# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 16:33:43 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-[3-(1H-benzimidazol-2-yl)-1H-pyrazol-4-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1c[nH]nc1c2[nH]c3ccccc3n2)c4ccccc4
#
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
 L0F  L0F  N-[3-(1H-benzimidazol-2-yl)-1H-pyrazol-4-yl]benzamide  ligand  36  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L0F
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
 L0F  O1   O  O     0  -0.469  -3.3076  -1.7924   0.0125
 L0F  C2   C  C     0   0.543  -2.6102  -0.7893   0.0025
 L0F  N3   N  NH1   0  -0.781  -1.2626  -0.8572  -0.0120
 L0F  C4   C  CR5   0   0.108  -0.5259  -2.0284  -0.0070
 L0F  C5   C  CR15  0  -0.006  -0.8961  -3.3569  -0.0027
 L0F  N6   N  NR15  0  -0.417   0.2609  -4.0521   0.0022
 L0F  N8   N  N     0  -0.272   1.3395  -3.3026   0.0017
 L0F  C9   C  CR5   0   0.113   0.8868  -2.0578  -0.0036
 L0F  C10  C  CR5   0   0.521   1.7587  -0.9075  -0.0064
 L0F  N11  N  N     0  -0.558   1.3221   0.3293  -0.0212
 L0F  C12  C  CR56  0   0.191   2.4500   1.1116  -0.0186
 L0F  C13  C  CR16  0  -0.338   2.5851   2.4991  -0.0297
 L0F  C14  C  CR16  0  -0.269   3.8654   3.0229  -0.0234
 L0F  C15  C  CR16  0  -0.278   4.9966   2.1925  -0.0063
 L0F  C16  C  CR16  0  -0.311   4.8823   0.8129   0.0049
 L0F  C17  C  CR56  0   0.316   3.5935   0.2940  -0.0017
 L0F  N18  N  NR15  0  -0.706   3.1104  -0.9880   0.0055
 L0F  C20  C  CR6   0  -0.054  -3.2075   0.5811   0.0049
 L0F  C21  C  CR16  0  -0.263  -4.5986   0.6719  -0.0151
 L0F  C22  C  CR16  0  -0.241  -5.2269   1.9070  -0.0127
 L0F  C23  C  CR16  0  -0.250  -4.4728   3.0724   0.0104
 L0F  C24  C  CR16  0  -0.236  -3.0870   2.9933   0.0317
 L0F  C25  C  CR16  0  -0.295  -2.4574   1.7580   0.0296
 L0F  H7   H  HNR5  0   0.432   0.3509  -5.0561   0.0054
 L0F  H19  H  HNR5  0   0.424   3.6506  -1.8393   0.0208
 L0F  H26  H  HNH1  0   0.455  -0.6839  -0.0233  -0.0255
 L0F  H27  H  HCR5  0   0.304  -1.8519  -3.8471  -0.0047
 L0F  H28  H  HCR6  0   0.256   1.7151   3.1427  -0.0438
 L0F  H29  H  HCR6  0   0.255   4.0010   4.0963  -0.0316
 L0F  H30  H  HCR6  0   0.257   5.9812   2.6415  -0.0010
 L0F  H31  H  HCR6  0   0.269   5.7543   0.1725   0.0185
 L0F  H32  H  HCR6  0   0.261  -5.1945  -0.2302  -0.0335
 L0F  H33  H  HCR6  0   0.264  -6.3074   1.9594  -0.0284
 L0F  H34  H  HCR6  0   0.266  -4.9615   4.0379   0.0125
 L0F  H35  H  HCR6  0   0.268  -2.4896   3.8950   0.0517
 L0F  H36  H  HCR6  0   0.239  -1.3747   1.7512   0.0498

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
 L0F  C2   O1   double    1.222  0.020  1.222
 L0F  C20  C2   single    1.495  0.020  1.495
