# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 14:30:36 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-chloranyl-4-[[4-(1-methylpyrazol-4-yl)-2-oxidanylidene-1~{H}-quinolin-6-yl]amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)C2=CC(=O)Nc3ccc(Nc4ccnc(Cl)c4C#N)cc23
#
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
 VHB  VHB  "2-chloranyl-4-[[4-(1-methylpyrazol-4-yl)-2-oxidanylidene-1H-quinolin-6-yl]amino]pyridine-3-carbonitrile"
  ligand  40  27  .  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_VHB
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
 VHB  C10  C   CR6   0   0.292  29.4778  -31.6041  -11.0943
 VHB  C11  C   CR6   0   0.517  29.0792  -30.8508  -13.3870
 VHB  C12  C   CR6   0  -0.088  28.7340  -29.8068  -14.2785
 VHB  C13  C   CSP   0   0.029  28.5363  -28.4895  -13.7968
 VHB  C14  C   CR6   0   0.145  28.5927  -30.1110  -15.6344
 VHB  C15  C   CR16  0  -0.052  29.0973  -32.2746  -15.3148
 VHB  C16  C   CR16  0  -0.385  29.2663  -32.1211  -13.9630
 VHB  C17  C   CR16  0  -0.271  28.5421  -32.6152  -10.8512
 VHB  C18  C   CR16  0  -0.317  28.7682  -33.5412   -9.8609
 VHB  CL   CL  CL    0  -0.065  28.1612  -28.8307  -16.7113
 VHB  N4   N   NS    0  -0.228  28.4018  -27.4210  -13.3838
 VHB  N5   N   N     0  -0.408  28.7582  -31.2900  -16.1588
 VHB  N3   N   NH1   0  -0.781  29.2261  -30.6150  -12.0726
 VHB  C7   C   CR66  0   0.392  29.9272  -33.4672   -9.0807
 VHB  N2   N   NR16  0  -0.757  30.1247  -34.3602   -8.0636
 VHB  C6   C   CR6   0   0.539  31.1942  -34.3601   -7.2058
 VHB  O    O   O     0  -0.481  31.2809  -35.1813   -6.3030
 VHB  C5   C   CR16  0  -0.560  32.1887  -33.3433   -7.4843
 VHB  C9   C   CR16  0  -0.408  30.6288  -31.5369  -10.3398
 VHB  C8   C   CR66  0   0.008  30.8832  -32.4667   -9.3244
 VHB  C4   C   CR6   0   0.254  32.0705  -32.4450   -8.4927
 VHB  C2   C   CR5   0  -0.187  33.1368  -31.4697   -8.7073
 VHB  C1   C   CR15  0   0.032  33.7522  -31.0883   -9.8855
 VHB  C3   C   CR15  0  -0.077  33.8374  -30.7500   -7.7189
 VHB  N1   N   N     0  -0.271  34.7814  -29.9991   -8.2475
 VHB  N    N   NR5   0  -0.262  34.7202  -30.2223   -9.5578
 VHB  C    C   CH3   0  -0.518  35.6379  -29.5682  -10.4639
 VHB  H1   H   HCR6  0   0.288  29.2449  -33.2497  -15.7625
 VHB  H2   H   HCR6  0   0.301  29.5520  -32.9721  -13.3624
 VHB  H3   H   HCR6  0   0.287  27.6294  -32.6599  -11.4316
 VHB  H4   H   HCR6  0   0.286  28.0382  -34.3164   -9.6644
 VHB  H5   H   HNH1  0   0.421  29.1944  -29.6600  -11.7454
 VHB  H6   H   HNR6  0   0.417  29.4208  -35.0708   -7.9083
 VHB  H7   H   HCR6  0   0.270  33.0727  -33.3534   -6.8605
 VHB  H8   H   HCR6  0   0.281  31.3320  -30.7375  -10.5283
 VHB  H9   H   HCR5  0   0.302  33.5882  -31.3936  -10.9071
 VHB  H10  H   HCR5  0   0.263  33.6621  -30.7479   -6.6533
 VHB  H11  H   HCH3  0   0.270  36.2857  -28.9198   -9.8827
 VHB  H12  H   HCH3  0   0.262  36.2466  -30.3021  -10.9886
 VHB  H13  H   HCH3  0   0.263  35.0939  -28.9694  -11.1916

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
 VHB  CL   C14  single    1.728  0.020  1.728
 VHB  N5   C14  aromatic  1.301  0.020  1.301
 VHB  N5   C15  aromatic  1.340  0.020  1.340
