# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 18:41:09 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-(4-hydroxy-5-phenyl-1H-pyrazol-3-yl)-1H-benzimidazole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2[nH]c(nc2c1)c3n[nH]c(c3O)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
 6NH  6NH  2-(4-hydroxy-5-phenyl-1H-pyrazol-3-yl)-1H-benzimidazole-5-carboximidamide  ligand  38  24  .  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_6NH
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
 6NH  C1    C  CR6   0   0.032   4.8020  -0.3866   0.0298
 6NH  C2    C  CR16  0  -0.311   4.9812   1.0075   0.1163
 6NH  C3    C  CR16  0  -0.300   3.9117   1.8837   0.1578
 6NH  C4    C  CR56  0   0.320   2.6421   1.3265   0.1079
 6NH  C5    C  CR56  0   0.224   2.4385  -0.0625   0.0279
 6NH  C6    C  CR16  0  -0.378   3.5241  -0.9283  -0.0067
 6NH  C7    C  C     0   0.338   5.9707  -1.3098  -0.0105
 6NH  N1    N  NH2   0  -0.824   7.1349  -0.7595  -0.4672
 6NH  N2    N  N     0  -0.655   5.8234  -2.5075   0.4110
 6NH  N3    N  NR15  0  -0.712   1.3862   1.8711   0.1210
 6NH  N4    N  N     0  -0.571   1.0913  -0.3280  -0.0053
 6NH  C8    C  CR5   0   0.545   0.5060   0.8450   0.0527
 6NH  C5'   C  CR5   0   0.028  -0.9270   0.9664   0.0457
 6NH  C4'   C  CR5   0   0.131  -1.7990  -0.1381  -0.0139
 6NH  O4'   O  OH1   0  -0.634  -1.4616  -1.4300  -0.0815
 6NH  C3'   C  CR5   0   0.301  -3.0700   0.4097  -0.0064
 6NH  N2'   N  NR15  0  -0.493  -2.8620   1.7540   0.0528
 6NH  N1'   N  N     0  -0.260  -1.6000   2.1089   0.0905
 6NH  C1B   C  CR6   0   0.068  -4.3949  -0.1940  -0.0689
 6NH  C2B   C  CR16  0  -0.308  -5.4830   0.5187  -0.5802
 6NH  C3B   C  CR16  0  -0.239  -6.7451  -0.0532  -0.6214
 6NH  C4B   C  CR16  0  -0.264  -6.9419  -1.3498  -0.1656
 6NH  C5B   C  CR16  0  -0.236  -5.8646  -2.0691   0.3351
 6NH  C6B   C  CR16  0  -0.324  -4.6021  -1.4985   0.3879
 6NH  H2    H  HCR6  0   0.260   5.9805   1.4179   0.1761
 6NH  H3    H  HCR6  0   0.272   4.0661   2.9515   0.2321
 6NH  H6    H  HCR6  0   0.257   3.3831  -1.9988  -0.0706
 6NH  HN11  H  HNH2  0   0.394   7.0791   0.0052  -1.1194
 6NH  HN12  H  HNH2  0   0.390   7.9034  -1.3865  -0.6463
 6NH  HN2   H  H     0   0.322   6.6771  -3.0460   0.2911
 6NH  HN3   H  HNR5  0   0.427   1.1514   2.8505   0.1709
 6NH  H4'   H  HOH1  0   0.477  -0.4829  -1.4743  -0.0776
 6NH  H2'   H  HNR5  0   0.431  -3.5725   2.4668   0.1166
 6NH  H2B   H  HCR6  0   0.253  -5.3499   1.5223  -0.9654
 6NH  H3B   H  HCR6  0   0.262  -7.5760   0.5152  -1.0186
 6NH  H4B   H  HCR6  0   0.260  -7.9271  -1.7962  -0.2006
 6NH  H5B   H  HCR6  0   0.261  -6.0089  -3.0792   0.6957
 6NH  H6B   H  HCR6  0   0.257  -3.7807  -2.0686   0.7998

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
 6NH  C1   C2    aromatic  1.408  0.020  1.408
 6NH  C1   C6    aromatic  1.388  0.020  1.388
