# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 16:17:49 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 6-methoxy-2-(1H-pyrazol-5-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc([nH]c2c1)c3[nH]ncc3
#
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
 62O  62O  6-methoxy-2-(1H-pyrazol-5-yl)-1H-benzimidazole  ligand  26  16  .  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_62O
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
 62O  C1   C  CR56  0   0.362   0.7898   0.4467   0.0039
 62O  C2   C  CR56  0   0.132   0.6502  -0.9514   0.0243
 62O  C7   C  CR5   0   0.469  -1.3245  -0.1598   0.0238
 62O  C8   C  CR6   0   0.378   3.1479   0.2744  -0.0015
 62O  C9   C  CR16  0  -0.391   3.0314  -1.1295   0.0184
 62O  C10  C  CR5   0   0.353  -2.7679  -0.0697   0.0317
 62O  C12  C  CR15  0  -0.487  -3.6985  -1.0898   0.0263
 62O  C14  C  CH3   0  -0.435   5.5252   0.1607  -0.0007
 62O  C15  C  CR15  0  -0.094  -4.9351  -0.4334   0.0396
 62O  N3   N  NR15  0  -0.730  -0.4921   0.9225   0.0023
 62O  C4   C  CR16  0  -0.419   2.0189   1.0867  -0.0095
 62O  N5   N  N     0  -0.472  -0.6790  -1.2936   0.0359
 62O  C6   C  CR16  0  -0.329   1.7923  -1.7455   0.0310
 62O  O11  O  O2    0  -0.476   4.3334   0.9195  -0.0135
 62O  N13  N  NR15  0  -0.517  -3.4765   1.0794   0.0467
 62O  N16  N  N     0  -0.249  -4.7852   0.8805   0.0519
 62O  H1   H  HCR6  0   0.279   3.9136  -1.7541   0.0250
 62O  H2   H  HCR5  0   0.271  -3.5015  -2.1481   0.0136
 62O  H3   H  HCH3  0   0.259   6.3454   0.8744  -0.0108
 62O  H4   H  HCH3  0   0.227   5.6088  -0.4558   0.8980
 62O  H5   H  HCH3  0   0.227   5.6113  -0.4836  -0.8794
 62O  H6   H  HCR5  0   0.268  -5.9224  -0.8688   0.0400
 62O  H7   H  HNR5  0   0.421  -0.7521   1.8957  -0.0056
 62O  H8   H  HCR6  0   0.272   2.1098   2.1652  -0.0243
 62O  H10  H  HCR6  0   0.261   1.7200  -2.8251   0.0462
 62O  H11  H  HNR5  0   0.422  -3.1322   2.0266   0.0572

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
 62O  N16  C15  aromatic  1.322  0.020  1.322
 62O  N16  N13  aromatic  1.324  0.020  1.324
 62O  C15  C12  aromatic  1.400  0.020  1.400
 62O  N13  C10  aromatic  1.350  0.020  1.350
 62O  C12  C10  aromatic  1.381  0.020  1.381
 62O  C10  C7   single    1.446  0.020  1.446
 62O  C7   N3   aromatic  1.365  0.020  1.365
 62O  C7   N5   aromatic  1.305  0.020  1.305
 62O  N3   C1   aromatic  1.367  0.020  1.367
 62O  N5   C2   aromatic  1.373  0.020  1.373
 62O  C1   C2   aromatic  1.405  0.020  1.405
 62O  C1   C4   aromatic  1.386  0.020  1.386
 62O  C2   C6   aromatic  1.391  0.020  1.391
 62O  C4   C8   aromatic  1.391  0.020  1.391
 62O  C14  O11  single    1.413  0.020  1.413
 62O  C6   C9   aromatic  1.384  0.020  1.384
 62O  C8   C9   aromatic  1.409  0.020  1.409
 62O  C8   O11  single    1.350  0.020  1.350
 62O  C9   H1   single    0.930  0.020  1.080
 62O  C12  H2   single    0.930  0.020  1.080
 62O  C14  H3   single    0.970  0.020  1.090
 62O  C14  H4   single    0.970  0.020  1.090
 62O  C14  H5   single    0.970  0.020  1.090
 62O  C15  H6   single    0.930  0.020  1.080
 62O  N3   H7   single    0.860  0.020  1.020
 62O  C4   H8   single    0.930  0.020  1.080
 62O  C6   H10  single    0.930  0.020  1.080
 62O  N13  H11  single    0.860  0.020  1.020

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
 62O  C4   C1   N3   132.13  3.000
 62O  C4   C1   C2   123.21  3.000
 62O  N3   C1   C2   104.66  3.000
 62O  C6   C2   N5   130.74  3.000
 62O  C6   C2   C1   119.11  3.000
 62O  N5   C2   C1   110.14  3.000
 62O  N5   C7   N3   112.79  3.000
 62O  N5   C7   C10  123.21  3.000
 62O  N3   C7   C10  123.99  3.000
 62O  O11  C8   C4   115.71  3.000
 62O  O11  C8   C9   123.30  3.000
 62O  C4   C8   C9   120.99  3.000
 62O  H1   C9   C6   118.26  3.000
 62O  H1   C9   C8   120.56  3.000
 62O  C6   C9   C8   121.18  3.000
 62O  N13  C10  C12  105.97  3.000