 L0F  C2   N3   single    1.349  0.020  1.349
 L0F  H26  N3   single    0.860  0.020  1.020
 L0F  N3   C4   single    1.384  0.020  1.384
 L0F  C9   C4   aromatic  1.413  0.020  1.413
 L0F  C4   C5   aromatic  1.379  0.020  1.379
 L0F  C5   H27  single    0.930  0.020  1.080
 L0F  C5   N6   aromatic  1.350  0.020  1.350
 L0F  N8   N6   aromatic  1.313  0.020  1.313
 L0F  N6   H7   single    0.860  0.020  1.020
 L0F  C9   N8   aromatic  1.325  0.020  1.325
 L0F  C10  C9   single    1.443  0.020  1.443
 L0F  N11  C10  aromatic  1.312  0.020  1.312
 L0F  C10  N18  aromatic  1.354  0.020  1.354
 L0F  C12  N11  aromatic  1.373  0.020  1.373
 L0F  C13  C12  aromatic  1.394  0.020  1.394
 L0F  C12  C17  aromatic  1.406  0.020  1.406
 L0F  H28  C13  single    0.930  0.020  1.080
 L0F  C14  C13  aromatic  1.383  0.020  1.383
 L0F  H29  C14  single    0.930  0.020  1.080
 L0F  C14  C15  aromatic  1.403  0.020  1.403
 L0F  H30  C15  single    0.930  0.020  1.080
 L0F  C15  C16  aromatic  1.384  0.020  1.384
 L0F  C16  C17  aromatic  1.389  0.020  1.389
 L0F  C16  H31  single    0.930  0.020  1.080
 L0F  C17  N18  aromatic  1.370  0.020  1.370
 L0F  N18  H19  single    0.860  0.020  1.020
 L0F  C21  C20  aromatic  1.394  0.020  1.394
 L0F  C25  C20  aromatic  1.396  0.020  1.396
 L0F  C22  C21  aromatic  1.386  0.020  1.386
 L0F  C21  H32  single    0.930  0.020  1.080
 L0F  H33  C22  single    0.930  0.020  1.080
 L0F  C23  C22  aromatic  1.388  0.020  1.388
 L0F  H34  C23  single    0.930  0.020  1.080
 L0F  C23  C24  aromatic  1.388  0.020  1.388
 L0F  H35  C24  single    0.930  0.020  1.080
 L0F  C24  C25  aromatic  1.386  0.020  1.386
 L0F  C25  H36  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
 L0F  C20  C2   N3   116.43  3.000
 L0F  N3   C2   O1   121.93  3.000
 L0F  C20  C2   O1   121.64  3.000
 L0F  H26  N3   C4   113.07  3.000
 L0F  C4   N3   C2   125.05  3.000
 L0F  H26  N3   C2   121.88  3.000
 L0F  C9   C4   C5   104.38  3.000
 L0F  C5   C4   N3   132.26  3.000
 L0F  C9   C4   N3   123.36  3.000
 L0F  H27  C5   N6   121.85  3.000
 L0F  N6   C5   C4   105.43  3.000
 L0F  H27  C5   C4   132.72  3.000
 L0F  H7   N6   N8   119.67  3.000
 L0F  H7   N6   C5   126.12  3.000
 L0F  N8   N6   C5   114.20  3.000
 L0F  C9   N8   N6   104.81  3.000
 L0F  C10  C9   N8   122.85  3.000
 L0F  C10  C9   C4   125.97  3.000
 L0F  N8   C9   C4   111.18  3.000
 L0F  N18  C10  N11  112.85  3.000
 L0F  N18  C10  C9   123.75  3.000
 L0F  N11  C10  C9   123.39  3.000
 L0F  C12  N11  C10  105.30  3.000
 L0F  C17  C12  C13  120.00  3.000
 L0F  C17  C12  N11  109.69  3.000
 L0F  C13  C12  N11  130.31  3.000
 L0F  H28  C13  C14  121.26  3.000
 L0F  C14  C13  C12  117.81  3.000
