0.750  -0.5450  -0.0429  -0.0294
 5JE  N2   N  NR5   0  -0.552  -1.9290  -0.0309  -0.0273
 5JE  N3   N  NR15  0  -0.740   0.1876   1.0953  -0.0257
 5JE  N4   N  N     0  -0.492   0.1593  -1.1319  -0.0321
 5JE  C5   C  CR15  0  -0.096  -2.7294  -1.1523  -0.0301
 5JE  C6   C  CR15  0   0.102  -2.7616   1.0508  -0.0243
 5JE  C7   C  CR56  0   0.343   1.5061   0.7057  -0.0257
 5JE  C8   C  CR56  0   0.164   1.4656  -0.6974  -0.0298
 5JE  C9   C  CR15  0  -0.206  -4.0027  -0.6809  -0.0278
 5JE  N10  N  N     0  -0.438  -4.0088   0.6911  -0.0241
 5JE  C11  C  CR16  0  -0.302   2.6934   1.4234  -0.0212
 5JE  C12  C  CR16  0  -0.331   2.6530  -1.4255  -0.0306
 5JE  C13  C  CR16  0  -0.278   3.8639   0.6821  -0.0216
 5JE  C14  C  CR16  0  -0.268   3.8439  -0.7195  -0.0270
 5JE  H3   H  HNR5  0   0.432  -0.1450   2.0469  -0.0248
 5JE  H5   H  HCR5  0   0.307  -2.3210  -2.1476  -0.0289
 5JE  H6   H  HCR5  0   0.297  -2.4044   2.0688  -0.0230
 5JE  H9   H  HCR5  0   0.267  -4.9160  -1.2547  -0.0301
 5JE  H11  H  HCR6  0   0.271   2.7093   2.5050  -0.0175
 5JE  H12  H  HCR6  0   0.258   2.6412  -2.5075  -0.0342
 5JE  H13  H  HCR6  0   0.258   4.8154   1.1972  -0.0185
 5JE  H14  H  HCR6  0   0.256   4.7815  -1.2598  -0.0284

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
 5JE  C1   N2   single    1.384  0.020  1.384
 5JE  C1   N3   aromatic  1.354  0.020  1.354
 5JE  C1   N4   aromatic  1.297  0.020  1.297
 5JE  N2   C5   aromatic  1.378  0.020  1.378
 5JE  N2   C6   aromatic  1.365  0.020  1.365
 5JE  N3   C7   aromatic  1.375  0.020  1.375
 5JE  N4   C8   aromatic  1.377  0.020  1.377
 5JE  C5   C9   aromatic  1.358  0.020  1.358
 5JE  C6   N10  aromatic  1.298  0.020  1.298
 5JE  C7   C8   aromatic  1.404  0.020  1.404
 5JE  C7   C11  aromatic  1.387  0.020  1.387
 5JE  C8   C12  aromatic  1.393  0.020  1.393
 5JE  C9   N10  aromatic  1.372  0.020  1.372
 5JE  C11  C13  aromatic  1.385  0.020  1.385
 5JE  C12  C14  aromatic  1.384  0.020  1.384
 5JE  C13  C14  aromatic  1.402  0.020  1.402
 5JE  N3   H3   single    0.860  0.020  1.020
 5JE  C5   H5   single    0.930  0.020  1.080
 5JE  C6   H6   single    0.930  0.020  1.080
 5JE  C9   H9   single    0.930  0.020  1.080
 5JE  C11  H11  single    0.930  0.020  1.080
 5JE  C12  H12  single    0.930  0.020  1.080
 5JE  C13  H13  single    0.930  0.020  1.080
 5JE  C14  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
 5JE  N4   C1   N3   114.34  3.000
 5JE  N4   C1   N2   123.39  3.000
 5JE  N3   C1   N2   122.27  3.000
 5JE  C6   N2   C5   106.90  3.000
 5JE  C6   N2   C1   128.08  3.000
 5JE  C5   N2   C1   125.02  3.000
 5JE  H3   N3   C7   125.73  3.000
 5JE  H3   N3   C1   127.97  3.000
 5JE  C7   N3   C1   106.30  3.000
 5JE  C8   N4   C1   104.49  3.000
 5JE  H5   C5   C9   132.62  3.000
 5JE  H5   C5   N2   122.18  3.000
 5JE  C9   C5   N2   105.20  3.000
 5JE  H6   C6   N10  125.43  3.000
 5JE  H6   C6   N2   123.07  3.000
 5JE  N10  C6   N2   111.50  3.000
 5JE  C11  C7   C8   122.81  3.000
 5JE  C11  C7   N3   132.38  3.000
 5JE  C8   C7   N3   104.81  3.000
 5JE  C12  C8   C7   119.86  3.000
 5JE  C12  C8   N4   130.08  3.000
 5JE  C7   C8   N4   110.06  3.000
