# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:05:12 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)c2n[nH]cc2C(=O)Nc3[nH]c4ccccc4n3
#
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
 3H6  3H6  N-(1H-benzimidazol-2-yl)-3-(4-fluorophenyl)-1H-pyrazole-4-carboxamide  ligand  36  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3H6
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
 3H6  C11  C  CR56  0   0.345   3.9077   0.8311   0.2422
 3H6  C13  C  CR5   0  -0.328  -1.1943  -1.6790   0.1502
 3H6  C14  C  CR15  0   0.046  -1.1513  -3.0578   0.2574
 3H6  C17  C  CR5   0   0.290  -2.5796  -1.3726   0.0970
 3H6  C18  C  CR6   0   0.056  -3.2582  -0.0779  -0.0384
 3H6  C10  C  CR16  0  -0.311   4.6849   1.9328   0.5671
 3H6  N12  N  NR15  0  -0.715   2.5596   0.5846   0.3438
 3H6  O01  O  O     0  -0.451  -0.1599   0.3844   0.6461
 3H6  C02  C  C     0   0.491  -0.0606  -0.7567   0.2306
 3H6  C04  C  CR5   0   0.680   2.3610  -0.6697  -0.1248
 3H6  N05  N  N     0  -0.515   3.4500  -1.2660  -0.5252
 3H6  C06  C  CR56  0   0.154   4.4474  -0.3445  -0.3066
 3H6  C07  C  CR16  0  -0.339   5.8175  -0.4315  -0.5419
 3H6  C08  C  CR16  0  -0.272   6.6031   0.6632  -0.2188
 3H6  C09  C  CR16  0  -0.282   6.0467   1.8274   0.3268
 3H6  N15  N  NR15  0  -0.420  -2.4163  -3.4697   0.2645
 3H6  N16  N  N     0  -0.273  -3.2950  -2.4796   0.1610
 3H6  C19  C  CR16  0  -0.272  -2.7918   0.8987  -0.9165
 3H6  C20  C  CR16  0  -0.403  -3.4626   2.1022  -1.0659
 3H6  C21  C  CR6   0   0.521  -4.6096   2.3176  -0.3259
 3H6  F22  F  F     0  -0.313  -5.2641   3.4805  -0.4664
 3H6  C23  C  CR16  0  -0.402  -5.1059   1.3715   0.5491
 3H6  C24  C  CR16  0  -0.268  -4.4229   0.1725   0.6856
 3H6  H1   H  HCR5  0   0.315  -0.3307  -3.7493   0.3641
 3H6  H2   H  HCR6  0   0.266   4.2538   2.8315   0.9882
 3H6  H3   H  HNR5  0   0.427   1.8389   1.2016   0.6854
 3H6  H4   H  HNH1  0   0.430   1.1512  -2.1995  -0.6053
 3H6  H6   H  HCR6  0   0.253   6.2521  -1.3288  -0.9632
 3H6  H7   H  HCR6  0   0.252   7.6709   0.6206  -0.3907
 3H6  H8   H  HCR6  0   0.254   6.6929   2.6614   0.5669
 3H6  H9   H  HNR5  0   0.435  -2.7398  -4.4223   0.3356
 3H6  H10  H  HCR6  0   0.263  -1.9068   0.7226  -1.5124
 3H6  H11  H  HCR6  0   0.282  -3.1004   2.8555  -1.7531
 3H6  H12  H  HCR6  0   0.282  -6.0069   1.5634   1.1168
 3H6  H13  H  HCR6  0   0.265  -4.8012  -0.5721   1.3732
 3H6  N03  N  NH1   0  -0.746   1.1330  -1.2830  -0.1825

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
 3H6  C14  N15  aromatic  1.330  0.020  1.330
 3H6  C14  C13  aromatic  1.384  0.020  1.384
 3H6  O01  C02  double    1.218  0.020  1.218
