# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 18:41:22 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 2-(1-methyl-1H-pyrazol-4-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2[nH]c3ccccc3n2
#
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
 S0D  S0D  2-(1-methyl-1H-pyrazol-4-yl)-1H-benzimidazole  ligand  25  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S0D
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
 S0D  C15  C  CR16  0  -0.280  -4.3763  -0.4843  -0.0619
 S0D  C14  C  CR16  0  -0.270  -4.2634   0.9124   0.0010
 S0D  C12  C  CR16  0  -0.316  -3.2568  -1.2998  -0.0851
 S0D  C13  C  CR16  0  -0.347  -3.0285   1.5363   0.0413
 S0D  C8   C  CR15  0  -0.085   2.3328  -1.3384  -0.0025
 S0D  C6   C  CR15  0   0.056   2.4434   0.8573   0.0048
 S0D  C2   C  CR5   0  -0.218   1.5301  -0.1809   0.0019
 S0D  C9   C  CR56  0   0.332  -2.0222  -0.6648  -0.0435
 S0D  C10  C  CR56  0   0.142  -1.8883   0.7333   0.0184
 S0D  C1   C  CR5   0   0.451   0.0930  -0.0549   0.0010
 S0D  N5   N  N     0  -0.269   3.6129  -1.0301  -0.0026
 S0D  N3   N  NR15  0  -0.727  -0.7357  -1.1340  -0.0522
 S0D  N4   N  N     0  -0.485  -0.5602   1.0787   0.0449
 S0D  N7   N  NR5   0  -0.265   3.6590   0.3006   0.0027
 S0D  H1   H  HCR6  0   0.254  -5.3600  -0.9344  -0.0938
 S0D  H2   H  HCR6  0   0.252  -5.1634   1.5132   0.0190
 S0D  H3   H  HCR6  0   0.264  -3.3448  -2.3772  -0.1334
 S0D  H4   H  HCR6  0   0.252  -2.9463   2.6147   0.0872
 S0D  H5   H  HCR5  0   0.259   2.0282  -2.3744  -0.0020
 S0D  H6   H  HCR5  0   0.298   2.2973   1.9250   0.0100
 S0D  H7   H  HCH3  0   0.265   5.4342   0.8016  -0.9784
 S0D  H8   H  HCH3  0   0.261   4.7669   2.0461   0.0912
 S0D  H9   H  HCH3  0   0.267   5.5628   0.6255   0.7835
 S0D  H10  H  HNR5  0   0.416  -0.4601  -2.1018  -0.0997
 S0D  C11  C  CH3   0  -0.507   4.9332   0.9798  -0.0291

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
 S0D  C11  N7   single    1.444  0.020  1.444
 S0D  N7   N5   aromatic  1.332  0.020  1.332
 S0D  N7   C6   aromatic  1.337  0.020  1.337
 S0D  N5   C8   aromatic  1.317  0.020  1.317
 S0D  C6   C2   aromatic  1.383  0.020  1.383
 S0D  C8   C2   aromatic  1.409  0.020  1.409
 S0D  C2   C1   single    1.443  0.020  1.443
 S0D  C1   N4   aromatic  1.309  0.020  1.309
 S0D  C1   N3   aromatic  1.362  0.020  1.362
 S0D  N4   C10  aromatic  1.372  0.020  1.372
 S0D  N3   C9   aromatic  1.369  0.020  1.369
 S0D  C10  C9   aromatic  1.406  0.020  1.406
 S0D  C10  C13  aromatic  1.395  0.020  1.395
 S0D  C9   C12  aromatic  1.389  0.020  1.389
 S0D  C13  C14  aromatic  1.384  0.020  1.384
 S0D  C12  C15  aromatic  1.385  0.020  1.385
 S0D  C14  C15  aromatic  1.403  0.020  1.403
 S0D  C15  H1   single    0.930  0.020  1.080
 S0D  C14  H2   single    0.930  0.020  1.080
 S0D  C12  H3   single    0.930  0.020  1.080
 S0D  C13  H4   single    0.930  0.020  1.080
 S0D  C8   H5   single    0.930  0.020  1.080
 S0D  C6   H6   single    0.930  0.020  1.080
 S0D  C11  H7   single    0.970  0.020  1.090
 S0D  C11  H8   single    0.970  0.020  1.090
 S0D  C11  H9   single    0.970  0.020  1.090
 S0D  N3   H10  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
 S0D  H1   C15  C12  119.29  3.000
 S0D  H1   C15  C14  119.25  3.000
 S0D  C12  C15  C14  121.46  3.000
 S0D  H2   C14  C13  119.42  3.000
 S0D  H2   C14  C15  119.11  3.000
 S0D  C13  C14  C15  121.46  3.000
 S0D  H3   C12  C9   121.93  3.000
 S0D  H3   C12  C15  121.41  3.000
 S0D  C9   C12  C15  116.66  3.000
 S0D  H4   C13  C10  120.81  3.000
 S0D  H4   C13  C14  121.19  3.000
 S0D  C10  C13  C14  117.99  3.000
 S0D  H5   C8   N5   119.93  3.000
 S0D  H5   C8   C2   128.87  3.000
 S0D  N5   C8   C2   111.20  3.000
 S0D  H6   C6   N7   122.40  3.000
 S0D  H6   C6   C2   130.87  3.000
