# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 17:00:54 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-chloranyl-4-[(1-methyl-2-oxidanylidene-quinolin-6-yl)amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C=Cc2cc(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
 VHQ  VHQ  "2-chloranyl-4-[(1-methyl-2-oxidanylidene-quinolin-6-yl)amino]pyridine-3-carbonitrile"
  ligand  33  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VHQ
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
 VHQ  C1   C   CR6   0  -0.094  -73.4952  48.1901  13.1916
 VHQ  C11  C   CH3   0  -0.567  -78.8592  50.4368  19.4884
 VHQ  C2   C   CR6   0   0.519  -74.6161  48.4019  14.0300
 VHQ  C7   C   CR66  0   0.035  -76.9793  47.5244  18.0941
 VHQ  C6   C   CR16  0  -0.381  -76.0519  47.2703  17.0809
 VHQ  C5   C   CR6   0   0.311  -75.5702  48.2931  16.2913
 VHQ  C4   C   CR16  0  -0.051  -75.6721  49.3574  12.1020
 VHQ  C3   C   CR16  0  -0.388  -75.7332  49.0073  13.4266
 VHQ  C8   C   CR66  0   0.392  -77.4564  48.8305  18.3042
 VHQ  C9   C   CR16  0  -0.326  -76.9599  49.8602  17.4932
 VHQ  C10  C   CR16  0  -0.279  -76.0224  49.5956  16.5186
 VHQ  C12  C   CR6   0   0.548  -78.8847  48.0841  20.1252
 VHQ  C14  C   CR16  0  -0.128  -77.4762  46.4776  18.9329
 VHQ  C15  C   CSP   0   0.030  -72.3224  47.5862  13.7068
 VHQ  N3   N   NS    0  -0.228  -71.3927  47.0888  14.1740
 VHQ  N    N   N     0  -0.408  -74.6081  49.1659  11.3099
 VHQ  C    C   CR6   0   0.147  -73.5751  48.5971  11.8582
 VHQ  CL   CL  CL    0  -0.064  -72.1993  48.3363  10.8473
 VHQ  N1   N   NH1   0  -0.785  -74.5863  48.0201  15.3203
 VHQ  N2   N   NR6   0  -0.602  -78.3850  49.0750  19.2964
 VHQ  O    O   O     0  -0.483  -79.7047  48.3306  20.9990
 VHQ  C13  C   CR16  0  -0.440  -78.3763  46.7431  19.8927
 VHQ  H1   H   HCH3  0   0.285  -79.5949  50.4470  20.2825
 VHQ  H2   H   HCH3  0   0.259  -78.0375  51.0963  19.7657
 VHQ  H3   H   HCH3  0   0.259  -79.3239  50.8121  18.5771
 VHQ  H4   H   HCR6  0   0.279  -75.7095  46.2538  16.9263
 VHQ  H5   H   HCR6  0   0.289  -76.5333  49.8170  11.6330
 VHQ  H6   H   HCR6  0   0.305  -76.6432  49.1846  13.9804
 VHQ  H7   H   HCR6  0   0.295  -77.2806  50.8826  17.6260
 VHQ  H8   H   HCR6  0   0.292  -75.6302  50.4175  15.9335
 VHQ  H9   H   HCR6  0   0.280  -77.1121  45.4687  18.7803
 VHQ  H10  H   HNH1  0   0.423  -73.8159  47.4435  15.6276
 VHQ  H11  H   HCR6  0   0.277  -78.7611  45.9644  20.5367

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
 VHQ  CL   C    single    1.727  0.020  1.727
 VHQ  N    C    aromatic  1.301  0.020  1.301
