# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 15:08:47 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-chloranyl-4-[[4-(4-methylpiperazin-1-yl)-2-oxidanylidene-1~{H}-quinolin-6-yl]amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)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
 VH5  VH5  "2-chloranyl-4-[[4-(4-methylpiperazin-1-yl)-2-oxidanylidene-1H-quinolin-6-yl]amino]pyridine-3-carbonitrile"
  ligand  47  28  .  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_VH5
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
 VH5  C1   C   CR6   0  -0.093  -26.9034   9.6627  13.5118
 VH5  C2   C   CR6   0   0.518  -25.8037   9.7333  14.4006
 VH5  C3   C   CR16  0  -0.388  -24.5856   9.2214  13.9166
 VH5  C4   C   CR16  0  -0.052  -24.5356   8.6884  12.6546
 VH5  C5   C   CR6   0   0.308  -24.9769  10.2564  16.6507
 VH5  C6   C   CR16  0  -0.296  -24.6323  11.4503  17.2917
 VH5  C8   C   CR66  0   0.366  -23.1874  10.2366  18.7827
 VH5  C9   C   CR66  0  -0.005  -23.4677   9.0460  18.0980
 VH5  C12  C   CR16  0  -0.573  -22.0971   7.8536  19.7023
 VH5  C19  C   CSP   0   0.030  -28.1755  10.1438  13.9071
 VH5  N5   N   NS    0  -0.228  -29.1956  10.5406  14.2706
 VH5  N    N   N     0  -0.408  -25.5780   8.6136  11.8153
 VH5  C    C   CR6   0   0.146  -26.7051   9.0943  12.2514
 VH5  CL   CL  CL    0  -0.065  -28.0563   9.0118  11.1776
 VH5  N1   N   NH1   0  -0.785  -25.9424  10.2786  15.6228
 VH5  C10  C   CR16  0  -0.368  -24.4138   9.0686  17.0690
 VH5  C11  C   CR6   0   0.487  -22.8356   7.8210  18.5610
 VH5  N3   N   NT    0  -0.513  -23.0624   6.6644  17.8352
 VH5  C17  C   CH2   0  -0.342  -22.5156   6.6216  16.4784
 VH5  C16  C   CH2   0  -0.279  -23.1916   5.5244  15.6839
 VH5  N4   N   NT    0  -0.412  -23.0199   4.2471  16.3433
 VH5  C18  C   CH3   0  -0.516  -23.6028   3.1672  15.5814
 VH5  C15  C   CH2   0  -0.276  -23.5405   4.2955  17.6937
 VH5  C14  C   CH2   0  -0.320  -22.8657   5.3899  18.5012
 VH5  C13  C   CR6   0   0.523  -21.8414   9.0714  20.4379
 VH5  O    O   O     0  -0.489  -21.1685   9.1320  21.4601
 VH5  N2   N   NR16  0  -0.759  -22.3760  10.2081  19.8833
 VH5  C7   C   CR16  0  -0.313  -23.7649  11.4385  18.3587
 VH5  H1   H   HCR6  0   0.306  -23.6859   9.2595  14.5122
 VH5  H2   H   HCR6  0   0.288  -23.5975   8.2991  12.2784
 VH5  H3   H   HCR6  0   0.280  -25.0686  12.3844  16.9615
 VH5  H4   H   HCR6  0   0.280  -21.6200   6.9632  20.0879
 VH5  H5   H   HNH1  0   0.421  -26.8033  10.7633  15.8336
 VH5  H6   H   HCR6  0   0.304  -24.7271   8.1374  16.6145
 VH5  H7   H   HCH2  0   0.240  -21.4340   6.4322  16.5212
 VH5  H8   H   HCH2  0   0.270  -22.6515   7.5769  15.9763
 VH5  H9   H   HCH2  0   0.198  -24.2572   5.7802  15.5454
 VH5  H10  H   HCH2  0   0.242  -22.7399   5.4786  14.6902
 VH5  H12  H   HCH3  0   0.233  -23.4063   2.2135  16.0734