 3H6  N15  N16  aromatic  1.328  0.020  1.328
 3H6  C13  C02  single    1.464  0.020  1.464
 3H6  C13  C17  aromatic  1.420  0.020  1.420
 3H6  C02  N03  single    1.368  0.020  1.368
 3H6  N16  C17  aromatic  1.320  0.020  1.320
 3H6  C10  C09  aromatic  1.387  0.020  1.387
 3H6  C10  C11  aromatic  1.387  0.020  1.387
 3H6  N12  C11  aromatic  1.374  0.020  1.374
 3H6  N12  C04  aromatic  1.354  0.020  1.354
 3H6  C09  C08  aromatic  1.401  0.020  1.401
 3H6  C11  C06  aromatic  1.405  0.020  1.405
 3H6  C17  C18  single    1.468  0.020  1.468
 3H6  C04  N03  single    1.374  0.020  1.374
 3H6  C04  N05  aromatic  1.305  0.020  1.305
 3H6  C08  C07  aromatic  1.386  0.020  1.386
 3H6  C06  N05  aromatic  1.375  0.020  1.375
 3H6  C06  C07  aromatic  1.393  0.020  1.393
 3H6  C19  C18  aromatic  1.394  0.020  1.394
 3H6  C19  C20  aromatic  1.386  0.020  1.386
 3H6  C18  C24  aromatic  1.394  0.020  1.394
 3H6  C20  C21  aromatic  1.382  0.020  1.382
 3H6  C24  C23  aromatic  1.387  0.020  1.387
 3H6  C21  C23  aromatic  1.381  0.020  1.381
 3H6  C21  F22  single    1.342  0.020  1.342
 3H6  C14  H1   single    0.930  0.020  1.080
 3H6  C10  H2   single    0.930  0.020  1.080
 3H6  N12  H3   single    0.860  0.020  1.020
 3H6  N03  H4   single    0.860  0.020  1.020
 3H6  C07  H6   single    0.930  0.020  1.080
 3H6  C08  H7   single    0.930  0.020  1.080
 3H6  C09  H8   single    0.930  0.020  1.080
 3H6  N15  H9   single    0.860  0.020  1.020
 3H6  C19  H10  single    0.930  0.020  1.080
 3H6  C20  H11  single    0.930  0.020  1.080
 3H6  C23  H12  single    0.930  0.020  1.080
 3H6  C24  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
 3H6  C06  C11  N12  104.81  3.000
 3H6  C06  C11  C10  122.74  3.000
 3H6  N12  C11  C10  132.45  3.000
 3H6  C02  C13  C17  128.44  3.000
 3H6  C17  C13  C14  104.38  3.000
 3H6  C02  C13  C14  126.84  3.000
 3H6  H1   C14  N15  121.63  3.000
 3H6  H1   C14  C13  132.09  3.000
 3H6  N15  C14  C13  106.22  3.000
 3H6  N16  C17  C18  119.59  3.000
 3H6  C18  C17  C13  130.15  3.000
 3H6  N16  C17  C13  110.25  3.000
 3H6  C24  C18  C19  118.74  3.000
 3H6  C24  C18  C17  119.78  3.000
 3H6  C19  C18  C17  121.43  3.000
 3H6  H2   C10  C09  121.45  3.000
 3H6  H2   C10  C11  121.85  3.000
 3H6  C09  C10  C11  116.70  3.000
 3H6  H3   N12  C04  125.41  3.000
 3H6  H3   N12  C11  128.05  3.000
 3H6  C04  N12  C11  106.53  3.000
 3H6  N03  C02  O01  122.30  3.000
 3H6  N03  C02  C13  114.62  3.000
 3H6  O01  C02  C13  123.08  3.000
 3H6  N05  C04  N03  121.96  3.000
 3H6  N05  C04  N12  114.03  3.000
 3H6  N03  C04  N12  124.01  3.000
 3H6  C06  N05  C04  104.50  3.000