 VHQ  N    C4   aromatic  1.340  0.020  1.340
 VHQ  C    C1   aromatic  1.396  0.020  1.396
 VHQ  C4   C3   aromatic  1.371  0.020  1.371
 VHQ  C1   C15  single    1.416  0.020  1.416
 VHQ  C1   C2   aromatic  1.416  0.020  1.416
 VHQ  C15  N3   triple    1.153  0.020  1.153
 VHQ  C3   C2   aromatic  1.407  0.020  1.407
 VHQ  C2   N1   single    1.346  0.020  1.346
 VHQ  N1   C5   single    1.409  0.020  1.409
 VHQ  C5   C10  aromatic  1.397  0.020  1.397
 VHQ  C5   C6   aromatic  1.379  0.020  1.379
 VHQ  C10  C9   aromatic  1.378  0.020  1.378
 VHQ  C6   C7   aromatic  1.397  0.020  1.397
 VHQ  C9   C8   aromatic  1.402  0.020  1.402
 VHQ  C7   C8   aromatic  1.406  0.020  1.406
 VHQ  C7   C14  single    1.431  0.020  1.431
 VHQ  C8   N2   single    1.381  0.020  1.381
 VHQ  C14  C13  double    1.342  0.020  1.342
 VHQ  N2   C11  single    1.455  0.020  1.455
 VHQ  N2   C12  single    1.385  0.020  1.385
 VHQ  C13  C12  single    1.453  0.020  1.453
 VHQ  C12  O    double    1.223  0.020  1.223
 VHQ  C11  H1   single    0.970  0.020  1.090
 VHQ  C11  H2   single    0.970  0.020  1.090
 VHQ  C11  H3   single    0.970  0.020  1.090
 VHQ  C6   H4   single    0.930  0.020  1.080
 VHQ  C4   H5   single    0.930  0.020  1.080
 VHQ  C3   H6   single    0.930  0.020  1.080
 VHQ  C9   H7   single    0.930  0.020  1.080
 VHQ  C10  H8   single    0.930  0.020  1.080
 VHQ  C14  H9   single    0.930  0.020  1.080
 VHQ  N1   H10  single    0.860  0.020  1.020
 VHQ  C13  H11  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
 VHQ  C    C1   C15  121.27  3.000
 VHQ  C15  C1   C2   120.27  3.000
 VHQ  C    C1   C2   118.46  3.000
 VHQ  H3   C11  H2   109.03  3.000
 VHQ  H3   C11  H1   108.69  3.000
 VHQ  H2   C11  H1   108.67  3.000
 VHQ  H3   C11  N2   110.56  3.000
 VHQ  H2   C11  N2   110.76  3.000
 VHQ  H1   C11  N2   109.10  3.000
 VHQ  N1   C2   C3   123.43  3.000
 VHQ  N1   C2   C1   120.51  3.000
 VHQ  C3   C2   C1   116.05  3.000
 VHQ  C14  C7   C8   118.31  3.000
 VHQ  C14  C7   C6   121.52  3.000
 VHQ  C8   C7   C6   120.17  3.000
 VHQ  H4   C6   C5   120.24  3.000
 VHQ  H4   C6   C7   118.94  3.000
 VHQ  C5   C6   C7   120.82  3.000
 VHQ  N1   C5   C10  121.24  3.000
 VHQ  C10  C5   C6   119.02  3.000
 VHQ  N1   C5   C6   119.66  3.000
 VHQ  H5   C4   N    115.85  3.000
 VHQ  H5   C4   C3   119.42  3.000
 VHQ  N    C4   C3   124.73  3.000
 VHQ  H6   C3   C4   119.40  3.000
 VHQ  H6   C3   C2   121.32  3.000
 VHQ  C4   C3   C2   119.26  3.000
 VHQ  N2   C8   C9   121.59  3.000
 VHQ  N2   C8   C7   120.00  3.000
 VHQ  C9   C8   C7   118.41  3.000
 VHQ  H7   C9   C10  118.09  3.000
