# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:51:37 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-[(1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2cc(Nc3ncccc3C#N)ccc12
#
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
 NQE  NQE  2-[(1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)amino]pyridine-3-carbonitrile  ligand  34  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NQE
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
 NQE  C1   C  CR5   0   0.656  -28.0933  32.5658   -8.5273
 NQE  C2   C  CH3   0  -0.536  -29.7416  31.3071   -9.9195
 NQE  C3   C  CR56  0   0.353  -27.2520  31.1187  -10.0367
 NQE  C4   C  CR16  0  -0.369  -27.0690  30.1775  -11.0275
 NQE  C6   C  CR16  0  -0.361  -24.6807  30.4410  -10.6837
 NQE  C7   C  CR16  0  -0.310  -24.8820  31.3740   -9.6704
 NQE  C9   C  CR6   0   0.555  -26.0621  28.6539  -13.5104
 NQE  C10  C  CR16  0  -0.025  -27.7135  29.1798  -15.0033
 NQE  C12  C  CR16  0  -0.117  -26.2301  27.4345  -15.5939
 NQE  N4   N  NS    0  -0.244  -23.5571  26.2090  -13.7021
 NQE  C13  C  CR6   0  -0.150  -25.5861  27.6379  -14.3796
 NQE  C11  C  CR16  0  -0.363  -27.3206  28.2181  -15.9220
 NQE  N3   N  N     0  -0.456  -27.1115  29.3947  -13.8439
 NQE  N2   N  NH1   0  -0.779  -25.4414  28.8782  -12.3254
 NQE  C5   C  CR6   0   0.350  -25.7501  29.8489  -11.3588
 NQE  C8   C  CR56  0   0.321  -26.1825  31.7138   -9.3632
 NQE  N    N  NR5   0  -0.581  -26.7210  32.5923   -8.4483
 NQE  C    C  CH3   0  -0.535  -25.9659  33.4267   -7.5500
 NQE  N1   N  NR5   0  -0.586  -28.4053  31.6513   -9.5083
 NQE  O    O  O     0  -0.504  -28.8780  33.2194   -7.8628
 NQE  H1   H  HCH3  0   0.269  -30.4538  31.8800   -9.3333
 NQE  H2   H  HCH3  0   0.254  -29.8911  31.5372  -10.9741
 NQE  H3   H  HCH3  0   0.255  -29.9321  30.2460   -9.7599
 NQE  H4   H  HCR6  0   0.284  -27.9092  29.7156  -11.5219
 NQE  H5   H  HCR6  0   0.269  -23.6677  30.1709  -10.9548
 NQE  H6   H  HCR6  0   0.276  -24.0375  31.8172   -9.1599
 NQE  H7   H  HCR6  0   0.277  -28.5639  29.8177  -15.2168
 NQE  H8   H  HCR6  0   0.295  -25.8722  26.6670  -16.2667
 NQE  H9   H  HCR6  0   0.279  -27.8484  28.0908  -16.8552
 NQE  H10  H  HNH1  0   0.416  -24.5564  28.4156  -12.1844
 NQE  H11  H  HCH3  0   0.268  -26.6540  34.0090   -6.9449
 NQE  H12  H  HCH3  0   0.255  -25.3476  32.8204   -6.8884
 NQE  H13  H  HCH3  0   0.255  -25.3237  34.1103   -8.1050
 NQE  C14  C  CSP   0   0.030  -24.4699  26.8411  -14.0162

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
 NQE  C11  C12  aromatic  1.382  0.020  1.382
 NQE  C11  C10  aromatic  1.387  0.020  1.387
 NQE  C12  C13  aromatic  1.390  0.020  1.390
 NQE  C10  N3   aromatic  1.324  0.020  1.324
 NQE  C13  C14  single    1.419  0.020  1.419
 NQE  C13  C9   aromatic  1.419  0.020  1.419
 NQE  N3   C9   aromatic  1.327  0.020  1.327
 NQE  C14  N4   triple    1.154  0.020  1.154
 NQE  C9   N2   single    1.356  0.020  1.356
 NQE  N2   C5   single    1.404  0.020  1.404
 NQE  C5   C6   aromatic  1.396  0.020  1.396
 NQE  C5   C4   aromatic  1.399  0.020  1.399