 L0F  H28  C13  C12  120.93  3.000
 L0F  H29  C14  C15  119.09  3.000
 L0F  C15  C14  C13  121.47  3.000
 L0F  H29  C14  C13  119.44  3.000
 L0F  H30  C15  C16  119.25  3.000
 L0F  C16  C15  C14  121.55  3.000
 L0F  H30  C15  C14  119.20  3.000
 L0F  H31  C16  C17  121.78  3.000
 L0F  H31  C16  C15  121.56  3.000
 L0F  C17  C16  C15  116.66  3.000
 L0F  N18  C17  C16  132.57  3.000
 L0F  N18  C17  C12  104.92  3.000
 L0F  C16  C17  C12  122.51  3.000
 L0F  H19  N18  C17  126.95  3.000
 L0F  H19  N18  C10  125.81  3.000
 L0F  C17  N18  C10  107.24  3.000
 L0F  C25  C20  C21  118.79  3.000
 L0F  C25  C20  C2   123.94  3.000
 L0F  C21  C20  C2   117.28  3.000
 L0F  H32  C21  C22  119.59  3.000
 L0F  H32  C21  C20  119.72  3.000
 L0F  C22  C21  C20  120.69  3.000
 L0F  H33  C22  C23  120.14  3.000
 L0F  C23  C22  C21  120.13  3.000
 L0F  H33  C22  C21  119.73  3.000
 L0F  H34  C23  C24  120.11  3.000
 L0F  C24  C23  C22  119.65  3.000
 L0F  H34  C23  C22  120.24  3.000
 L0F  H35  C24  C25  119.47  3.000
 L0F  C25  C24  C23  120.27  3.000
 L0F  H35  C24  C23  120.27  3.000
 L0F  H36  C25  C24  117.36  3.000
 L0F  H36  C25  C20  122.17  3.000
 L0F  C24  C25  C20  120.48  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
 L0F  CONST_01  N6   N8   C9   C4     0.00   0.0  0
 L0F  CONST_02  N11  C10  C9   C4     0.00   0.0  0
 L0F  CONST_03  N18  C10  C9   C4   180.00   0.0  0
 L0F  CONST_04  N8   N6   C5   C4     0.00   0.0  0
 L0F  CONST_05  N8   C9   C4   C5     0.00   0.0  0
 L0F  CONST_06  C10  C9   C4   C5   180.00   0.0  0
 L0F  CONST_07  C9   N8   N6   C5     0.00   0.0  0
 L0F  CONST_08  C9   C4   C5   N6     0.00   0.0  0
 L0F  CONST_09  C10  C9   N8   N6   180.00   0.0  0
 L0F  CONST_10  N11  C10  C9   N8   180.00   0.0  0
 L0F  CONST_11  N18  C10  C9   N8     0.00   0.0  0
 L0F  CONST_12  C12  N11  C10  C9   180.00   0.0  0
 L0F  CONST_13  C17  N18  C10  C9   180.00   0.0  0
 L0F  CONST_14  C13  C12  N11  C10  180.00   0.0  0
 L0F  CONST_15  C17  C12  N11  C10    0.00   0.0  0
 L0F  CONST_16  C12  C17  N18  C10    0.00   0.0  0
 L0F  CONST_17  C16  C17  N18  C10  180.00   0.0  0
 L0F  CONST_18  C17  N18  C10  N11    0.00   0.0  0
 L0F  CONST_19  C14  C13  C12  N11  180.00   0.0  0
 L0F  CONST_20  C16  C17  C12  N11  180.00   0.0  0
 L0F  CONST_21  N18  C17  C12  N11    0.00   0.0  0
 L0F  CONST_22  N18  C10  N11  C12    0.00   0.0  0
 L0F  CONST_23  C15  C14  C13  C12    0.00   0.0  0
 L0F  CONST_24  C15  C16  C17  C12    0.00   0.0  0
 L0F  CONST_25  C16  C17  C12  C13    0.00   0.0  0
 L0F  CONST_26  N18  C17  C12  C13  180.00   0.0  0
 L0F  CONST_27  C16  C15  C14  C13    0.00   0.0  0
 L0F  CONST_28  C17  C12  C13  C14    0.00   0.0  0
