# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 00:51:03 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(C(=O)Nc2[nH]c3ccccc3n2)c(C)n1
#
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
 3H5  3H5  N-(1H-benzimidazol-2-yl)-1,3-dimethyl-1H-pyrazole-4-carboxamide  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_3H5
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
 3H5  C11  C  CR5   0   0.708   1.1775  -0.4223   0.0964
 3H5  C13  C  CR56  0   0.206   3.1429   0.5113  -0.0056
 3H5  C14  C  CR16  0  -0.214   4.2805   1.2977  -0.0888
 3H5  C15  C  CR16  0  -0.321   5.5032   0.6463  -0.0375
 3H5  C16  C  CR16  0  -0.262   5.5750  -0.7426   0.0893
 3H5  C02  C  CR5   0   0.321  -3.5604   1.0455  -0.0839
 3H5  N03  N  N     0  -0.262  -4.7050   0.3857  -0.0562
 3H5  N04  N  NR5   0  -0.312  -4.3840  -0.9086  -0.1032
 3H5  C05  C  CH3   0  -0.474  -5.4001  -1.9220  -0.0537
 3H5  C06  C  CR15  0   0.016  -3.0796  -1.0858  -0.1579
 3H5  C07  C  CR5   0  -0.286  -2.4772   0.1570  -0.1279
 3H5  C08  C  C     0   0.528  -1.0782   0.5292  -0.1118
 3H5  O09  O  O     0  -0.546  -0.6685   1.6487  -0.3008
 3H5  N10  N  NH1   0  -0.698  -0.1958  -0.5163   0.1518
 3H5  N12  N  NR15  0  -0.734   1.7975   0.7925  -0.0371
 3H5  C17  C  CR16  0  -0.297   4.4348  -1.5198   0.1648
 3H5  C18  C  CR56  0   0.116   3.1994  -0.8961   0.1247
 3H5  N19  N  N     0  -0.454   1.9522  -1.4370   0.1936
 3H5  H1   H  HCR6  0   0.266   4.2436   2.3734  -0.1874
 3H5  H2   H  HCR6  0   0.259   6.4114   1.2291  -0.0911
 3H5  H3   H  HCR6  0   0.257   6.5484  -1.2117   0.1322
 3H5  H4   H  HCH3  0   0.213  -2.8762   2.8625   0.8099
 3H5  H5   H  HCH3  0   0.289  -3.0484   2.9595  -0.9018
 3H5  H6   H  HCH3  0   0.235  -4.5087   2.9418   0.1111
 3H5  H7   H  HCH3  0   0.306  -6.2608  -1.5858  -0.6035
 3H5  H8   H  HCH3  0   0.288  -5.0802  -2.8417  -0.5104
 3H5  H9   H  HCH3  0   0.233  -5.6989  -2.1414   0.9607
 3H5  H10  H  HCR5  0   0.315  -2.7041  -2.0873  -0.1059
 3H5  H11  H  HNH1  0   0.438  -0.5075  -1.3973   0.5023
 3H5  H12  H  HNR5  0   0.386   1.2111   1.6085  -0.1118
 3H5  H13  H  HCR6  0   0.235   4.4766  -2.5922   0.2627
 3H5  C01  C  CH3   0  -0.755  -3.5068   2.5323  -0.0134

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
 3H5  C15  C14  aromatic  1.386  0.020  1.386
 3H5  C15  C16  aromatic  1.397  0.020  1.397
 3H5  C14  C13  aromatic  1.385  0.020  1.385
 3H5  C16  C17  aromatic  1.382  0.020  1.382
 3H5  C13  C18  aromatic  1.415  0.020  1.415
 3H5  C13  N12  aromatic  1.375  0.020  1.375
 3H5  C17  C18  aromatic  1.384  0.020  1.384
 3H5  C18  N19  aromatic  1.361  0.020  1.361
 3H5  N12  C11  aromatic  1.370  0.020  1.370
 3H5  N19  C11  aromatic  1.280  0.020  1.280
 3H5  C11  N10  single    1.378  0.020  1.378
 3H5  O09  C08  double    1.207  0.020  1.207
 3H5  N10  C08  single    1.393  0.020  1.393
 3H5  C08  C07  single    1.448  0.020  1.448
 3H5  C01  C02  single    1.489  0.020  1.489
