# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 20:23:34 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-chloranyl-4-[(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(Nc3ccnc(Cl)c3C#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
 NQK  NQK  2-chloranyl-4-[(1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)amino]pyridine-3-carbonitrile  ligand  34  22  .  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_NQK
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
 NQK  N1   N   N     0  -0.413  25.8970   -9.4386  11.3923
 NQK  C2   C   CR6   0   0.516  26.1654   -9.9267  14.1628
 NQK  N3   N   NR5   0  -0.582  22.5740   -9.2955  19.4222
 NQK  C4   C   CR16  0  -0.053  24.9145   -9.1673  12.2642
 NQK  N4   N   NR5   0  -0.585  23.0988  -11.3895  18.9861
 NQK  C5   C   CR6   0   0.146  26.9861   -9.9451  11.8904
 NQK  C6   C   CR6   0   0.257  25.3527   -9.8756  16.4680
 NQK  C13  C   CH3   0  -0.537  23.1331  -12.8287  19.0296
 NQK  C12  C   CR16  0  -0.359  24.7560  -10.9311  17.1592
 NQK  C10  C   CR5   0   0.661  22.3078  -10.5961  19.7867
 NQK  C11  C   CR56  0   0.348  23.8433  -10.6039  18.1397
 NQK  N2   N   NH1   0  -0.777  26.3156  -10.1756  15.4732
 NQK  C9   C   CR56  0   0.343  23.5110   -9.2731  18.4169
 NQK  C8   C   CR16  0  -0.319  24.0990   -8.2302  17.7302
 NQK  C1   C   CR6   0  -0.087  27.2024  -10.2166  13.2430
 NQK  C3   C   CR16  0  -0.384  24.9883   -9.3818  13.6158
 NQK  C7   C   CR16  0  -0.292  25.0386   -8.5502  16.7535
 NQK  O    O   O     0  -0.497  21.5291  -10.9700  20.6440
 NQK  CL   CL  CL    0  -0.067  28.2593  -10.3038  10.7784
 NQK  C    C   CSP   0   0.030  28.4254  -10.7656  13.6983
 NQK  N    N   NS    0  -0.232  29.4061  -11.2071  14.1156
 NQK  H1   H   HCR6  0   0.289  24.0084   -8.7537  11.8397
 NQK  H2   H   HCH3  0   0.270  21.2216   -8.4538  20.7420
 NQK  H3   H   HCH3  0   0.257  22.7043   -7.5181  20.5190
 NQK  H4   H   HCH3  0   0.257  21.4621   -7.5352  19.2531
 NQK  H5   H   HCH3  0   0.270  22.4553  -13.1770  19.8029
 NQK  H6   H   HCH3  0   0.257  22.8208  -13.2510  18.0749
 NQK  H7   H   HCH3  0   0.257  24.1374  -13.1817  19.2612
 NQK  H8   H   HCR6  0   0.287  25.0058  -11.9577  16.9244
 NQK  H9   H   HNH1  0   0.417  27.1438  -10.6652  15.7790
 NQK  H10  H   HCR6  0   0.281  23.8567   -7.1978  17.9435
 NQK  H11  H   HCR6  0   0.300  24.1429   -9.1396  14.2423
 NQK  H12  H   HCR6  0   0.276  25.5347   -7.7556  16.2118
 NQK  C14  C   CH3   0  -0.536  21.9611   -8.1343  20.0139

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
 NQK  CL   C5   single    1.728  0.020  1.728
 NQK  N1   C5   aromatic  1.300  0.020  1.300
 NQK  N1   C4   aromatic  1.341  0.020  1.341
 NQK  C5   C1   aromatic  1.396  0.020  1.396
 NQK  C4   C3   aromatic  1.370  0.020  1.370
 NQK  C1   C    single    1.416  0.020  1.416
 NQK  C1   C2   aromatic  1.416  0.020  1.416
 NQK  C    N    triple    1.154  0.020  1.154
 NQK  C3   C2   aromatic  1.408  0.020  1.408
 NQK  C2   N2   single    1.342  0.020  1.342
 NQK  N2   C6   single    1.417  0.020  1.417
 NQK  C6   C7   aromatic  1.392  0.020  1.392