 3H6  C07  C06  N05  130.14  3.000
 3H6  C07  C06  C11  119.74  3.000
 3H6  N05  C06  C11  110.12  3.000
 3H6  H6   C07  C08  121.20  3.000
 3H6  H6   C07  C06  120.83  3.000
 3H6  C08  C07  C06  117.97  3.000
 3H6  H7   C08  C09  119.11  3.000
 3H6  H7   C08  C07  119.42  3.000
 3H6  C09  C08  C07  121.47  3.000
 3H6  H8   C09  C08  119.32  3.000
 3H6  H8   C09  C10  119.29  3.000
 3H6  C08  C09  C10  121.38  3.000
 3H6  H9   N15  N16  119.84  3.000
 3H6  H9   N15  C14  126.71  3.000
 3H6  N16  N15  C14  113.45  3.000
 3H6  N15  N16  C17  105.70  3.000
 3H6  H10  C19  C20  118.57  3.000
 3H6  H10  C19  C18  120.46  3.000
 3H6  C20  C19  C18  120.96  3.000
 3H6  H11  C20  C21  120.62  3.000
 3H6  H11  C20  C19  120.73  3.000
 3H6  C21  C20  C19  118.65  3.000
 3H6  C23  C21  F22  119.00  3.000
 3H6  F22  C21  C20  118.94  3.000
 3H6  C23  C21  C20  122.06  3.000
 3H6  H12  C23  C24  120.79  3.000
 3H6  H12  C23  C21  120.68  3.000
 3H6  C24  C23  C21  118.54  3.000
 3H6  H13  C24  C23  119.04  3.000
 3H6  H13  C24  C18  119.91  3.000
 3H6  C23  C24  C18  121.05  3.000
 3H6  H4   N03  C04  114.00  3.000
 3H6  H4   N03  C02  119.43  3.000
 3H6  C04  N03  C02  126.54  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
 3H6  CONST_01  C08  C09  C10  C11     0.00   0.0  0
 3H6  CONST_02  N05  C04  N12  C11     0.00   0.0  0
 3H6  CONST_03  C04  N05  C06  C11     0.00   0.0  0
 3H6  CONST_04  C08  C07  C06  C11     0.00   0.0  0
 3H6  CONST_05  N16  N15  C14  C13     0.00   0.0  0
 3H6  CONST_06  N15  N16  C17  C13     0.00   0.0  0
 3H6  CONST_09  C17  N16  N15  C14     0.00   0.0  0
 3H6  CONST_10  N16  C17  C13  C14     0.00   0.0  0
 3H6  CONST_11  C18  C17  C13  C14   180.00   0.0  0
 3H6  CONST_12  N15  C14  C13  C17     0.00   0.0  0
 3H6  CONST_13  C20  C19  C18  C17   180.00   0.0  0
 3H6  CONST_14  C23  C24  C18  C17   180.00   0.0  0
 3H6  CONST_15  N15  N16  C17  C18   180.00   0.0  0
 3H6  CONST_16  C21  C20  C19  C18     0.00   0.0  0
 3H6  CONST_17  C21  C23  C24  C18     0.00   0.0  0
 3H6  CONST_18  C07  C08  C09  C10     0.00   0.0  0
 3H6  CONST_19  C04  N12  C11  C10   180.00   0.0  0
 3H6  CONST_20  N05  C06  C11  C10   180.00   0.0  0
 3H6  CONST_21  C07  C06  C11  C10     0.00   0.0  0
 3H6  CONST_22  C09  C10  C11  N12   180.00   0.0  0
 3H6  CONST_23  N05  C06  C11  N12     0.00   0.0  0
 3H6  CONST_24  C07  C06  C11  N12   180.00   0.0  0
 3H6  CONST_25  C06  N05  C04  N12     0.00   0.0  0
 3H6  CONST_26  C06  C11  N12  C04     0.00   0.0  0
 3H6  CONST_27  C07  C06  N05  C04   180.00   0.0  0
 3H6  CONST_28  C08  C07  C06  N05   180.00   0.0  0
 3H6  CONST_29  C09  C10  C11  C06     0.00   0.0  0