 3H5  C07  C02  aromatic  1.402  0.020  1.402
 3H5  C07  C06  aromatic  1.381  0.020  1.381
 3H5  C02  N03  aromatic  1.321  0.020  1.321
 3H5  N03  N04  aromatic  1.334  0.020  1.334
 3H5  C06  N04  aromatic  1.318  0.020  1.318
 3H5  N04  C05  single    1.436  0.020  1.436
 3H5  C14  H1   single    0.930  0.020  1.080
 3H5  C15  H2   single    0.930  0.020  1.080
 3H5  C16  H3   single    0.930  0.020  1.080
 3H5  C01  H4   single    0.970  0.020  1.090
 3H5  C01  H5   single    0.970  0.020  1.090
 3H5  C01  H6   single    0.970  0.020  1.090
 3H5  C05  H7   single    0.970  0.020  1.090
 3H5  C05  H8   single    0.970  0.020  1.090
 3H5  C05  H9   single    0.970  0.020  1.090
 3H5  C06  H10  single    0.930  0.020  1.080
 3H5  N10  H11  single    0.860  0.020  1.020
 3H5  N12  H12  single    0.860  0.020  1.020
 3H5  C17  H13  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
 3H5  N19  C11  N12  115.86  3.000
 3H5  N19  C11  N10  123.10  3.000
 3H5  N12  C11  N10  121.02  3.000
 3H5  C18  C13  N12  104.16  3.000
 3H5  N12  C13  C14  133.32  3.000
 3H5  C18  C13  C14  122.51  3.000
 3H5  H1   C14  C15  120.07  3.000
 3H5  H1   C14  C13  122.84  3.000
 3H5  C15  C14  C13  117.09  3.000
 3H5  H2   C15  C16  119.85  3.000
 3H5  H2   C15  C14  119.09  3.000
 3H5  C16  C15  C14  121.06  3.000
 3H5  H3   C16  C17  119.77  3.000
 3H5  H3   C16  C15  118.77  3.000
 3H5  C17  C16  C15  121.46  3.000
 3H5  C07  C02  N03  110.70  3.000
 3H5  N03  C02  C01  121.91  3.000
 3H5  C07  C02  C01  127.33  3.000
 3H5  N04  N03  C02  105.98  3.000
 3H5  C06  N04  C05  127.39  3.000
 3H5  C05  N04  N03  120.87  3.000
 3H5  C06  N04  N03  111.72  3.000
 3H5  H9   C05  H8   107.90  3.000
 3H5  H9   C05  H7   108.81  3.000
 3H5  H8   C05  H7   106.75  3.000
 3H5  H9   C05  N04  111.81  3.000
 3H5  H8   C05  N04  112.23  3.000
 3H5  H7   C05  N04  109.16  3.000
 3H5  H10  C06  C07  133.43  3.000
 3H5  H10  C06  N04  118.09  3.000
 3H5  C07  C06  N04  108.05  3.000
 3H5  C08  C07  C06  130.76  3.000
 3H5  C06  C07  C02  103.53  3.000
 3H5  C08  C07  C02  125.70  3.000
 3H5  N10  C08  O09  120.70  3.000
 3H5  N10  C08  C07  114.92  3.000
 3H5  O09  C08  C07  124.38  3.000
 3H5  H11  N10  C08  122.07  3.000
 3H5  H11  N10  C11  112.68  3.000
 3H5  C08  N10  C11  124.93  3.000
 3H5  H12  N12  C13  137.46  3.000
 3H5  H12  N12  C11  117.51  3.000
 3H5  C13  N12  C11  105.02  3.000
 3H5  H13  C17  C18  119.05  3.000
 3H5  H13  C17  C16  122.18  3.000
 3H5  C18  C17  C16  118.77  3.000
 3H5  N19  C18  C17  129.58  3.000
 3H5  N19  C18  C13  111.31  3.000
 3H5  C17  C18  C13  119.11  3.000
 3H5  C18  N19  C11  103.63  3.000
 3H5  H6   C01  H5   109.48  3.000
 3H5  H6   C01  H4   109.40  3.000
 3H5  H5   C01  H4   104.75  3.000
 3H5  H6   C01  C02  110.34  3.000
 3H5  H5   C01  C02  111.64  3.000
 3H5  H4   C01  C02  111.07  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
 3H5  CONST_01  C14  C13  N12  C11  180.00   0.0  0
 3H5  CONST_02  C18  C13  N12  C11    0.00   0.0  0