 VHQ  H7   C9   C8   121.28  3.000
 VHQ  C10  C9   C8   120.61  3.000
 VHQ  H8   C10  C9   118.88  3.000
 VHQ  H8   C10  C5   120.17  3.000
 VHQ  C9   C10  C5   120.94  3.000
 VHQ  C13  C12  O    122.33  3.000
 VHQ  O    C12  N2   121.67  3.000
 VHQ  C13  C12  N2   115.99  3.000
 VHQ  H9   C14  C13  120.68  3.000
 VHQ  H9   C14  C7   118.83  3.000
 VHQ  C13  C14  C7   120.49  3.000
 VHQ  N3   C15  C1   180.00  3.000
 VHQ  C    N    C4   116.36  3.000
 VHQ  CL   C    N    116.87  3.000
 VHQ  N    C    C1   125.14  3.000
 VHQ  CL   C    C1   117.99  3.000
 VHQ  H10  N1   C5   115.68  3.000
 VHQ  H10  N1   C2   118.07  3.000
 VHQ  C5   N1   C2   126.17  3.000
 VHQ  C12  N2   C8   123.09  3.000
 VHQ  C12  N2   C11  118.24  3.000
 VHQ  C8   N2   C11  118.67  3.000
 VHQ  H11  C13  C14  121.47  3.000
 VHQ  H11  C13  C12  116.41  3.000
 VHQ  C14  C13  C12  122.12  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
 VHQ  CONST_01  C4   N    C    C1      0.00   0.0  0
 VHQ  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 VHQ  CONST_03  N    C    C1   C2      0.00   0.0  0
 VHQ  CONST_04  N    C4   C3   C2      0.00   0.0  0
 VHQ  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 VHQ  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 VHQ  CONST_07  C9   C10  C5   C6      0.00   0.0  0
 VHQ  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 VHQ  CONST_09  C8   C9   C10  C5      0.00   0.0  0
 VHQ  CONST_10  C8   C7   C6   C5      0.00   0.0  0
 VHQ  CONST_11  C    N    C4   C3      0.00   0.0  0
 VHQ  CONST_12  C    C1   C2   C3      0.00   0.0  0
 VHQ  CONST_13  C13  C12  N2   C8      0.00   0.0  0
 VHQ  CONST_14  CL   C    C1   C2    180.00   0.0  0
 VHQ  CONST_15  N1   C5   C6   C7    180.00   0.0  0
 VHQ  CONST_16  CL   C    N    C4    180.00   0.0  0
 VHQ  CONST_17  N1   C2   C3   C4    180.00   0.0  0
 VHQ  CONST_18  C15  C1   C2   C3    180.00   0.0  0
 VHQ  CONST_19  N1   C5   C10  C9    180.00   0.0  0
 VHQ  CONST_20  N    C    C1   C15   180.00   0.0  0
 VHQ  CONST_21  N1   C2   C1   C     180.00   0.0  0
 VHQ  CONST_22  C13  C12  N2   C11   180.00   0.0  0
 VHQ  CONST_23  O    C12  N2   C8    180.00   0.0  0
 VHQ  CONST_24  H6   C3   C2   C1    180.00   0.0  0
 VHQ  CONST_25  H5   C4   C3   C2    180.00   0.0  0
 VHQ  CONST_26  H7   C9   C8   C7    180.00   0.0  0
 VHQ  CONST_27  H8   C10  C5   C6    180.00   0.0  0
 VHQ  CONST_28  H7   C9   C10  C5    180.00   0.0  0
 VHQ  CONST_29  H8   C10  C9   C8    180.00   0.0  0
 VHQ  CONST_30  H4   C6   C7   C8    180.00   0.0  0
 VHQ  CONST_31  H4   C6   C5   C10   180.00   0.0  0