 VH5  H13  H   HCH3  0   0.193  -24.6923   3.2630  15.4551
 VH5  H14  H   HCH3  0   0.233  -23.1555   3.1292  14.5870
 VH5  H15  H   HCH2  0   0.196  -24.6315   4.4634  17.7078
 VH5  H16  H   HCH2  0   0.242  -23.3554   3.3366  18.1832
 VH5  H17  H   HCH2  0   0.221  -21.7992   5.1534  18.6241
 VH5  H18  H   HCH2  0   0.259  -23.3153   5.4289  19.4940
 VH5  H19  H   HNR6  0   0.412  -22.1954  11.0780  20.3668
 VH5  H20  H   HCR6  0   0.283  -23.5298  12.3596  18.8770

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
 VH5  CL   C    single    1.728  0.020  1.728
 VH5  N    C    aromatic  1.301  0.020  1.301
 VH5  N    C4   aromatic  1.340  0.020  1.340
 VH5  C    C1   aromatic  1.397  0.020  1.397
 VH5  C4   C3   aromatic  1.371  0.020  1.371
 VH5  C1   C19  single    1.416  0.020  1.416
 VH5  C1   C2   aromatic  1.416  0.020  1.416
 VH5  C19  N5   triple    1.153  0.020  1.153
 VH5  C3   C2   aromatic  1.407  0.020  1.407
 VH5  C2   N1   single    1.345  0.020  1.345
 VH5  N1   C5   single    1.410  0.020  1.410
 VH5  C16  C17  single    1.514  0.020  1.514
 VH5  C16  N4   single    1.448  0.020  1.448
 VH5  C18  N4   single    1.444  0.020  1.444
 VH5  C17  N3   single    1.463  0.020  1.463
 VH5  N4   C15  single    1.448  0.020  1.448
 VH5  C5   C10  aromatic  1.379  0.020  1.379
 VH5  C5   C6   aromatic  1.398  0.020  1.398
 VH5  C10  C9   aromatic  1.398  0.020  1.398
 VH5  C6   C7   aromatic  1.375  0.020  1.375
 VH5  N3   C11  single    1.384  0.020  1.384
 VH5  N3   C14  single    1.451  0.020  1.451
 VH5  C15  C14  single    1.518  0.020  1.518
 VH5  C9   C11  single    1.454  0.020  1.454
 VH5  C9   C8   aromatic  1.402  0.020  1.402
 VH5  C7   C8   aromatic  1.399  0.020  1.399
 VH5  C11  C12  double    1.360  0.020  1.360
 VH5  C8   N2   single    1.368  0.020  1.368
 VH5  C12  C13  single    1.446  0.020  1.446
 VH5  N2   C13  single    1.373  0.020  1.373
 VH5  C13  O    double    1.225  0.020  1.225
 VH5  C3   H1   single    0.930  0.020  1.080
 VH5  C4   H2   single    0.930  0.020  1.080
 VH5  C6   H3   single    0.930  0.020  1.080
 VH5  C12  H4   single    0.930  0.020  1.080
 VH5  N1   H5   single    0.860  0.020  1.020
 VH5  C10  H6   single    0.930  0.020  1.080
 VH5  C17  H7   single    0.970  0.020  1.090
 VH5  C17  H8   single    0.970  0.020  1.090
 VH5  C16  H9   single    0.970  0.020  1.090
 VH5  C16  H10  single    0.970  0.020  1.090
 VH5  C18  H12  single    0.970  0.020  1.090
 VH5  C18  H13  single    0.970  0.020  1.090
 VH5  C18  H14  single    0.970  0.020  1.090
 VH5  C15  H15  single    0.970  0.020  1.090
 VH5  C15  H16  single    0.970  0.020  1.090
 VH5  C14  H17  single    0.970  0.020  1.090
 VH5  C14  H18  single    0.970  0.020  1.090
 VH5  N2   H19  single    0.860  0.020  1.020
 VH5  C7   H20  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