 3H5  CONST_03  C13  C18  N19  C11    0.00   0.0  0
 3H5  CONST_04  C17  C18  N19  C11  180.00   0.0  0
 3H5  CONST_05  C16  C15  C14  C13    0.00   0.0  0
 3H5  CONST_06  C16  C17  C18  C13    0.00   0.0  0
 3H5  CONST_07  N19  C11  N12  C13    0.00   0.0  0
 3H5  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 3H5  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 3H5  CONST_10  N19  C18  C13  C14  180.00   0.0  0
 3H5  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 3H5  CONST_12  N12  C13  C14  C15  180.00   0.0  0
 3H5  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 3H5  CONST_14  N19  C18  C17  C16  180.00   0.0  0
 3H5  CONST_15  N04  C06  C07  C02    0.00   0.0  0
 3H5  CONST_16  C06  N04  N03  C02    0.00   0.0  0
 3H5  CONST_17  C06  C07  C02  N03    0.00   0.0  0
 3H5  CONST_18  C07  C06  N04  N03    0.00   0.0  0
 3H5  CONST_19  C07  C02  N03  N04    0.00   0.0  0
 3H5  CONST_20  C17  C18  C13  N12  180.00   0.0  0
 3H5  CONST_21  N19  C18  C13  N12    0.00   0.0  0
 3H5  CONST_22  C18  N19  C11  N12    0.00   0.0  0
 3H5  CONST_23  N10  C11  N12  C13  180.00   0.0  0
 3H5  CONST_24  C06  C07  C02  C01  180.00   0.0  0
 3H5  CONST_25  N04  N03  C02  C01  180.00   0.0  0
 3H5  CONST_26  C05  N04  N03  C02  180.00   0.0  0
 3H5  CONST_27  C08  C07  C02  N03  180.00   0.0  0
 3H5  CONST_28  C08  C07  C06  N04  180.00   0.0  0
 3H5  CONST_29  C07  C06  N04  C05  180.00   0.0  0
 3H5  CONST_30  C18  N19  C11  N10  180.00   0.0  0
 3H5  CONST_31  H2   C15  C14  C13  180.00   0.0  0
 3H5  CONST_32  H13  C17  C18  C13  180.00   0.0  0
 3H5  CONST_33  H3   C16  C15  C14  180.00   0.0  0
 3H5  CONST_34  H12  N12  C13  C14    0.00   0.0  0
 3H5  CONST_35  H1   C14  C15  C16  180.00   0.0  0
 3H5  CONST_36  H10  C06  C07  C02  180.00   0.0  0
 3H5  CONST_37  C07  C08  N10  C11  180.00   0.0  0
 3H5  CONST_38  N12  C11  N10  C08    0.00   0.0  0
 3H5  CONST_39  N19  C11  N10  C08  180.00   0.0  0
 3H5  CONST_41  O09  C08  N10  C11    0.00   0.0  0
 3H5  Var_01    O09  C08  C07  C02  -14.06  30.0  2
 3H5  Var_02    H4   C01  C02  N03  124.40  30.0  2
 3H5  Var_03    H7   C05  N04  N03   37.16  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
 3H5  plan-1  C02  0.020
 3H5  plan-1  N03  0.020
 3H5  plan-1  N04  0.020
 3H5  plan-1  C05  0.020
 3H5  plan-1  C06  0.020
 3H5  plan-1  C07  0.020
 3H5  plan-1  C08  0.020
 3H5  plan-1  H10  0.020
 3H5  plan-1  C01  0.020
 3H5  plan-2  C11  0.020
 3H5  plan-2  C13  0.020
 3H5  plan-2  C14  0.020
 3H5  plan-2  C15  0.020
 3H5  plan-2  C16  0.020
 3H5  plan-2  N10  0.020
 3H5  plan-2  N12  0.020
 3H5  plan-2  C17  0.020
 3H5  plan-2  C18  0.020
 3H5  plan-2  N19  0.020
 3H5  plan-2  H1   0.020
 3H5  plan-2  H2   0.020
 3H5  plan-2  H3   0.020
 3H5  plan-2  H12  0.020
 3H5  plan-2  H13  0.020
 3H5  plan-3  C11  0.020
 3H5  plan-3  C07  0.020
 3H5  plan-3  C08  0.020
 3H5  plan-3  O09  0.020
 3H5  plan-3  N10  0.020
 3H5  plan-3  H11  0.020