 NQK  C6   C12  aromatic  1.396  0.020  1.396
 NQK  C7   C8   aromatic  1.393  0.020  1.393
 NQK  C12  C11  aromatic  1.379  0.020  1.379
 NQK  C8   C9   aromatic  1.380  0.020  1.380
 NQK  C11  C9   aromatic  1.399  0.020  1.399
 NQK  C11  N4   single    1.374  0.020  1.374
 NQK  C9   N3   single    1.374  0.020  1.374
 NQK  N4   C13  single    1.440  0.020  1.440
 NQK  N4   C10  single    1.377  0.020  1.377
 NQK  N3   C10  single    1.377  0.020  1.377
 NQK  N3   C14  single    1.440  0.020  1.440
 NQK  C10  O    double    1.217  0.020  1.217
 NQK  C4   H1   single    0.930  0.020  1.080
 NQK  C14  H2   single    0.970  0.020  1.090
 NQK  C14  H3   single    0.970  0.020  1.090
 NQK  C14  H4   single    0.970  0.020  1.090
 NQK  C13  H5   single    0.970  0.020  1.090
 NQK  C13  H6   single    0.970  0.020  1.090
 NQK  C13  H7   single    0.970  0.020  1.090
 NQK  C12  H8   single    0.930  0.020  1.080
 NQK  N2   H9   single    0.860  0.020  1.020
 NQK  C8   H10  single    0.930  0.020  1.080
 NQK  C3   H11  single    0.930  0.020  1.080
 NQK  C7   H12  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
 NQK  C5   N1   C4   116.31  3.000
 NQK  C3   C2   C1   116.05  3.000
 NQK  C3   C2   N2   123.00  3.000
 NQK  C1   C2   N2   120.94  3.000
 NQK  C9   N3   C10  109.93  3.000
 NQK  C10  N3   C14  124.79  3.000
 NQK  C9   N3   C14  125.27  3.000
 NQK  H1   C4   C3   119.44  3.000
 NQK  H1   C4   N1   115.81  3.000
 NQK  C3   C4   N1   124.75  3.000
 NQK  C11  N4   C10  109.88  3.000
 NQK  C10  N4   C13  124.88  3.000
 NQK  C11  N4   C13  125.24  3.000
 NQK  CL   C5   C1   117.96  3.000
 NQK  C1   C5   N1   125.20  3.000
 NQK  CL   C5   N1   116.84  3.000
 NQK  C7   C6   N2   119.95  3.000
 NQK  C7   C6   C12  121.47  3.000
 NQK  N2   C6   C12  118.57  3.000
 NQK  H7   C13  H6   108.96  3.000
 NQK  H7   C13  H5   108.67  3.000
 NQK  H6   C13  H5   108.71  3.000
 NQK  H7   C13  N4   110.62  3.000
 NQK  H6   C13  N4   110.73  3.000
 NQK  H5   C13  N4   109.10  3.000
 NQK  H8   C12  C11  122.15  3.000
 NQK  H8   C12  C6   120.74  3.000
 NQK  C11  C12  C6   117.11  3.000
 NQK  O    C10  N4   126.88  3.000
 NQK  O    C10  N3   126.90  3.000
 NQK  N4   C10  N3   106.22  3.000
 NQK  C9   C11  C12  121.58  3.000
 NQK  C9   C11  N4   107.04  3.000
 NQK  C12  C11  N4   131.38  3.000
 NQK  H9   N2   C6   116.59  3.000
 NQK  H9   N2   C2   118.52  3.000
 NQK  C6   N2   C2   124.77  3.000
 NQK  C8   C9   C11  121.25  3.000
 NQK  C11  C9   N3   106.93  3.000
 NQK  C8   C9   N3   131.81  3.000
 NQK  H10  C8   C7   120.58  3.000
 NQK  H10  C8   C9   121.84  3.000
 NQK  C7   C8   C9   117.57  3.000
 NQK  C    C1   C5   121.38  3.000
 NQK  C    C1   C2   120.20  3.000
 NQK  C5   C1   C2   118.42  3.000
 NQK  H11  C3   C4   119.67  3.000
 NQK  H11  C3   C2   121.06  3.000
 NQK  C4   C3   C2   119.26  3.000
 NQK  H12  C7   C8   119.45  3.000
 NQK  H12  C7   C6   119.55  3.000
 NQK  C8   C7   C6   121.00  3.000
 NQK  N    C    C1   180.00  3.000
 NQK  H4   C14  H3   108.97  3.000
 NQK  H4   C14  H2   108.55  3.000
 NQK  H3   C14  H2   108.67  3.000