 6NH  C1   C7    single    1.490  0.020  1.490
 6NH  C2   C3    aromatic  1.383  0.020  1.383
 6NH  C2   H2    single    0.930  0.020  1.080
 6NH  C3   C4    aromatic  1.387  0.020  1.387
 6NH  C3   H3    single    0.930  0.020  1.080
 6NH  C4   C5    aromatic  1.406  0.020  1.406
 6NH  C4   N3    aromatic  1.369  0.020  1.369
 6NH  C5   C6    aromatic  1.389  0.020  1.389
 6NH  C5   N4    aromatic  1.373  0.020  1.373
 6NH  C6   H6    single    0.930  0.020  1.080
 6NH  C7   N1    single    1.366  0.020  1.366
 6NH  C7   N2    double    1.278  0.020  1.278
 6NH  N1   HN11  single    0.890  0.020  1.040
 6NH  N1   HN12  single    0.890  0.020  1.040
 6NH  N2   HN2   single    0.890  0.020  1.040
 6NH  N3   C8    aromatic  1.354  0.020  1.354
 6NH  N3   HN3   single    0.860  0.020  1.020
 6NH  N4   C8    aromatic  1.312  0.020  1.312
 6NH  C8   C5'   single    1.438  0.020  1.438
 6NH  C5'  C4'   aromatic  1.408  0.020  1.408
 6NH  C5'  N1'   aromatic  1.327  0.020  1.327
 6NH  C4'  O4'   single    1.337  0.020  1.337
 6NH  C4'  C3'   aromatic  1.384  0.020  1.384
 6NH  O4'  H4'   single    0.850  0.020  0.980
 6NH  C3'  N2'   aromatic  1.362  0.020  1.362
 6NH  C3'  C1B   single    1.457  0.020  1.457
 6NH  N2'  N1'   aromatic  1.311  0.020  1.311
 6NH  N2'  H2'   single    0.860  0.020  1.020
 6NH  C1B  C2B   aromatic  1.398  0.020  1.398
 6NH  C1B  C6B   aromatic  1.398  0.020  1.398
 6NH  C2B  C3B   aromatic  1.386  0.020  1.386
 6NH  C2B  H2B   single    0.930  0.020  1.080
 6NH  C3B  C4B   aromatic  1.388  0.020  1.388
 6NH  C3B  H3B   single    0.930  0.020  1.080
 6NH  C4B  C5B   aromatic  1.389  0.020  1.389
 6NH  C4B  H4B   single    0.930  0.020  1.080
 6NH  C5B  C6B   aromatic  1.386  0.020  1.386
 6NH  C5B  H5B   single    0.930  0.020  1.080
 6NH  C6B  H6B   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
 6NH  C7    C1   C6    118.65  3.000
 6NH  C7    C1   C2    121.02  3.000
 6NH  C6    C1   C2    120.33  3.000
 6NH  H2    C2   C3    118.17  3.000
 6NH  H2    C2   C1    119.76  3.000
 6NH  C3    C2   C1    122.05  3.000
 6NH  H3    C3   C4    121.98  3.000
 6NH  H3    C3   C2    121.14  3.000
 6NH  C4    C3   C2    116.87  3.000
 6NH  N3    C4   C5    105.11  3.000
 6NH  N3    C4   C3    132.80  3.000
 6NH  C5    C4   C3    122.10  3.000
 6NH  N4    C5   C6    130.21  3.000
 6NH  N4    C5   C4    109.53  3.000
 6NH  C6    C5   C4    120.26  3.000
 6NH  H6    C6   C5    121.09  3.000
 6NH  H6    C6   C1    120.51  3.000
 6NH  C5    C6   C1    118.39  3.000
 6NH  N2    C7   N1    125.86  3.000
 6NH  N2    C7   C1    118.77  3.000
 6NH  N1    C7   C1    115.33  3.000
 6NH  HN12  N1   HN11  113.56  3.000
 6NH  HN12  N1   C7    117.30  3.000
 6NH  HN11  N1   C7    118.38  3.000
 6NH  HN2   N2   C7    111.14  3.000
 6NH  HN3   N3   C8    125.97  3.000
 6NH  HN3   N3   C4    126.90  3.000
 6NH  C8    N3   C4    107.13  3.000
