# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 04:23:08 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-chloranyl-4-[[1-methyl-3-[(3~{R})-3-oxidanylbutyl]-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)CCN1C(=O)N(C)c2ccc(Nc3ccnc(Cl)c3C#N)cc12
#
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
 NQN  NQN  2-chloranyl-4-[[1-methyl-3-[(3~{R})-3-oxidanylbutyl]-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile  ligand  44  26  .  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_NQN
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
 NQN  C2   C   CR6   0  -0.087  27.2125  -10.2768  13.2221
 NQN  C3   C   CR6   0   0.516  26.1794   -9.9790  14.1436
 NQN  C4   C   CR16  0  -0.384  25.0025   -9.4320  13.5982
 NQN  C5   C   CR6   0   0.258  25.3706   -9.9259  16.4501
 NQN  C10  C   CR16  0  -0.354  24.7773  -10.9836  17.1403
 NQN  C11  C   CR5   0   0.672  22.3231  -10.6585  19.7653
 NQN  C6   C   CR16  0  -0.294  25.0508   -8.6019  16.7358
 NQN  C7   C   CR16  0  -0.318  24.1085   -8.2872  17.7112
 NQN  N1   N   NH1   0  -0.778  26.3336  -10.2228  15.4549
 NQN  C1   C   CR6   0   0.146  26.9934  -10.0095  11.8689
 NQN  N    N   N     0  -0.413  25.9047   -9.5006  11.3724
 NQN  C17  C   CSP   0   0.030  28.4336  -10.8320  13.6751
 NQN  N4   N   NS    0  -0.232  29.4114  -11.2835  14.0885
 NQN  C    C   CR16  0  -0.053  24.9257   -9.2223  12.2460
 NQN  C9   C   CR56  0   0.348  23.8628  -10.6627  18.1218
 NQN  N2   N   NR5   0  -0.593  23.1288  -11.4501  18.9778
 NQN  C13  C   CH2   0  -0.313  23.1274  -12.8957  19.0011
 NQN  C14  C   CH2   0  -0.487  22.2565  -13.4862  17.8978
 NQN  C15  C   CH1   0   0.038  22.2630  -15.0143  17.8570
 NQN  O1   O   OH1   0  -0.672  21.8349  -15.5708  19.0870
 NQN  C16  C   CH3   0  -0.688  23.6305  -15.5952  17.5429
 NQN  O    O   O     0  -0.500  21.5385  -11.0377  20.6152
 NQN  N3   N   NR5   0  -0.587  22.5855   -9.3575  19.4010
 NQN  C12  C   CH3   0  -0.537  21.9707   -8.1970  19.9922
 NQN  C8   C   CR56  0   0.340  23.5242   -9.3331  18.3970
 NQN  H1   H   HCR6  0   0.300  24.1597   -9.1845  14.2260
 NQN  H2   H   HCR6  0   0.279  25.0313  -12.0078  16.8996
 NQN  H3   H   HCR6  0   0.276  25.5438   -7.8053  16.1943
 NQN  H4   H   HCR6  0   0.281  23.8602   -7.2563  17.9254
 NQN  H5   H   HNH1  0   0.417  27.1587  -10.7191  15.7585
 NQN  H6   H   HCR6  0   0.289  24.0199   -8.8071  11.8224
 NQN  H7   H   HCH2  0   0.270  22.7763  -13.2140  19.9807
 NQN  H8   H   HCH2  0   0.262  24.1629  -13.2291  18.9143
 NQN  H9   H   HCH2  0   0.238  22.5809  -13.1116  16.9225
 NQN  H10  H   HCH2  0   0.248  21.2286  -13.1341  18.0322
 NQN  H11  H   HCH1  0   0.216  21.5799  -15.3117  17.0493
 NQN  H12  H   HOH1  0   0.449  20.9338  -15.2769  19.2543
 NQN  H13  H   HCH3  0   0.241  23.5704  -16.6754  17.4059