 S0D  N7   C6   C2   106.73  3.000
 S0D  C1   C2   C6   126.33  3.000
 S0D  C1   C2   C8   129.75  3.000
 S0D  C6   C2   C8   103.92  3.000
 S0D  N3   C9   C10  104.57  3.000
 S0D  C10  C9   C12  122.73  3.000
 S0D  N3   C9   C12  132.71  3.000
 S0D  N4   C10  C9   110.08  3.000
 S0D  C9   C10  C13  119.69  3.000
 S0D  N4   C10  C13  130.23  3.000
 S0D  N4   C1   N3   112.58  3.000
 S0D  N3   C1   C2   122.49  3.000
 S0D  N4   C1   C2   124.94  3.000
 S0D  N7   N5   C8   105.53  3.000
 S0D  H10  N3   C1   126.64  3.000
 S0D  H10  N3   C9   125.90  3.000
 S0D  C1   N3   C9   107.46  3.000
 S0D  C1   N4   C10  105.32  3.000
 S0D  N5   N7   C11  120.03  3.000
 S0D  N5   N7   C6   112.62  3.000
 S0D  C11  N7   C6   127.32  3.000
 S0D  H9   C11  H8   109.02  3.000
 S0D  H9   C11  H7   109.39  3.000
 S0D  H8   C11  H7   109.15  3.000
 S0D  H9   C11  N7   109.95  3.000
 S0D  H8   C11  N7   108.92  3.000
 S0D  H7   C11  N7   110.38  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
 S0D  CONST_01  N3   C9   C12  C15   180.00   0.0  0
 S0D  CONST_02  C10  C9   C12  C15     0.00   0.0  0
 S0D  CONST_03  C10  C13  C14  C15     0.00   0.0  0
 S0D  CONST_04  N4   C10  C13  C14   180.00   0.0  0
 S0D  CONST_05  C9   C10  C13  C14     0.00   0.0  0
 S0D  CONST_06  C9   C12  C15  C14     0.00   0.0  0
 S0D  CONST_07  C1   N3   C9   C12   180.00   0.0  0
 S0D  CONST_08  N4   C10  C9   C12   180.00   0.0  0
 S0D  CONST_09  C13  C10  C9   C12     0.00   0.0  0
 S0D  CONST_10  C13  C14  C15  C12     0.00   0.0  0
 S0D  CONST_11  C1   N4   C10  C13   180.00   0.0  0
 S0D  CONST_12  N3   C9   C10  C13   180.00   0.0  0
 S0D  CONST_13  C6   N7   N5   C8      0.00   0.0  0
 S0D  CONST_14  N7   C6   C2   C8      0.00   0.0  0
 S0D  CONST_15  N4   C1   C2   C8    180.00   0.0  0
 S0D  CONST_16  N3   C1   C2   C8      0.00   0.0  0
 S0D  CONST_17  N5   C8   C2   C6      0.00   0.0  0
 S0D  CONST_18  N4   C1   C2   C6      0.00   0.0  0
 S0D  CONST_19  N3   C1   C2   C6    180.00   0.0  0
 S0D  CONST_20  N5   N7   C6   C2      0.00   0.0  0
 S0D  CONST_21  N7   N5   C8   C2      0.00   0.0  0
 S0D  CONST_22  C10  N4   C1   C2    180.00   0.0  0
 S0D  CONST_23  C9   N3   C1   C2    180.00   0.0  0
 S0D  CONST_24  N4   C1   N3   C9      0.00   0.0  0
 S0D  CONST_25  C1   N4   C10  C9      0.00   0.0  0
 S0D  CONST_26  N3   C1   N4   C10     0.00   0.0  0
 S0D  CONST_27  C1   N3   C9   C10     0.00   0.0  0
 S0D  CONST_28  N7   C6   C2   C1    180.00   0.0  0
 S0D  CONST_29  N5   C8   C2   C1    180.00   0.0  0
 S0D  CONST_30  N4   C10  C9   N3      0.00   0.0  0
 S0D  CONST_31  C11  N7   N5   C8    180.00   0.0  0
 S0D  CONST_32  C11  N7   C6   C2    180.00   0.0  0
 S0D  CONST_33  H4   C13  C14  C15   180.00   0.0  0
 S0D  CONST_34  H3   C12  C15  C14   180.00   0.0  0
 S0D  CONST_35  H10  N3   C9   C12     0.00   0.0  0
 S0D  CONST_36  H2   C14  C15  C12   180.00   0.0  0
 S0D  CONST_37  H1   C15  C14  C13   180.00   0.0  0
 S0D  CONST_38  H6   C6   C2   C8    180.00   0.0  0
 S0D  CONST_39  H5   C8   C2   C6    180.00   0.0  0
 S0D  Var_01    H7   C11  N7   C6   -111.81  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
 S0D  plan-1  C8   0.020
 S0D  plan-1  C6   0.020
 S0D  plan-1  C2   0.020
 S0D  plan-1  C1   0.020
 S0D  plan-1  N5   0.020
 S0D  plan-1  N7   0.020
 S0D  plan-1  H5   0.020
 S0D  plan-1  H6   0.020
 S0D  plan-1  C11  0.020
 S0D  plan-2  C15  0.020
 S0D  plan-2  C14  0.020
 S0D  plan-2  C12  0.020
 S0D  plan-2  C13  0.020
 S0D  plan-2  C2   0.020
 S0D  plan-2  C9   0.020
 S0D  plan-2  C10  0.020
 S0D  plan-2  C1   0.020
 S0D  plan-2  N3   0.020
 S0D  plan-2  N4   0.020
 S0D  plan-2  H1   0.020
 S0D  plan-2  H2   0.020
 S0D  plan-2  H3   0.020
 S0D  plan-2  H4   0.020
 S0D  plan-2  H10  0.020