 VHB  C14  C12  aromatic  1.397  0.020  1.397
 VHB  C15  C16  aromatic  1.371  0.020  1.371
 VHB  C12  C13  single    1.416  0.020  1.416
 VHB  C12  C11  aromatic  1.416  0.020  1.416
 VHB  C13  N4   triple    1.153  0.020  1.153
 VHB  C16  C11  aromatic  1.407  0.020  1.407
 VHB  C11  N3   single    1.343  0.020  1.343
 VHB  N3   C10  single    1.414  0.020  1.414
 VHB  C10  C17  aromatic  1.399  0.020  1.399
 VHB  C10  C9   aromatic  1.378  0.020  1.378
 VHB  C17  C18  aromatic  1.374  0.020  1.374
 VHB  C    N    single    1.446  0.020  1.446
 VHB  C9   C8   aromatic  1.400  0.020  1.400
 VHB  C18  C7   aromatic  1.399  0.020  1.399
 VHB  C1   N    aromatic  1.340  0.020  1.340
 VHB  C1   C2   aromatic  1.383  0.020  1.383
 VHB  N    N1   aromatic  1.331  0.020  1.331
 VHB  C8   C7   aromatic  1.405  0.020  1.405
 VHB  C8   C4   single    1.450  0.020  1.450
 VHB  C7   N2   single    1.368  0.020  1.368
 VHB  C2   C4   single    1.461  0.020  1.461
 VHB  C2   C3   aromatic  1.409  0.020  1.409
 VHB  C4   C5   double    1.356  0.020  1.356
 VHB  N2   C6   single    1.371  0.020  1.371
 VHB  N1   C3   aromatic  1.317  0.020  1.317
 VHB  C5   C6   single    1.449  0.020  1.449
 VHB  C6   O    double    1.223  0.020  1.223
 VHB  C15  H1   single    0.930  0.020  1.080
 VHB  C16  H2   single    0.930  0.020  1.080
 VHB  C17  H3   single    0.930  0.020  1.080
 VHB  C18  H4   single    0.930  0.020  1.080
 VHB  N3   H5   single    0.860  0.020  1.020
 VHB  N2   H6   single    0.860  0.020  1.020
 VHB  C5   H7   single    0.930  0.020  1.080
 VHB  C9   H8   single    0.930  0.020  1.080
 VHB  C1   H9   single    0.930  0.020  1.080
 VHB  C3   H10  single    0.930  0.020  1.080
 VHB  C    H11  single    0.970  0.020  1.090
 VHB  C    H12  single    0.970  0.020  1.090
 VHB  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
 VHB  C9   C10  N3   119.57  3.000
 VHB  C9   C10  C17  119.92  3.000
 VHB  N3   C10  C17  120.46  3.000
 VHB  N3   C11  C16  122.98  3.000
 VHB  N3   C11  C12  120.89  3.000
 VHB  C16  C11  C12  116.13  3.000
 VHB  C14  C12  C13  121.24  3.000
 VHB  C13  C12  C11  120.38  3.000
 VHB  C14  C12  C11  118.38  3.000
 VHB  N4   C13  C12  180.00  3.000
 VHB  N5   C14  CL   116.88  3.000
 VHB  N5   C14  C12  125.16  3.000
 VHB  CL   C14  C12  117.96  3.000
 VHB  H1   C15  N5   115.82  3.000
 VHB  H1   C15  C16  119.44  3.000
 VHB  N5   C15  C16  124.74  3.000
 VHB  H2   C16  C15  119.52  3.000
 VHB  H2   C16  C11  121.25  3.000
 VHB  C15  C16  C11  119.22  3.000
 VHB  H3   C17  C18  119.81  3.000
 VHB  H3   C17  C10  120.04  3.000
 VHB  C18  C17  C10  120.14  3.000
 VHB  H4   C18  C7   119.68  3.000
 VHB  H4   C18  C17  120.14  3.000
 VHB  C7   C18  C17  120.16  3.000
 VHB  C15  N5   C14  116.37  3.000
 VHB  H5   N3   C11  118.65  3.000
 VHB  H5   N3   C10  116.30  3.000
 VHB  C11  N3   C10  125.01  3.000
 VHB  C8   C7   N2   119.71  3.000
 VHB  N2   C7   C18  119.99  3.000
 VHB  C8   C7   C18  120.30  3.000
 VHB  H6   N2   C6   116.53  3.000
 VHB  H6   N2   C7   118.16  3.000
 VHB  C6   N2   C7   125.30  3.000
 VHB  C5   C6   O    124.34  3.000
 VHB  O    C6   N2   121.12  3.000
 VHB  C5   C6   N2   114.52  3.000
 VHB  H7   C5   C4   120.42  3.000