 VH5  C    C1   C19  121.17  3.000
 VH5  C19  C1   C2   120.37  3.000
 VH5  C    C1   C2   118.46  3.000
 VH5  N1   C2   C3   123.31  3.000
 VH5  N1   C2   C1   120.69  3.000
 VH5  C3   C2   C1   116.00  3.000
 VH5  H1   C3   C4   119.42  3.000
 VH5  H1   C3   C2   121.25  3.000
 VH5  C4   C3   C2   119.32  3.000
 VH5  H2   C4   N    115.85  3.000
 VH5  H2   C4   C3   119.42  3.000
 VH5  N    C4   C3   124.73  3.000
 VH5  C10  C5   N1   120.93  3.000
 VH5  C10  C5   C6   119.71  3.000
 VH5  N1   C5   C6   119.30  3.000
 VH5  H3   C6   C7   119.89  3.000
 VH5  H3   C6   C5   119.84  3.000
 VH5  C7   C6   C5   120.25  3.000
 VH5  C7   C8   N2   120.43  3.000
 VH5  N2   C8   C9   119.60  3.000
 VH5  C7   C8   C9   119.94  3.000
 VH5  C11  C9   C10  122.83  3.000
 VH5  C11  C9   C8   118.24  3.000
 VH5  C10  C9   C8   118.75  3.000
 VH5  H4   C12  C13  115.74  3.000
 VH5  H4   C12  C11  121.28  3.000
 VH5  C13  C12  C11  122.91  3.000
 VH5  N5   C19  C1   180.00  3.000
 VH5  C    N    C4   116.32  3.000
 VH5  CL   C    N    116.85  3.000
 VH5  N    C    C1   125.17  3.000
 VH5  CL   C    C1   117.98  3.000
 VH5  H5   N1   C5   116.03  3.000
 VH5  H5   N1   C2   118.16  3.000
 VH5  C5   N1   C2   125.80  3.000
 VH5  H6   C10  C9   119.40  3.000
 VH5  H6   C10  C5   119.69  3.000
 VH5  C9   C10  C5   120.89  3.000
 VH5  N3   C11  C12  123.30  3.000
 VH5  C12  C11  C9   118.89  3.000
 VH5  N3   C11  C9   117.76  3.000
 VH5  C14  N3   C17  110.43  3.000
 VH5  C14  N3   C11  118.10  3.000
 VH5  C17  N3   C11  116.70  3.000
 VH5  H8   C17  H7   107.00  3.000
 VH5  H8   C17  C16  109.78  3.000
 VH5  H7   C17  C16  109.57  3.000
 VH5  H8   C17  N3   110.83  3.000
 VH5  H7   C17  N3   109.67  3.000
 VH5  C16  C17  N3   109.93  3.000
 VH5  H10  C16  H9   107.13  3.000
 VH5  H10  C16  N4   109.17  3.000
 VH5  H9   C16  N4   112.08  3.000
 VH5  H10  C16  C17  108.85  3.000
 VH5  H9   C16  C17  109.19  3.000
 VH5  N4   C16  C17  110.33  3.000
 VH5  C15  N4   C18  111.83  3.000
 VH5  C15  N4   C16  110.65  3.000
 VH5  C18  N4   C16  111.81  3.000
 VH5  H14  C18  H13  107.71  3.000
 VH5  H14  C18  H12  107.86  3.000
 VH5  H13  C18  H12  107.82  3.000
 VH5  H14  C18  N4   109.96  3.000
 VH5  H13  C18  N4   113.25  3.000
 VH5  H12  C18  N4   110.06  3.000
 VH5  H16  C15  H15  107.17  3.000
 VH5  H16  C15  C14  108.61  3.000
 VH5  H15  C15  C14  108.84  3.000
 VH5  H16  C15  N4   109.12  3.000
 VH5  H15  C15  N4   111.85  3.000
 VH5  C14  C15  N4   111.12  3.000
 VH5  H18  C14  H17  107.81  3.000
 VH5  H18  C14  C15  109.07  3.000
 VH5  H17  C14  C15  109.61  3.000
 VH5  H18  C14  N3   109.30  3.000
 VH5  H17  C14  N3   111.82  3.000
 VH5  C15  C14  N3   109.19  3.000
 VH5  N2   C13  O    120.65  3.000
 VH5  O    C13  C12  124.29  3.000
 VH5  N2   C13  C12  115.03  3.000