 6NH  C8    N4   C5    105.29  3.000
 6NH  C5'   C8   N4    121.31  3.000
 6NH  C5'   C8   N3    125.74  3.000
 6NH  N4    C8   N3    112.94  3.000
 6NH  N1'   C5'  C4'   111.27  3.000
 6NH  N1'   C5'  C8    125.31  3.000
 6NH  C4'   C5'  C8    123.43  3.000
 6NH  C3'   C4'  O4'   127.91  3.000
 6NH  C3'   C4'  C5'   104.94  3.000
 6NH  O4'   C4'  C5'   127.14  3.000
 6NH  H4'   O4'  C4'   107.19  3.000
 6NH  C1B   C3'  N2'   123.35  3.000
 6NH  C1B   C3'  C4'   132.12  3.000
 6NH  N2'   C3'  C4'   104.52  3.000
 6NH  H2'   N2'  N1'   119.00  3.000
 6NH  H2'   N2'  C3'   126.37  3.000
 6NH  N1'   N2'  C3'   114.54  3.000
 6NH  N2'   N1'  C5'   104.72  3.000
 6NH  C6B   C1B  C2B   118.70  3.000
 6NH  C6B   C1B  C3'   120.49  3.000
 6NH  C2B   C1B  C3'   120.81  3.000
 6NH  H2B   C2B  C3B   118.92  3.000
 6NH  H2B   C2B  C1B   120.46  3.000
 6NH  C3B   C2B  C1B   120.61  3.000
 6NH  H3B   C3B  C4B   120.14  3.000
 6NH  H3B   C3B  C2B   119.55  3.000
 6NH  C4B   C3B  C2B   120.30  3.000
 6NH  H4B   C4B  C5B   120.28  3.000
 6NH  H4B   C4B  C3B   120.24  3.000
 6NH  C5B   C4B  C3B   119.48  3.000
 6NH  H5B   C5B  C6B   119.53  3.000
 6NH  H5B   C5B  C4B   120.00  3.000
 6NH  C6B   C5B  C4B   120.46  3.000
 6NH  H6B   C6B  C5B   119.29  3.000
 6NH  H6B   C6B  C1B   120.26  3.000
 6NH  C5B   C6B  C1B   120.44  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
 6NH  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 6NH  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 6NH  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 6NH  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 6NH  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 6NH  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 6NH  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 6NH  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 6NH  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 6NH  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 6NH  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 6NH  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 6NH  CONST_13  C5'   C8   N3   C4   180.00   0.0  0
 6NH  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 6NH  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 6NH  CONST_16  C5'   C8   N4   C5   180.00   0.0  0
 6NH  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 6NH  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 6NH  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 6NH  CONST_20  C4'   C5'  C8   N3   180.00   0.0  0
 6NH  CONST_21  N1'   C5'  C8   N3     0.00   0.0  0
 6NH  CONST_22  C4'   C5'  C8   N4     0.00   0.0  0
 6NH  CONST_23  N1'   C5'  C8   N4   180.00   0.0  0
 6NH  CONST_24  C3'   C4'  C5'  C8   180.00   0.0  0
 6NH  CONST_25  N2'   N1'  C5'  C8   180.00   0.0  0
 6NH  CONST_26  N2'   C3'  C4'  C5'    0.00   0.0  0
 6NH  CONST_27  C1B   C3'  C4'  C5'  180.00   0.0  0