 NQN  H14  H   HCH3  0   0.229  24.0205  -15.1656  16.6199
 NQN  H15  H   HCH3  0   0.228  24.3532  -15.4018  18.3374
 NQN  H16  H   HCH3  0   0.270  21.2441   -8.5170  20.7330
 NQN  H17  H   HCH3  0   0.257  22.7163   -7.5722  20.4831
 NQN  H18  H   HCH3  0   0.257  21.4571   -7.6066  19.2343
 NQN  CL   CL  CL    0  -0.067  28.2613  -10.3787  10.7543

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
 NQN  CL   C1   single    1.728  0.020  1.728
 NQN  N    C1   aromatic  1.300  0.020  1.300
 NQN  N    C    aromatic  1.341  0.020  1.341
 NQN  C1   C2   aromatic  1.397  0.020  1.397
 NQN  C    C4   aromatic  1.371  0.020  1.371
 NQN  C2   C17  single    1.416  0.020  1.416
 NQN  C2   C3   aromatic  1.416  0.020  1.416
 NQN  C17  N4   triple    1.154  0.020  1.154
 NQN  C4   C3   aromatic  1.408  0.020  1.408
 NQN  C3   N1   single    1.343  0.020  1.343
 NQN  N1   C5   single    1.416  0.020  1.416
 NQN  C5   C6   aromatic  1.392  0.020  1.392
 NQN  C5   C10  aromatic  1.395  0.020  1.395
 NQN  C6   C7   aromatic  1.392  0.020  1.392
 NQN  C10  C9   aromatic  1.379  0.020  1.379
 NQN  C7   C8   aromatic  1.380  0.020  1.380
 NQN  C16  C15  single    1.519  0.020  1.519
 NQN  C14  C15  single    1.529  0.020  1.529
 NQN  C14  C13  single    1.525  0.020  1.525
 NQN  C15  O1   single    1.416  0.020  1.416
 NQN  C9   C8   aromatic  1.399  0.020  1.399
 NQN  C9   N2   single    1.375  0.020  1.375
 NQN  C8   N3   single    1.375  0.020  1.375
 NQN  C13  N2   single    1.446  0.020  1.446
 NQN  N2   C11  single    1.377  0.020  1.377
 NQN  N3   C11  single    1.376  0.020  1.376
 NQN  N3   C12  single    1.440  0.020  1.440
 NQN  C11  O    double    1.217  0.020  1.217
 NQN  C4   H1   single    0.930  0.020  1.080
 NQN  C10  H2   single    0.930  0.020  1.080
 NQN  C6   H3   single    0.930  0.020  1.080
 NQN  C7   H4   single    0.930  0.020  1.080
 NQN  N1   H5   single    0.860  0.020  1.020
 NQN  C    H6   single    0.930  0.020  1.080
 NQN  C13  H7   single    0.970  0.020  1.090
 NQN  C13  H8   single    0.970  0.020  1.090
 NQN  C14  H9   single    0.970  0.020  1.090
 NQN  C14  H10  single    0.970  0.020  1.090
 NQN  C15  H11  single    0.970  0.020  1.090
 NQN  O1   H12  single    0.850  0.020  0.980
 NQN  C16  H13  single    0.970  0.020  1.090
 NQN  C16  H14  single    0.970  0.020  1.090
 NQN  C16  H15  single    0.970  0.020  1.090
 NQN  C12  H16  single    0.970  0.020  1.090
 NQN  C12  H17  single    0.970  0.020  1.090
 NQN  C12  H18  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
 NQN  C17  C2   C1   121.36  3.000
 NQN  C17  C2   C3   120.23  3.000
 NQN  C1   C2   C3   118.42  3.000
 NQN  N1   C3   C4   123.02  3.000
 NQN  N1   C3   C2   120.91  3.000
 NQN  C4   C3   C2   116.07  3.000
 NQN  H1   C4   C    119.66  3.000