 VHB  H7   C5   C6   116.31  3.000
 VHB  C4   C5   C6   123.23  3.000
 VHB  H8   C9   C8   119.96  3.000
 VHB  H8   C9   C10  118.94  3.000
 VHB  C8   C9   C10  121.10  3.000
 VHB  C4   C8   C9   123.70  3.000
 VHB  C4   C8   C7   117.93  3.000
 VHB  C9   C8   C7   118.36  3.000
 VHB  C2   C4   C8   121.57  3.000
 VHB  C2   C4   C5   119.21  3.000
 VHB  C8   C4   C5   119.22  3.000
 VHB  C3   C2   C1   103.62  3.000
 VHB  C3   C2   C4   126.93  3.000
 VHB  C1   C2   C4   129.35  3.000
 VHB  H9   C1   N    121.63  3.000
 VHB  H9   C1   C2   131.39  3.000
 VHB  N    C1   C2   106.94  3.000
 VHB  H10  C3   N1   120.75  3.000
 VHB  H10  C3   C2   127.76  3.000
 VHB  N1   C3   C2   111.47  3.000
 VHB  N    N1   C3   105.47  3.000
 VHB  C    N    N1   120.80  3.000
 VHB  N1   N    C1   112.49  3.000
 VHB  C    N    C1   126.71  3.000
 VHB  H13  C    H12  109.16  3.000
 VHB  H13  C    H11  109.13  3.000
 VHB  H12  C    H11  109.10  3.000
 VHB  H13  C    N    110.53  3.000
 VHB  H12  C    N    110.62  3.000
 VHB  H11  C    N    108.27  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
 VHB  CONST_01  C7   C18  C17  C10     0.00   0.0  0
 VHB  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 VHB  CONST_03  N5   C14  C12  C11     0.00   0.0  0
 VHB  CONST_04  N5   C15  C16  C11     0.00   0.0  0
 VHB  CONST_05  C15  N5   C14  C12     0.00   0.0  0
 VHB  CONST_06  C15  C16  C11  C12     0.00   0.0  0
 VHB  CONST_07  C16  C15  N5   C14     0.00   0.0  0
 VHB  CONST_08  C16  C11  C12  C14     0.00   0.0  0
 VHB  CONST_09  C8   C9   C10  C17     0.00   0.0  0
 VHB  CONST_10  C8   C7   C18  C17     0.00   0.0  0
 VHB  CONST_11  C9   C10  C17  C18     0.00   0.0  0
 VHB  CONST_12  C9   C8   C7   C18     0.00   0.0  0
 VHB  CONST_13  C2   C4   C8   C7    180.00   0.0  0
 VHB  CONST_14  C2   C4   C8   C9      0.00   0.0  0
 VHB  CONST_17  N1   N    C1   C2      0.00   0.0  0
 VHB  CONST_18  N    N1   C3   C2      0.00   0.0  0
 VHB  CONST_19  C3   N1   N    C1      0.00   0.0  0
 VHB  CONST_20  N1   C3   C2   C1      0.00   0.0  0
 VHB  CONST_21  N    C1   C2   C3      0.00   0.0  0
 VHB  CONST_24  N    C1   C2   C4    180.00   0.0  0
 VHB  CONST_25  N1   C3   C2   C4    180.00   0.0  0
 VHB  CONST_26  C5   C6   N2   C7      0.00   0.0  0
 VHB  CONST_27  CL   C14  C12  C11   180.00   0.0  0
 VHB  CONST_28  N5   C14  C12  C13   180.00   0.0  0
 VHB  CONST_29  C16  C11  C12  C13   180.00   0.0  0
 VHB  CONST_30  N3   C11  C12  C14   180.00   0.0  0
 VHB  CONST_31  CL   C14  N5   C15   180.00   0.0  0
 VHB  CONST_32  N3   C11  C16  C15   180.00   0.0  0
 VHB  CONST_33  N3   C10  C17  C18   180.00   0.0  0
 VHB  CONST_34  C8   C9   C10  N3    180.00   0.0  0
 VHB  CONST_35  C    N    C1   C2    180.00   0.0  0
 VHB  CONST_36  C    N    N1   C3    180.00   0.0  0
 VHB  CONST_37  O    C6   N2   C7    180.00   0.0  0
 VHB  CONST_38  H4   C18  C17  C10   180.00   0.0  0
 VHB  CONST_39  H1   C15  C16  C11   180.00   0.0  0
 VHB  CONST_40  H2   C16  C11  C12   180.00   0.0  0
 VHB  CONST_41  H1   C15  N5   C14   180.00   0.0  0
 VHB  CONST_42  H8   C9   C10  C17   180.00   0.0  0
 VHB  CONST_43  H2   C16  C15  N5    180.00   0.0  0
 VHB  CONST_44  H3   C17  C18  C7    180.00   0.0  0