 NQK  H4   C14  N3   110.57  3.000
 NQK  H3   C14  N3   110.87  3.000
 NQK  H2   C14  N3   109.15  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
 NQK  CONST_01  C2   C1   C5   N1     0.00   0.0  0
 NQK  CONST_02  C2   C3   C4   N1     0.00   0.0  0
 NQK  CONST_03  C1   C5   N1   C4     0.00   0.0  0
 NQK  CONST_04  C1   C2   C3   C4     0.00   0.0  0
 NQK  CONST_05  C3   C4   N1   C5     0.00   0.0  0
 NQK  CONST_06  C3   C2   C1   C5     0.00   0.0  0
 NQK  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 NQK  CONST_08  C9   C11  C12  C6     0.00   0.0  0
 NQK  CONST_09  C8   C7   C6   C12    0.00   0.0  0
 NQK  CONST_10  C8   C9   C11  C12    0.00   0.0  0
 NQK  CONST_11  C7   C6   C12  C11    0.00   0.0  0
 NQK  CONST_12  C7   C8   C9   C11    0.00   0.0  0
 NQK  CONST_13  N4   C11  C9   N3     0.00   0.0  0
 NQK  CONST_14  C11  N4   C10  N3     0.00   0.0  0
 NQK  CONST_15  C9   N3   C10  N4     0.00   0.0  0
 NQK  CONST_16  C9   C11  N4   C10    0.00   0.0  0
 NQK  CONST_17  C11  C9   N3   C10    0.00   0.0  0
 NQK  CONST_18  C    C1   C5   N1   180.00   0.0  0
 NQK  CONST_19  CL   C5   C1   C2   180.00   0.0  0
 NQK  CONST_20  CL   C5   N1   C4   180.00   0.0  0
 NQK  CONST_21  N2   C2   C3   C4   180.00   0.0  0
 NQK  CONST_22  N2   C2   C1   C5   180.00   0.0  0
 NQK  CONST_23  N2   C6   C12  C11  180.00   0.0  0
 NQK  CONST_24  C8   C7   C6   N2   180.00   0.0  0
 NQK  CONST_25  C    C1   C2   C3   180.00   0.0  0
 NQK  CONST_26  C13  N4   C10  N3   180.00   0.0  0
 NQK  CONST_27  C14  N3   C10  N4   180.00   0.0  0
 NQK  CONST_28  C11  C9   N3   C14  180.00   0.0  0
 NQK  CONST_29  C9   C11  N4   C13  180.00   0.0  0
 NQK  CONST_30  O    C10  N4   C11  180.00   0.0  0
 NQK  CONST_31  O    C10  N3   C9   180.00   0.0  0
 NQK  CONST_32  H11  C3   C4   N1   180.00   0.0  0
 NQK  CONST_33  H1   C4   C3   C2   180.00   0.0  0
 NQK  CONST_34  H10  C8   C9   N3     0.00   0.0  0
 NQK  CONST_35  H8   C12  C11  N4     0.00   0.0  0
 NQK  CONST_36  H12  C7   C6   C12  180.00   0.0  0
 NQK  CONST_37  O    C10  N3   C14    0.00   0.0  0
 NQK  CONST_38  O    C10  N4   C13    0.00   0.0  0
 NQK  Var_01    C7   C6   N2   C2   -66.29  30.0  2
 NQK  Var_02    C1   C2   N2   C6   177.69  30.0  2
 NQK  Var_03    H5   C13  N4   C10   -1.15  30.0  3
 NQK  Var_04    H2   C14  N3   C10   -3.35  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
 NQK  plan-1  N1   0.020
 NQK  plan-1  C2   0.020
 NQK  plan-1  C4   0.020
 NQK  plan-1  C5   0.020
 NQK  plan-1  N2   0.020
 NQK  plan-1  C1   0.020
 NQK  plan-1  C3   0.020
 NQK  plan-1  CL   0.020
 NQK  plan-1  C    0.020
 NQK  plan-1  N    0.020
 NQK  plan-1  H1   0.020
 NQK  plan-1  H11  0.020
 NQK  plan-2  N3   0.020
 NQK  plan-2  N4   0.020
 NQK  plan-2  C6   0.020
 NQK  plan-2  C13  0.020
 NQK  plan-2  C12  0.020
 NQK  plan-2  C10  0.020
 NQK  plan-2  C11  0.020
 NQK  plan-2  N2   0.020
 NQK  plan-2  C9   0.020
 NQK  plan-2  C8   0.020
 NQK  plan-2  C7   0.020
 NQK  plan-2  O    0.020
 NQK  plan-2  H8   0.020
 NQK  plan-2  H10  0.020
 NQK  plan-2  H12  0.020
 NQK  plan-2  C14  0.020