 NQE  C6   C7   aromatic  1.392  0.020  1.392
 NQE  C4   C3   aromatic  1.379  0.020  1.379
 NQE  C7   C8   aromatic  1.379  0.020  1.379
 NQE  C3   C8   aromatic  1.397  0.020  1.397
 NQE  C3   N1   single    1.376  0.020  1.376
 NQE  C8   N    single    1.378  0.020  1.378
 NQE  N1   C2   single    1.440  0.020  1.440
 NQE  N1   C1   single    1.377  0.020  1.377
 NQE  N    C    single    1.440  0.020  1.440
 NQE  N    C1   single    1.375  0.020  1.375
 NQE  C1   O    double    1.218  0.020  1.218
 NQE  C2   H1   single    0.970  0.020  1.090
 NQE  C2   H2   single    0.970  0.020  1.090
 NQE  C2   H3   single    0.970  0.020  1.090
 NQE  C4   H4   single    0.930  0.020  1.080
 NQE  C6   H5   single    0.930  0.020  1.080
 NQE  C7   H6   single    0.930  0.020  1.080
 NQE  C10  H7   single    0.930  0.020  1.080
 NQE  C12  H8   single    0.930  0.020  1.080
 NQE  C11  H9   single    0.930  0.020  1.080
 NQE  N2   H10  single    0.860  0.020  1.020
 NQE  C    H11  single    0.970  0.020  1.090
 NQE  C    H12  single    0.970  0.020  1.090
 NQE  C    H13  single    0.970  0.020  1.090

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
 NQE  O    C1   N1   126.79  3.000
 NQE  O    C1   N    126.95  3.000
 NQE  N1   C1   N    106.26  3.000
 NQE  H3   C2   H2   108.87  3.000
 NQE  H3   C2   H1   108.66  3.000
 NQE  H2   C2   H1   108.73  3.000
 NQE  H3   C2   N1   110.68  3.000
 NQE  H2   C2   N1   110.69  3.000
 NQE  H1   C2   N1   109.17  3.000
 NQE  N1   C3   C8   106.96  3.000
 NQE  N1   C3   C4   130.66  3.000
 NQE  C8   C3   C4   122.39  3.000
 NQE  H4   C4   C5   121.68  3.000
 NQE  H4   C4   C3   121.21  3.000
 NQE  C5   C4   C3   117.11  3.000
 NQE  H5   C6   C5   119.31  3.000
 NQE  H5   C6   C7   118.99  3.000
 NQE  C5   C6   C7   121.70  3.000
 NQE  H6   C7   C8   122.03  3.000
 NQE  H6   C7   C6   120.34  3.000
 NQE  C8   C7   C6   117.63  3.000
 NQE  N2   C9   N3   119.28  3.000
 NQE  N2   C9   C13  119.99  3.000
 NQE  N3   C9   C13  120.73  3.000
 NQE  H7   C10  N3   115.70  3.000
 NQE  H7   C10  C11  119.98  3.000
 NQE  N3   C10  C11  124.32  3.000
 NQE  H8   C12  C11  121.04  3.000
 NQE  H8   C12  C13  119.61  3.000
 NQE  C11  C12  C13  119.35  3.000
 NQE  C14  C13  C12  120.42  3.000
 NQE  C14  C13  C9   120.60  3.000
 NQE  C12  C13  C9   118.98  3.000
 NQE  H9   C11  C12  121.60  3.000
 NQE  H9   C11  C10  121.06  3.000
 NQE  C12  C11  C10  117.35  3.000
 NQE  C10  N3   C9   119.28  3.000
 NQE  H10  N2   C5   114.44  3.000
 NQE  H10  N2   C9   116.61  3.000
 NQE  C5   N2   C9   127.95  3.000
 NQE  N2   C5   C6   117.23  3.000
 NQE  C6   C5   C4   120.52  3.000
 NQE  N2   C5   C4   122.19  3.000
 NQE  N    C8   C7   132.34  3.000
 NQE  N    C8   C3   107.01  3.000
 NQE  C7   C8   C3   120.64  3.000
 NQE  C    N    C8   125.36  3.000
 NQE  C    N    C1   124.78  3.000
 NQE  C8   N    C1   109.85  3.000
 NQE  H13  C    H12  108.89  3.000
 NQE  H13  C    H11  108.72  3.000
 NQE  H12  C    H11  108.64  3.000
 NQE  H13  C    N    110.78  3.000
 NQE  H12  C    N    110.72  3.000
 NQE  H11  C    N    109.04  3.000