 NQN  H1   C4   C3   121.09  3.000
 NQN  C    C4   C3   119.24  3.000
 NQN  N1   C5   C6   119.99  3.000
 NQN  C6   C5   C10  121.46  3.000
 NQN  N1   C5   C10  118.54  3.000
 NQN  H2   C10  C9   122.27  3.000
 NQN  H2   C10  C5   120.50  3.000
 NQN  C9   C10  C5   117.23  3.000
 NQN  N3   C11  O    127.02  3.000
 NQN  O    C11  N2   126.69  3.000
 NQN  N3   C11  N2   106.29  3.000
 NQN  H3   C6   C7   119.51  3.000
 NQN  H3   C6   C5   119.53  3.000
 NQN  C7   C6   C5   120.96  3.000
 NQN  H4   C7   C8   121.77  3.000
 NQN  H4   C7   C6   120.62  3.000
 NQN  C8   C7   C6   117.60  3.000
 NQN  H5   N1   C5   116.57  3.000
 NQN  H5   N1   C3   118.48  3.000
 NQN  C5   N1   C3   124.76  3.000
 NQN  N    C1   CL   116.85  3.000
 NQN  N    C1   C2   125.19  3.000
 NQN  CL   C1   C2   117.97  3.000
 NQN  C    N    C1   116.33  3.000
 NQN  N4   C17  C2   180.00  3.000
 NQN  H6   C    N    115.81  3.000
 NQN  H6   C    C4   119.44  3.000
 NQN  N    C    C4   124.75  3.000
 NQN  C8   C9   N2   107.00  3.000
 NQN  N2   C9   C10  131.57  3.000
 NQN  C8   C9   C10  121.42  3.000
 NQN  C13  N2   C9   125.66  3.000
 NQN  C13  N2   C11  124.40  3.000
 NQN  C9   N2   C11  109.83  3.000
 NQN  H8   C13  H7   106.76  3.000
 NQN  H8   C13  C14  111.48  3.000
 NQN  H7   C13  C14  110.72  3.000
 NQN  H8   C13  N2   107.65  3.000
 NQN  H7   C13  N2   107.90  3.000
 NQN  C14  C13  N2   112.10  3.000
 NQN  H10  C14  H9   106.12  3.000
 NQN  H10  C14  C15  109.19  3.000
 NQN  H9   C14  C15  108.49  3.000
 NQN  H10  C14  C13  108.84  3.000
 NQN  H9   C14  C13  110.07  3.000
 NQN  C15  C14  C13  113.84  3.000
 NQN  H11  C15  C16  107.71  3.000
 NQN  H11  C15  O1   110.13  3.000
 NQN  C16  C15  O1   107.55  3.000
 NQN  H11  C15  C14  106.71  3.000
 NQN  O1   C15  C14  111.61  3.000
 NQN  C16  C15  C14  113.06  3.000
 NQN  H12  O1   C15  108.30  3.000
 NQN  H15  C16  H14  108.04  3.000
 NQN  H15  C16  H13  107.67  3.000
 NQN  H14  C16  H13  107.68  3.000
 NQN  H15  C16  C15  112.21  3.000
 NQN  H14  C16  C15  110.27  3.000
 NQN  H13  C16  C15  110.81  3.000
 NQN  C8   N3   C12  125.24  3.000
 NQN  C12  N3   C11  124.86  3.000
 NQN  C8   N3   C11  109.89  3.000
 NQN  H18  C12  H17  108.98  3.000
 NQN  H18  C12  H16  108.60  3.000
 NQN  H17  C12  H16  108.64  3.000
 NQN  H18  C12  N3   110.63  3.000
 NQN  H17  C12  N3   110.79  3.000
 NQN  H16  C12  N3   109.16  3.000
 NQN  N3   C8   C9   106.98  3.000
 NQN  N3   C8   C7   131.71  3.000
 NQN  C9   C8   C7   121.32  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
 NQN  CONST_01  C    N    C1   C2     0.00   0.0  0
 NQN  CONST_02  C    C4   C3   C2     0.00   0.0  0
 NQN  CONST_03  N    C1   C2   C3     0.00   0.0  0
 NQN  CONST_04  N    C    C4   C3     0.00   0.0  0
 NQN  CONST_05  C1   N    C    C4     0.00   0.0  0