 VHQ  CONST_32  H4   C6   C7   C14     0.00   0.0  0
 VHQ  CONST_33  H6   C3   C4   N     180.00   0.0  0
 VHQ  CONST_34  H5   C4   N    C     180.00   0.0  0
 VHQ  CONST_35  H7   C9   C8   N2      0.00   0.0  0
 VHQ  CONST_36  O    C12  N2   C11     0.00   0.0  0
 VHQ  Var_01    C12  N2   C8   C7      0.32  30.0  1
 VHQ  Var_02    C12  C13  C14  C7      0.03  30.0  1
 VHQ  Var_03    C13  C14  C7   C6   -179.39  30.0  1
 VHQ  Var_04    C13  C14  C7   C8      0.09  30.0  1
 VHQ  Var_05    C12  N2   C8   C9   -179.24  30.0  1
 VHQ  Var_06    N2   C12  C13  C14     0.00  30.0  1
 VHQ  Var_07    C5   N1   C2   C1    173.01  30.0  2
 VHQ  Var_08    C9   C8   N2   C11     0.46  30.0  1
 VHQ  Var_09    C7   C8   N2   C11  -179.98  30.0  1
 VHQ  Var_10    C10  C5   N1   C2    -52.34  30.0  2
 VHQ  Var_11    C6   C5   N1   C2    130.93  30.0  2
 VHQ  Var_12    C3   C2   N1   C5     -7.79  30.0  2
 VHQ  Var_13    O    C12  C13  C14  -179.98  30.0  1
 VHQ  Var_14    H11  C13  C14  C7   -179.89  30.0  1
 VHQ  Var_15    H9   C14  C7   C6      0.69  30.0  1
 VHQ  Var_16    H9   C14  C7   C8   -179.82  30.0  1
 VHQ  Var_17    H9   C14  C13  C12   179.95  30.0  1
 VHQ  Var_18    H11  C13  C12  N2    179.94  30.0  1
 VHQ  Var_19    H10  N1   C2   C1    -10.29  30.0  2
 VHQ  Var_20    H10  N1   C5   C6    -45.83  30.0  2
 VHQ  Var_21    H10  N1   C2   C3    168.91  30.0  2
 VHQ  Var_22    H1   C11  N2   C8    178.59  30.0  3
 VHQ  Var_23    H2   C11  N2   C8    -61.84  30.0  3
 VHQ  Var_24    H3   C11  N2   C8     59.12  30.0  3
 VHQ  Var_25    H10  N1   C5   C10   130.90  30.0  2
 VHQ  Var_26    H1   C11  N2   C12    -1.70  30.0  3
 VHQ  Var_27    H2   C11  N2   C12   117.87  30.0  3
 VHQ  Var_28    H3   C11  N2   C12  -121.16  30.0  3
 VHQ  Var_29    H11  C13  C12  O      -0.05  30.0  1

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
 VHQ  plan-1  C1   0.020
 VHQ  plan-1  C2   0.020
 VHQ  plan-1  C4   0.020
 VHQ  plan-1  C3   0.020
 VHQ  plan-1  C15  0.020
 VHQ  plan-1  N3   0.020
 VHQ  plan-1  N    0.020
 VHQ  plan-1  C    0.020
 VHQ  plan-1  CL   0.020
 VHQ  plan-1  N1   0.020
 VHQ  plan-1  H5   0.020
 VHQ  plan-1  H6   0.020
 VHQ  plan-2  C7   0.020
 VHQ  plan-2  C6   0.020
 VHQ  plan-2  C5   0.020
 VHQ  plan-2  C8   0.020
 VHQ  plan-2  C9   0.020
 VHQ  plan-2  C10  0.020
 VHQ  plan-2  C14  0.020
 VHQ  plan-2  N1   0.020
 VHQ  plan-2  N2   0.020
 VHQ  plan-2  H4   0.020
 VHQ  plan-2  H7   0.020
 VHQ  plan-2  H8   0.020
 VHQ  plan-3  C11  0.020
 VHQ  plan-3  C8   0.020
 VHQ  plan-3  C12  0.020
 VHQ  plan-3  N2   0.020
 VHQ  plan-3  O    0.020
 VHQ  plan-3  C13  0.020