 3H6  CONST_30  C09  C08  C07  C06     0.00   0.0  0
 3H6  CONST_33  C23  C24  C18  C19     0.00   0.0  0
 3H6  CONST_34  C23  C21  C20  C19     0.00   0.0  0
 3H6  CONST_35  C24  C18  C19  C20     0.00   0.0  0
 3H6  CONST_36  C24  C23  C21  C20     0.00   0.0  0
 3H6  CONST_37  N03  C04  N12  C11   180.00   0.0  0
 3H6  CONST_38  C02  C13  C17  C18     0.00   0.0  0
 3H6  CONST_39  N15  C14  C13  C02   180.00   0.0  0
 3H6  CONST_40  N16  C17  C13  C02   180.00   0.0  0
 3H6  CONST_41  C06  N05  C04  N03   180.00   0.0  0
 3H6  CONST_42  F22  C21  C20  C19   180.00   0.0  0
 3H6  CONST_43  C24  C23  C21  F22   180.00   0.0  0
 3H6  CONST_44  H8   C09  C10  C11   180.00   0.0  0
 3H6  CONST_45  H6   C07  C06  C11   180.00   0.0  0
 3H6  CONST_46  H9   N15  C14  C13   180.00   0.0  0
 3H6  CONST_47  H1   C14  C13  C17   180.00   0.0  0
 3H6  CONST_48  H10  C19  C18  C17     0.00   0.0  0
 3H6  CONST_49  H13  C24  C18  C17     0.00   0.0  0
 3H6  CONST_50  H11  C20  C19  C18   180.00   0.0  0
 3H6  CONST_51  H12  C23  C24  C18   180.00   0.0  0
 3H6  CONST_52  H7   C08  C09  C10   180.00   0.0  0
 3H6  CONST_53  H3   N12  C11  C10     0.00   0.0  0
 3H6  CONST_54  H2   C10  C11  N12     0.00   0.0  0
 3H6  CONST_55  C04  N03  C02  C13   180.00   0.0  0
 3H6  CONST_56  C02  N03  C04  N12     0.00   0.0  0
 3H6  CONST_57  N05  C04  N03  C02   180.00   0.0  0
 3H6  CONST_58  H4   N03  C04  N12   180.00   0.0  0
 3H6  CONST_59  C04  N03  C02  O01     0.00   0.0  0
 3H6  Var_01    O01  C02  C13  C14  -150.23  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
 3H6  plan-1  C13  0.020
 3H6  plan-1  C14  0.020
 3H6  plan-1  C17  0.020
 3H6  plan-1  C18  0.020
 3H6  plan-1  C02  0.020
 3H6  plan-1  N15  0.020
 3H6  plan-1  N16  0.020
 3H6  plan-1  H1   0.020
 3H6  plan-1  H9   0.020
 3H6  plan-2  C17  0.020
 3H6  plan-2  C18  0.020
 3H6  plan-2  C19  0.020
 3H6  plan-2  C20  0.020
 3H6  plan-2  C21  0.020
 3H6  plan-2  F22  0.020
 3H6  plan-2  C23  0.020
 3H6  plan-2  C24  0.020
 3H6  plan-2  H10  0.020
 3H6  plan-2  H11  0.020
 3H6  plan-2  H12  0.020
 3H6  plan-2  H13  0.020
 3H6  plan-3  C11  0.020
 3H6  plan-3  C10  0.020
 3H6  plan-3  N12  0.020
 3H6  plan-3  C04  0.020
 3H6  plan-3  N05  0.020
 3H6  plan-3  C06  0.020
 3H6  plan-3  C07  0.020
 3H6  plan-3  C08  0.020
 3H6  plan-3  C09  0.020
 3H6  plan-3  H2   0.020
 3H6  plan-3  H3   0.020
 3H6  plan-3  H6   0.020
 3H6  plan-3  H7   0.020
 3H6  plan-3  H8   0.020
 3H6  plan-3  N03  0.020
 3H6  plan-4  C13  0.020
 3H6  plan-4  O01  0.020
 3H6  plan-4  C02  0.020
 3H6  plan-4  C04  0.020
 3H6  plan-4  H4   0.020
 3H6  plan-4  N03  0.020