 NQN  CONST_06  C1   C2   C3   C4     0.00   0.0  0
 NQN  CONST_07  C8   C7   C6   C5     0.00   0.0  0
 NQN  CONST_08  C8   C9   C10  C5     0.00   0.0  0
 NQN  CONST_09  C7   C6   C5   C10    0.00   0.0  0
 NQN  CONST_10  C7   C8   C9   C10    0.00   0.0  0
 NQN  CONST_11  C9   C10  C5   C6     0.00   0.0  0
 NQN  CONST_12  C9   C8   C7   C6     0.00   0.0  0
 NQN  CONST_13  C8   C9   N2   C11    0.00   0.0  0
 NQN  CONST_14  C9   C8   N3   C11    0.00   0.0  0
 NQN  CONST_15  N3   C11  N2   C9     0.00   0.0  0
 NQN  CONST_16  N3   C8   C9   N2     0.00   0.0  0
 NQN  CONST_17  C8   N3   C11  N2     0.00   0.0  0
 NQN  CONST_18  CL   C1   C2   C3   180.00   0.0  0
 NQN  CONST_19  C17  C2   C3   C4   180.00   0.0  0
 NQN  CONST_20  N1   C5   C6   C7   180.00   0.0  0
 NQN  CONST_21  C1   C2   C3   N1   180.00   0.0  0
 NQN  CONST_22  C    C4   C3   N1   180.00   0.0  0
 NQN  CONST_23  C9   C10  C5   N1   180.00   0.0  0
 NQN  CONST_24  C    N    C1   CL   180.00   0.0  0
 NQN  CONST_25  C17  C2   C1   N    180.00   0.0  0
 NQN  CONST_26  C12  N3   C8   C9   180.00   0.0  0
 NQN  CONST_27  O    C11  N2   C9   180.00   0.0  0
 NQN  CONST_28  C12  N3   C11  N2   180.00   0.0  0
 NQN  CONST_29  C8   C9   N2   C13  180.00   0.0  0
 NQN  CONST_30  N3   C11  N2   C13  180.00   0.0  0
 NQN  CONST_31  C8   N3   C11  O    180.00   0.0  0
 NQN  CONST_32  H1   C4   C3   C2   180.00   0.0  0
 NQN  CONST_33  H6   C    C4   C3   180.00   0.0  0
 NQN  CONST_34  H4   C7   C6   C5   180.00   0.0  0
 NQN  CONST_35  H3   C6   C5   C10  180.00   0.0  0
 NQN  CONST_36  H2   C10  C5   C6   180.00   0.0  0
 NQN  CONST_37  O    C11  N2   C13    0.00   0.0  0
 NQN  CONST_38  C12  N3   C11  O      0.00   0.0  0
 NQN  Var_01    C5   N1   C3   C2   178.28  30.0  2
 NQN  Var_02    C6   C5   N1   C3   -66.50  30.0  2
 NQN  Var_03    C14  C13  N2   C11   96.74  30.0  1
 NQN  Var_04    H16  C12  N3   C11   -2.41  30.0  3
 NQN  Var_05    C15  C14  C13  N2   178.09  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NQN  chir_01  C15  C16  C14  O1  positiv

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
 NQN  plan-1  C2   0.020
 NQN  plan-1  C3   0.020
 NQN  plan-1  C4   0.020
 NQN  plan-1  N1   0.020
 NQN  plan-1  C1   0.020
 NQN  plan-1  N    0.020
 NQN  plan-1  C17  0.020
 NQN  plan-1  N4   0.020
 NQN  plan-1  C    0.020
 NQN  plan-1  H1   0.020
 NQN  plan-1  H6   0.020
 NQN  plan-1  CL   0.020
 NQN  plan-2  C5   0.020
 NQN  plan-2  C10  0.020
 NQN  plan-2  C11  0.020
 NQN  plan-2  C6   0.020
 NQN  plan-2  C7   0.020
 NQN  plan-2  N1   0.020
 NQN  plan-2  C9   0.020
 NQN  plan-2  N2   0.020
 NQN  plan-2  C13  0.020
 NQN  plan-2  O    0.020
 NQN  plan-2  N3   0.020
 NQN  plan-2  C12  0.020
 NQN  plan-2  C8   0.020
 NQN  plan-2  H2   0.020
 NQN  plan-2  H3   0.020
 NQN  plan-2  H4   0.020