 NQE  C3   N1   C2   125.15  3.000
 NQE  C2   N1   C1   124.93  3.000
 NQE  C3   N1   C1   109.92  3.000
 NQE  C13  C14  N4   180.00  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
 NQE  CONST_01  C6   C5   C4   C3     0.00   0.0  0
 NQE  CONST_02  C6   C7   C8   C3     0.00   0.0  0
 NQE  CONST_03  C7   C6   C5   C4     0.00   0.0  0
 NQE  CONST_04  C7   C8   C3   C4     0.00   0.0  0
 NQE  CONST_05  C11  C12  C13  C9     0.00   0.0  0
 NQE  CONST_06  C11  C10  N3   C9     0.00   0.0  0
 NQE  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 NQE  CONST_08  C13  C9   N3   C10    0.00   0.0  0
 NQE  CONST_09  N3   C10  C11  C12    0.00   0.0  0
 NQE  CONST_10  N3   C9   C13  C12    0.00   0.0  0
 NQE  CONST_11  C8   C7   C6   C5     0.00   0.0  0
 NQE  CONST_12  C8   C3   C4   C5     0.00   0.0  0
 NQE  CONST_13  C8   C3   N1   C1     0.00   0.0  0
 NQE  CONST_14  C3   C8   N    C1     0.00   0.0  0
 NQE  CONST_15  N    C1   N1   C3     0.00   0.0  0
 NQE  CONST_16  N1   C1   N    C8     0.00   0.0  0
 NQE  CONST_17  N1   C3   C8   N      0.00   0.0  0
 NQE  CONST_18  N2   C5   C4   C3   180.00   0.0  0
 NQE  CONST_19  N2   C5   C6   C7   180.00   0.0  0
 NQE  CONST_20  N2   C9   N3   C10  180.00   0.0  0
 NQE  CONST_21  N2   C9   C13  C12  180.00   0.0  0
 NQE  CONST_22  C11  C12  C13  C14  180.00   0.0  0
 NQE  CONST_23  N3   C9   C13  C14  180.00   0.0  0
 NQE  CONST_24  C8   C3   N1   C2   180.00   0.0  0
 NQE  CONST_25  N    C1   N1   C2   180.00   0.0  0
 NQE  CONST_26  C    N    C8   C3   180.00   0.0  0
 NQE  CONST_27  O    C1   N1   C3   180.00   0.0  0
 NQE  CONST_28  O    C1   N    C8   180.00   0.0  0
 NQE  CONST_29  N1   C1   N    C    180.00   0.0  0
 NQE  CONST_30  H6   C7   C8   C3   180.00   0.0  0
 NQE  CONST_31  H5   C6   C5   C4   180.00   0.0  0
 NQE  CONST_32  H4   C4   C5   C6   180.00   0.0  0
 NQE  CONST_33  H8   C12  C13  C9   180.00   0.0  0
 NQE  CONST_34  H7   C10  N3   C9   180.00   0.0  0
 NQE  CONST_35  H9   C11  C12  C13  180.00   0.0  0
 NQE  CONST_36  O    C1   N1   C2     0.00   0.0  0
 NQE  CONST_37  O    C1   N    C      0.00   0.0  0
 NQE  Var_01    C9   N2   C5   C4    39.72  30.0  2
 NQE  Var_02    C5   N2   C9   C13  178.54  30.0  2
 NQE  Var_03    H1   C2   N1   C1    -0.11  30.0  3
 NQE  Var_04    H11  C    N    C1     0.92  30.0  3

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
 NQE  plan-1  C9   0.020
 NQE  plan-1  C10  0.020
 NQE  plan-1  C12  0.020
 NQE  plan-1  N4   0.020
 NQE  plan-1  C13  0.020
 NQE  plan-1  C11  0.020
 NQE  plan-1  N3   0.020
 NQE  plan-1  N2   0.020
 NQE  plan-1  H7   0.020
 NQE  plan-1  H8   0.020
 NQE  plan-1  H9   0.020
 NQE  plan-1  C14  0.020
 NQE  plan-2  C1   0.020
 NQE  plan-2  C2   0.020
 NQE  plan-2  C3   0.020
 NQE  plan-2  C4   0.020
 NQE  plan-2  C6   0.020
 NQE  plan-2  C7   0.020
 NQE  plan-2  N2   0.020
 NQE  plan-2  C5   0.020
 NQE  plan-2  C8   0.020
 NQE  plan-2  N    0.020
 NQE  plan-2  C    0.020
 NQE  plan-2  N1   0.020
 NQE  plan-2  O    0.020
 NQE  plan-2  H4   0.020
 NQE  plan-2  H5   0.020
 NQE  plan-2  H6   0.020