 6NH  CONST_28  C3'   N2'  N1'  C5'    0.00   0.0  0
 6NH  CONST_29  N2'   N1'  C5'  C4'    0.00   0.0  0
 6NH  CONST_30  N1'   N2'  C3'  C4'    0.00   0.0  0
 6NH  CONST_33  N1'   C5'  C4'  C3'    0.00   0.0  0
 6NH  CONST_34  C3B   C2B  C1B  C3'  180.00   0.0  0
 6NH  CONST_35  C5B   C6B  C1B  C3'  180.00   0.0  0
 6NH  CONST_38  C1B   C3'  N2'  N1'  180.00   0.0  0
 6NH  CONST_39  C4B   C3B  C2B  C1B    0.00   0.0  0
 6NH  CONST_40  C4B   C5B  C6B  C1B    0.00   0.0  0
 6NH  CONST_41  C5B   C6B  C1B  C2B    0.00   0.0  0
 6NH  CONST_42  C5B   C4B  C3B  C2B    0.00   0.0  0
 6NH  CONST_43  C6B   C1B  C2B  C3B    0.00   0.0  0
 6NH  CONST_44  C6B   C5B  C4B  C3B    0.00   0.0  0
 6NH  CONST_45  C7    C1   C2   C3   180.00   0.0  0
 6NH  CONST_46  C7    C1   C6   C5   180.00   0.0  0
 6NH  CONST_47  O4'   C4'  C5'  C8     0.00   0.0  0
 6NH  CONST_48  N1'   C5'  C4'  O4'  180.00   0.0  0
 6NH  CONST_49  N2'   C3'  C4'  O4'  180.00   0.0  0
 6NH  CONST_50  C1B   C3'  C4'  O4'    0.00   0.0  0
 6NH  CONST_51  H3    C3   C2   C1   180.00   0.0  0
 6NH  CONST_52  H6    C6   C1   C2   180.00   0.0  0
 6NH  CONST_53  HN3   N3   C4   C3     0.00   0.0  0
 6NH  CONST_54  H2    C2   C3   C4   180.00   0.0  0
 6NH  CONST_55  H2'   N2'  N1'  C5'  180.00   0.0  0
 6NH  CONST_56  H2B   C2B  C1B  C3'    0.00   0.0  0
 6NH  CONST_57  H6B   C6B  C1B  C3'    0.00   0.0  0
 6NH  CONST_58  H3B   C3B  C2B  C1B  180.00   0.0  0
 6NH  CONST_59  H5B   C5B  C6B  C1B  180.00   0.0  0
 6NH  CONST_60  H4B   C4B  C3B  C2B  180.00   0.0  0
 6NH  CONST_62  HN12  N1   C7   C1   180.00   0.0  0
 6NH  CONST_63  HN2   N2   C7   C1   180.00   0.0  0
 6NH  Var_01    N1    C7   C1   C2   -24.10  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
 6NH  plan-1  C8    0.020
 6NH  plan-1  C5'   0.020
 6NH  plan-1  C4'   0.020
 6NH  plan-1  O4'   0.020
 6NH  plan-1  C3'   0.020
 6NH  plan-1  N2'   0.020
 6NH  plan-1  N1'   0.020
 6NH  plan-1  C1B   0.020
 6NH  plan-1  H2'   0.020
 6NH  plan-2  C3'   0.020
 6NH  plan-2  C1B   0.020
 6NH  plan-2  C2B   0.020
 6NH  plan-2  C3B   0.020
 6NH  plan-2  C4B   0.020
 6NH  plan-2  C5B   0.020
 6NH  plan-2  C6B   0.020
 6NH  plan-2  H2B   0.020
 6NH  plan-2  H3B   0.020
 6NH  plan-2  H4B   0.020
 6NH  plan-2  H5B   0.020
 6NH  plan-2  H6B   0.020
 6NH  plan-3  C1    0.020
 6NH  plan-3  C2    0.020
 6NH  plan-3  C3    0.020
 6NH  plan-3  C4    0.020
 6NH  plan-3  C5    0.020
 6NH  plan-3  C6    0.020
 6NH  plan-3  C7    0.020
 6NH  plan-3  N3    0.020
 6NH  plan-3  N4    0.020
 6NH  plan-3  C8    0.020
 6NH  plan-3  C5'   0.020
 6NH  plan-3  H2    0.020
 6NH  plan-3  H3    0.020
 6NH  plan-3  H6    0.020
 6NH  plan-3  HN3   0.020
 6NH  plan-4  C1    0.020
 6NH  plan-4  C7    0.020
 6NH  plan-4  N1    0.020
 6NH  plan-4  N2    0.020
 6NH  plan-4  HN11  0.020
 6NH  plan-4  HN12  0.020
 6NH  plan-4  HN2   0.020