 5JE  H9   C9   N10  121.89  3.000
 5JE  H9   C9   C5   127.54  3.000
 5JE  N10  C9   C5   110.57  3.000
 5JE  C9   N10  C6   105.83  3.000
 5JE  H11  C11  C13  121.50  3.000
 5JE  H11  C11  C7   122.00  3.000
 5JE  C13  C11  C7   116.50  3.000
 5JE  H12  C12  C14  121.28  3.000
 5JE  H12  C12  C8   120.89  3.000
 5JE  C14  C12  C8   117.82  3.000
 5JE  H13  C13  C14  119.25  3.000
 5JE  H13  C13  C11  119.22  3.000
 5JE  C14  C13  C11  121.53  3.000
 5JE  H14  C14  C13  119.13  3.000
 5JE  H14  C14  C12  119.39  3.000
 5JE  C13  C14  C12  121.48  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
 5JE  CONST_01  C9   C5   N2   C1   180.00  0.0  0
 5JE  CONST_02  N10  C6   N2   C1   180.00  0.0  0
 5JE  CONST_03  C8   C7   N3   C1     0.00  0.0  0
 5JE  CONST_04  C11  C7   N3   C1   180.00  0.0  0
 5JE  CONST_05  C7   C8   N4   C1     0.00  0.0  0
 5JE  CONST_06  C12  C8   N4   C1   180.00  0.0  0
 5JE  CONST_07  C7   N3   C1   N2   180.00  0.0  0
 5JE  CONST_08  C8   N4   C1   N2   180.00  0.0  0
 5JE  CONST_09  N10  C9   C5   N2     0.00  0.0  0
 5JE  CONST_10  C9   N10  C6   N2     0.00  0.0  0
 5JE  CONST_11  C5   N2   C1   N3   180.00  0.0  0
 5JE  CONST_12  C6   N2   C1   N3     0.00  0.0  0
 5JE  CONST_13  C8   N4   C1   N3     0.00  0.0  0
 5JE  CONST_14  N4   C8   C7   N3     0.00  0.0  0
 5JE  CONST_15  C12  C8   C7   N3   180.00  0.0  0
 5JE  CONST_16  C13  C11  C7   N3   180.00  0.0  0
 5JE  CONST_17  C5   N2   C1   N4     0.00  0.0  0
 5JE  CONST_18  C6   N2   C1   N4   180.00  0.0  0
 5JE  CONST_19  C7   N3   C1   N4     0.00  0.0  0
 5JE  CONST_20  C11  C7   C8   N4   180.00  0.0  0
 5JE  CONST_21  C14  C12  C8   N4   180.00  0.0  0
 5JE  CONST_22  N10  C6   N2   C5     0.00  0.0  0
 5JE  CONST_23  C6   N10  C9   C5     0.00  0.0  0
 5JE  CONST_24  C9   C5   N2   C6     0.00  0.0  0
 5JE  CONST_25  C14  C12  C8   C7     0.00  0.0  0
 5JE  CONST_26  C14  C13  C11  C7     0.00  0.0  0
 5JE  CONST_27  C13  C11  C7   C8     0.00  0.0  0
 5JE  CONST_28  C13  C14  C12  C8     0.00  0.0  0
 5JE  CONST_29  C12  C8   C7   C11    0.00  0.0  0
 5JE  CONST_30  C12  C14  C13  C11    0.00  0.0  0
 5JE  CONST_31  H5   C5   N2   C1     0.00  0.0  0
 5JE  CONST_32  H6   C6   N2   C1     0.00  0.0  0
 5JE  CONST_33  H3   N3   C1   N2     0.00  0.0  0
 5JE  CONST_34  H9   C9   C5   N2   180.00  0.0  0
 5JE  CONST_35  H11  C11  C7   N3     0.00  0.0  0
 5JE  CONST_36  H12  C12  C8   N4     0.00  0.0  0
 5JE  CONST_37  H13  C13  C11  C7   180.00  0.0  0
 5JE  CONST_38  H14  C14  C12  C8   180.00  0.0  0

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
 5JE  plan-1  C1   0.020
 5JE  plan-1  N2   0.020
 5JE  plan-1  C5   0.020
 5JE  plan-1  C6   0.020
 5JE  plan-1  C9   0.020
 5JE  plan-1  N10  0.020
 5JE  plan-1  H5   0.020
 5JE  plan-1  H6   0.020
 5JE  plan-1  H9   0.020
 5JE  plan-2  C1   0.020
 5JE  plan-2  N2   0.020
 5JE  plan-2  N3   0.020
 5JE  plan-2  N4   0.020
 5JE  plan-2  C7   0.020
 5JE  plan-2  C8   0.020
 5JE  plan-2  C11  0.020
 5JE  plan-2  C12  0.020
 5JE  plan-2  C13  0.020
 5JE  plan-2  C14  0.020
 5JE  plan-2  H3   0.020
 5JE  plan-2  H11  0.020
 5JE  plan-2  H12  0.020
 5JE  plan-2  H13  0.020
 5JE  plan-2  H14  0.020