 VHB  CONST_45  H8   C9   C8   C7    180.00   0.0  0
 VHB  CONST_46  H4   C18  C7   N2      0.00   0.0  0
 VHB  CONST_47  H3   C17  C10  C9    180.00   0.0  0
 VHB  CONST_48  H4   C18  C7   C8    180.00   0.0  0
 VHB  CONST_49  H8   C9   C8   C4      0.00   0.0  0
 VHB  CONST_50  H9   C1   C2   C4      0.00   0.0  0
 VHB  CONST_51  H10  C3   C2   C4      0.00   0.0  0
 VHB  CONST_52  H10  C3   C2   C1    180.00   0.0  0
 VHB  CONST_53  H9   C1   C2   C3    180.00   0.0  0
 VHB  CONST_54  H9   C1   N    N1    180.00   0.0  0
 VHB  CONST_55  H10  C3   N1   N     180.00   0.0  0
 VHB  CONST_56  H6   N2   C6   C5    180.00   0.0  0
 VHB  CONST_57  H6   N2   C6   O       0.00   0.0  0
 VHB  Var_01    C6   N2   C7   C18  -177.69  30.0  1
 VHB  Var_02    C5   C4   C8   C7     -2.79  30.0  1
 VHB  Var_03    C4   C5   C6   N2      1.13  30.0  1
 VHB  Var_04    C8   C7   N2   C6      1.42  30.0  1
 VHB  Var_05    C8   C4   C5   C6      1.51  30.0  1
 VHB  Var_06    C2   C4   C5   C6   -179.08  30.0  1
 VHB  Var_07    C9   C8   C4   C5    176.22  30.0  1
 VHB  Var_08    C12  C11  N3   C10   175.43  30.0  3
 VHB  Var_09    C16  C11  N3   C10    -5.20  30.0  3
 VHB  Var_10    C17  C10  N3   C11   -62.98  30.0  2
 VHB  Var_11    C9   C10  N3   C11   119.66  30.0  2
 VHB  Var_12    C4   C5   C6   O     179.91  30.0  1
 VHB  Var_13    H6   N2   C7   C18     0.85  30.0  1
 VHB  Var_14    H7   C5   C6   N2   -176.59  30.0  1
 VHB  Var_15    H6   N2   C7   C8    179.96  30.0  1
 VHB  Var_16    H7   C5   C4   C8    179.15  30.0  1
 VHB  Var_17    H7   C5   C4   C2     -1.44  30.0  1
 VHB  Var_18    H5   N3   C11  C12    -7.20  30.0  2
 VHB  Var_19    H5   N3   C11  C16   172.17  30.0  2
 VHB  Var_20    H5   N3   C10  C17   119.59  30.0  1
 VHB  Var_21    H7   C5   C6   O       2.18  30.0  1
 VHB  Var_22    H5   N3   C10  C9    -57.77  30.0  1
 VHB  Var_23    H11  C    N    C1    179.19  30.0  2
 VHB  Var_24    H12  C    N    C1    -61.31  30.0  2
 VHB  Var_25    H13  C    N    C1     59.71  30.0  2
 VHB  Var_26    H11  C    N    N1     -1.14  30.0  2
 VHB  Var_27    H12  C    N    N1    118.36  30.0  2
 VHB  Var_28    H13  C    N    N1   -120.62  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
 VHB  plan-1  C4   0.020
 VHB  plan-1  C2   0.020
 VHB  plan-1  C1   0.020
 VHB  plan-1  C3   0.020
 VHB  plan-1  N1   0.020
 VHB  plan-1  N    0.020
 VHB  plan-1  C    0.020
 VHB  plan-1  H9   0.020
 VHB  plan-1  H10  0.020
 VHB  plan-2  C11  0.020
 VHB  plan-2  C12  0.020
 VHB  plan-2  C13  0.020
 VHB  plan-2  C14  0.020
 VHB  plan-2  C15  0.020
 VHB  plan-2  C16  0.020
 VHB  plan-2  CL   0.020
 VHB  plan-2  N4   0.020
 VHB  plan-2  N5   0.020
 VHB  plan-2  N3   0.020
 VHB  plan-2  H1   0.020
 VHB  plan-2  H2   0.020
 VHB  plan-3  C10  0.020
 VHB  plan-3  C17  0.020
 VHB  plan-3  C18  0.020
 VHB  plan-3  N3   0.020
 VHB  plan-3  C7   0.020
 VHB  plan-3  N2   0.020
 VHB  plan-3  C9   0.020
 VHB  plan-3  C8   0.020
 VHB  plan-3  C4   0.020
 VHB  plan-3  H3   0.020
 VHB  plan-3  H4   0.020
 VHB  plan-3  H8   0.020
 VHB  plan-4  C7   0.020
 VHB  plan-4  N2   0.020
 VHB  plan-4  C6   0.020
 VHB  plan-4  O    0.020
 VHB  plan-4  C5   0.020
 VHB  plan-4  H6   0.020