 62O  C12  C10  C7   128.80  3.000
 62O  N13  C10  C7   125.23  3.000
 62O  H2   C12  C15  128.51  3.000
 62O  H2   C12  C10  127.08  3.000
 62O  C15  C12  C10  104.41  3.000
 62O  H5   C14  H4   108.81  3.000
 62O  H5   C14  H3   108.67  3.000
 62O  H4   C14  H3   108.67  3.000
 62O  H5   C14  O11  112.07  3.000
 62O  H4   C14  O11  112.02  3.000
 62O  H3   C14  O11  106.48  3.000
 62O  H6   C15  N16  120.30  3.000
 62O  H6   C15  C12  128.24  3.000
 62O  N16  C15  C12  111.45  3.000
 62O  H7   N3   C7   127.48  3.000
 62O  H7   N3   C1   125.32  3.000
 62O  C7   N3   C1   107.20  3.000
 62O  H8   C4   C8   120.92  3.000
 62O  H8   C4   C1   122.33  3.000
 62O  C8   C4   C1   116.76  3.000
 62O  C7   N5   C2   105.21  3.000
 62O  H10  C6   C9   120.27  3.000
 62O  H10  C6   C2   120.98  3.000
 62O  C9   C6   C2   118.75  3.000
 62O  C14  O11  C8   118.95  3.000
 62O  H11  N13  N16  118.62  3.000
 62O  H11  N13  C10  128.37  3.000
 62O  N16  N13  C10  113.01  3.000
 62O  N13  N16  C15  105.15  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
 62O  CONST_01  C10  C7   N3   C1    180.00   0.0  0
 62O  CONST_02  N5   C7   N3   C1      0.00   0.0  0
 62O  CONST_03  C7   N5   C2   C1      0.00   0.0  0
 62O  CONST_04  C9   C6   C2   C1      0.00   0.0  0
 62O  CONST_05  C9   C8   C4   C1      0.00   0.0  0
 62O  CONST_06  C10  C7   N5   C2    180.00   0.0  0
 62O  CONST_07  N3   C7   N5   C2      0.00   0.0  0
 62O  CONST_08  C7   N3   C1   C2      0.00   0.0  0
 62O  CONST_09  C8   C4   C1   C2      0.00   0.0  0
 62O  CONST_10  C8   C9   C6   C2      0.00   0.0  0
 62O  CONST_11  N16  N13  C10  C7    180.00   0.0  0
 62O  CONST_12  C15  C12  C10  C7    180.00   0.0  0
 62O  CONST_13  C4   C1   N3   C7    180.00   0.0  0
 62O  CONST_14  C6   C2   N5   C7    180.00   0.0  0
 62O  CONST_15  N3   C1   C4   C8    180.00   0.0  0
 62O  CONST_16  N5   C2   C6   C9    180.00   0.0  0
 62O  CONST_17  C15  N16  N13  C10     0.00   0.0  0
 62O  CONST_18  N16  C15  C12  C10     0.00   0.0  0
 62O  CONST_19  N13  N16  C15  C12     0.00   0.0  0
 62O  CONST_20  N16  N13  C10  C12     0.00   0.0  0
 62O  CONST_21  N3   C7   C10  C12   180.00   0.0  0
 62O  CONST_22  N5   C7   C10  C12     0.00   0.0  0
 62O  CONST_23  N13  C10  C12  C15     0.00   0.0  0
 62O  CONST_24  N13  C10  C7   N3      0.00   0.0  0
 62O  CONST_25  N5   C2   C1   N3      0.00   0.0  0
 62O  CONST_26  C6   C2   C1   N3    180.00   0.0  0
 62O  CONST_27  N5   C2   C1   C4    180.00   0.0  0
 62O  CONST_28  C6   C2   C1   C4      0.00   0.0  0
 62O  CONST_29  C6   C9   C8   C4      0.00   0.0  0
 62O  CONST_30  N13  C10  C7   N5    180.00   0.0  0
 62O  CONST_31  O11  C8   C4   C1    180.00   0.0  0
 62O  CONST_32  O11  C8   C9   C6    180.00   0.0  0
 62O  CONST_33  H10  C6   C2   C1    180.00   0.0  0
 62O  CONST_34  H7   N3   C1   C2    180.00   0.0  0
 62O  CONST_35  H8   C4   C1   C2    180.00   0.0  0
 62O  CONST_36  H1   C9   C6   C2    180.00   0.0  0
 62O  CONST_37  H11  N13  C10  C7      0.00   0.0  0
 62O  CONST_38  H2   C12  C10  C7      0.00   0.0  0
 62O  CONST_39  H6   C15  C12  C10   180.00   0.0  0
 62O  Var_01    C4   C8   O11  C14   179.74  30.0  2
 62O  Var_02    H3   C14  O11  C8   -179.83  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
 62O  plan-1  C7   0.020
 62O  plan-1  C10  0.020
 62O  plan-1  C12  0.020
 62O  plan-1  C15  0.020
 62O  plan-1  N13  0.020
 62O  plan-1  N16  0.020
 62O  plan-1  H2   0.020
 62O  plan-1  H6   0.020
 62O  plan-1  H11  0.020
 62O  plan-2  C1   0.020
 62O  plan-2  C2   0.020
 62O  plan-2  C7   0.020
 62O  plan-2  C8   0.020
 62O  plan-2  C9   0.020
 62O  plan-2  C10  0.020
 62O  plan-2  N3   0.020
 62O  plan-2  C4   0.020
 62O  plan-2  N5   0.020
 62O  plan-2  C6   0.020
 62O  plan-2  O11  0.020
 62O  plan-2  H1   0.020
 62O  plan-2  H7   0.020
 62O  plan-2  H8   0.020
 62O  plan-2  H10  0.020