 L0F  CONST_29  C17  C16  C15  C14    0.00   0.0  0
 L0F  CONST_30  N18  C17  C16  C15  180.00   0.0  0
 L0F  CONST_31  C23  C22  C21  C20    0.00   0.0  0
 L0F  CONST_32  C23  C24  C25  C20    0.00   0.0  0
 L0F  CONST_33  C24  C25  C20  C21    0.00   0.0  0
 L0F  CONST_34  C24  C23  C22  C21    0.00   0.0  0
 L0F  CONST_35  C25  C20  C21  C22    0.00   0.0  0
 L0F  CONST_36  C25  C24  C23  C22    0.00   0.0  0
 L0F  CONST_37  C22  C21  C20  C2   180.00   0.0  0
 L0F  CONST_38  C24  C25  C20  C2   180.00   0.0  0
 L0F  CONST_39  N8   C9   C4   N3   180.00   0.0  0
 L0F  CONST_40  C10  C9   C4   N3     0.00   0.0  0
 L0F  CONST_41  N6   C5   C4   N3   180.00   0.0  0
 L0F  CONST_42  H7   N6   C5   C4   180.00   0.0  0
 L0F  CONST_43  H27  C5   N6   N8   180.00   0.0  0
 L0F  CONST_44  H19  N18  C10  C9     0.00   0.0  0
 L0F  CONST_45  H28  C13  C12  N11    0.00   0.0  0
 L0F  CONST_46  H29  C14  C13  C12  180.00   0.0  0
 L0F  CONST_47  H31  C16  C17  C12  180.00   0.0  0
 L0F  CONST_48  H30  C15  C14  C13  180.00   0.0  0
 L0F  CONST_49  H33  C22  C21  C20  180.00   0.0  0
 L0F  CONST_50  H35  C24  C25  C20  180.00   0.0  0
 L0F  CONST_51  H36  C25  C20  C21  180.00   0.0  0
 L0F  CONST_52  H34  C23  C22  C21  180.00   0.0  0
 L0F  CONST_53  H32  C21  C22  C23  180.00   0.0  0
 L0F  CONST_54  C20  C2   N3   C4   180.00   0.0  0
 L0F  CONST_55  C9   C4   N3   C2   180.00   0.0  0
 L0F  CONST_56  C5   C4   N3   C2     0.00   0.0  0
 L0F  CONST_57  H26  N3   C4   C5   180.00   0.0  0
 L0F  CONST_58  C4   N3   C2   O1     0.00   0.0  0
 L0F  Var_01    C21  C20  C2   O1    -1.57  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
 L0F  plan-1  N3   0.020
 L0F  plan-1  C4   0.020
 L0F  plan-1  C5   0.020
 L0F  plan-1  N6   0.020
 L0F  plan-1  N8   0.020
 L0F  plan-1  C9   0.020
 L0F  plan-1  C10  0.020
 L0F  plan-1  H7   0.020
 L0F  plan-1  H27  0.020
 L0F  plan-2  C2   0.020
 L0F  plan-2  C20  0.020
 L0F  plan-2  C21  0.020
 L0F  plan-2  C22  0.020
 L0F  plan-2  C23  0.020
 L0F  plan-2  C24  0.020
 L0F  plan-2  C25  0.020
 L0F  plan-2  H32  0.020
 L0F  plan-2  H33  0.020
 L0F  plan-2  H34  0.020
 L0F  plan-2  H35  0.020
 L0F  plan-2  H36  0.020
 L0F  plan-3  C9   0.020
 L0F  plan-3  C10  0.020
 L0F  plan-3  N11  0.020
 L0F  plan-3  C12  0.020
 L0F  plan-3  C13  0.020
 L0F  plan-3  C14  0.020
 L0F  plan-3  C15  0.020
 L0F  plan-3  C16  0.020
 L0F  plan-3  C17  0.020
 L0F  plan-3  N18  0.020
 L0F  plan-3  H19  0.020
 L0F  plan-3  H28  0.020
 L0F  plan-3  H29  0.020
 L0F  plan-3  H30  0.020
 L0F  plan-3  H31  0.020
 L0F  plan-4  O1   0.020
 L0F  plan-4  C2   0.020
 L0F  plan-4  N3   0.020
 L0F  plan-4  C4   0.020
 L0F  plan-4  C20  0.020
 L0F  plan-4  H26  0.020