 VH5  H19  N2   C13  116.71  3.000
 VH5  H19  N2   C8   118.21  3.000
 VH5  C13  N2   C8   124.97  3.000
 VH5  H20  C7   C8   119.75  3.000
 VH5  H20  C7   C6   120.06  3.000
 VH5  C8   C7   C6   120.19  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
 VH5  CONST_01  C4   N    C    C1      0.00   0.0  0
 VH5  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 VH5  CONST_03  N    C    C1   C2      0.00   0.0  0
 VH5  CONST_04  N    C4   C3   C2      0.00   0.0  0
 VH5  CONST_05  C    N    C4   C3      0.00   0.0  0
 VH5  CONST_06  C    C1   C2   C3      0.00   0.0  0
 VH5  CONST_07  C8   C9   C10  C5      0.00   0.0  0
 VH5  CONST_08  C8   C7   C6   C5      0.00   0.0  0
 VH5  CONST_09  C9   C10  C5   C6      0.00   0.0  0
 VH5  CONST_10  C9   C8   C7   C6      0.00   0.0  0
 VH5  CONST_11  C7   C6   C5   C10     0.00   0.0  0
 VH5  CONST_12  C7   C8   C9   C10     0.00   0.0  0
 VH5  CONST_13  C12  C13  N2   C8      0.00   0.0  0
 VH5  CONST_14  CL   C    C1   C2    180.00   0.0  0
 VH5  CONST_15  C19  C1   C2   C3    180.00   0.0  0
 VH5  CONST_16  CL   C    N    C4    180.00   0.0  0
 VH5  CONST_17  N1   C2   C3   C4    180.00   0.0  0
 VH5  CONST_18  N1   C5   C10  C9    180.00   0.0  0
 VH5  CONST_19  N    C    C1   C19   180.00   0.0  0
 VH5  CONST_20  N1   C2   C1   C     180.00   0.0  0
 VH5  CONST_21  C7   C6   C5   N1    180.00   0.0  0
 VH5  CONST_22  O    C13  N2   C8    180.00   0.0  0
 VH5  CONST_23  H1   C3   C2   C1    180.00   0.0  0
 VH5  CONST_24  H2   C4   C3   C2    180.00   0.0  0
 VH5  CONST_25  H20  C7   C6   C5    180.00   0.0  0
 VH5  CONST_26  H6   C10  C5   C6    180.00   0.0  0
 VH5  CONST_27  H6   C10  C9   C8    180.00   0.0  0
 VH5  CONST_28  H3   C6   C7   C8    180.00   0.0  0
 VH5  CONST_29  H20  C7   C8   C9    180.00   0.0  0
 VH5  CONST_30  H1   C3   C4   N     180.00   0.0  0
 VH5  CONST_31  H2   C4   N    C     180.00   0.0  0
 VH5  CONST_32  H3   C6   C5   C10   180.00   0.0  0
 VH5  CONST_33  H6   C10  C9   C11     0.00   0.0  0
 VH5  CONST_34  H20  C7   C8   N2      0.00   0.0  0
 VH5  CONST_35  H19  N2   C13  C12   180.00   0.0  0
 VH5  CONST_36  H19  N2   C13  O       0.00   0.0  0
 VH5  Var_01    N3   C11  C9   C8   -176.62  30.0  1
 VH5  Var_02    C12  C11  C9   C8      5.76  30.0  1
 VH5  Var_03    C17  N3   C11  C9     66.33  30.0  3
 VH5  Var_04    C14  N3   C11  C9   -158.32  30.0  3
 VH5  Var_05    C13  C12  C11  C9     -3.90  30.0  1
 VH5  Var_06    C13  N2   C8   C9     -3.36  30.0  1
 VH5  Var_07    C17  N3   C11  C12  -116.16  30.0  3
 VH5  Var_08    C14  N3   C11  C12    19.19  30.0  3
 VH5  Var_09    C10  C9   C11  C12  -169.33  30.0  1
 VH5  Var_10    N3   C11  C9   C10     8.29  30.0  1
 VH5  Var_11    C16  C17  N3   C11  -162.44  30.0  1
 VH5  Var_12    C15  C14  N3   C11   163.59  30.0  1
 VH5  Var_13    N2   C13  C12  C11    -1.38  30.0  1
 VH5  Var_14    N4   C16  C17  N3    -57.73  30.0  1
 VH5  Var_15    C13  C12  C11  N3    178.61  30.0  1
 VH5  Var_16    N4   C15  C14  N3     57.89  30.0  1
 VH5  Var_17    C15  N4   C16  C17    57.18  30.0  1
 VH5  Var_18    C15  C14  N3   C17   -58.47  30.0  1
 VH5  Var_19    C14  N3   C17  C16    58.97  30.0  1
 VH5  Var_20    C14  C15  N4   C16   -57.57  30.0  1
 VH5  Var_21    C7   C8   N2   C13   174.98  30.0  1
 VH5  Var_22    C5   N1   C2   C1    171.58  30.0  2
 VH5  Var_23    C10  C5   N1   C2    -53.25  30.0  2
 VH5  Var_24    C6   C5   N1   C2    129.60  30.0  2
 VH5  Var_25    C5   N1   C2   C3     -9.29  30.0  2
 VH5  Var_26    O    C13  C12  C11  -179.19  30.0  1
 VH5  Var_27    C18  N4   C16  C17  -177.46  30.0  1
 VH5  Var_28    C14  C15  N4   C18   177.08  30.0  1
 VH5  Var_29    H4   C12  C11  C9    179.27  30.0  1
 VH5  Var_30    H19  N2   C8   C9   -179.39  30.0  1
 VH5  Var_31    H7   C17  N3   C11    77.02  30.0  1
 VH5  Var_32    H8   C17  N3   C11   -40.90  30.0  1
 VH5  Var_33    H17  C14  N3   C11   -74.94  30.0  1
 VH5  Var_34    H18  C14  N3   C11    44.36  30.0  1
 VH5  Var_35    H9   C16  C17  N3     65.87  30.0  1
 VH5  Var_36    H10  C16  C17  N3   -177.50  30.0  1
 VH5  Var_37    H4   C12  C11  N3      1.79  30.0  1
 VH5  Var_38    H15  C15  C14  N3    -65.71  30.0  1
 VH5  Var_39    H16  C15  C14  N3    177.93  30.0  1
 VH5  Var_40    H17  C14  N3   C17    63.01  30.0  1
 VH5  Var_41    H18  C14  N3   C17  -177.70  30.0  1
 VH5  Var_42    H15  C15  N4   C16    64.28  30.0  1
 VH5  Var_43    H16  C15  N4   C16  -177.31  30.0  1
 VH5  Var_44    H7   C17  C16  N4     62.86  30.0  1
 VH5  Var_45    H8   C17  C16  N4   -179.90  30.0  1
 VH5  Var_46    H17  C14  C15  N4    -64.91  30.0  1
 VH5  Var_47    H18  C14  C15  N4    177.27  30.0  1
 VH5  Var_48    H9   C16  N4   C15   -64.73  30.0  1
 VH5  Var_49    H10  C16  N4   C15   176.75  30.0  1
 VH5  Var_50    H7   C17  N3   C14   -61.56  30.0  1
 VH5  Var_51    H8   C17  N3   C14  -179.49  30.0  1
 VH5  Var_52    H4   C12  C13  N2    175.61  30.0  1
 VH5  Var_53    H19  N2   C8   C7     -1.05  30.0  1
 VH5  Var_54    H5   N1   C2   C1     -9.46  30.0  2
 VH5  Var_55    H5   N1   C2   C3    169.67  30.0  2
 VH5  Var_56    H5   N1   C5   C6    -49.38  30.0  2
 VH5  Var_57    H5   N1   C5   C10   127.77  30.0  2
 VH5  Var_58    H12  C18  N4   C16   176.67  30.0  3
 VH5  Var_59    H13  C18  N4   C16   -62.56  30.0  3
 VH5  Var_60    H14  C18  N4   C16    57.99  30.0  3
 VH5  Var_61    H9   C16  N4   C18    60.63  30.0  1
 VH5  Var_62    H10  C16  N4   C18   -57.88  30.0  1
 VH5  Var_63    H15  C15  N4   C18   -61.07  30.0  1
 VH5  Var_64    H16  C15  N4   C18    57.34  30.0  1
 VH5  Var_65    H12  C18  N4   C15   -58.62  30.0  3
 VH5  Var_66    H13  C18  N4   C15    62.15  30.0  3
 VH5  Var_67    H14  C18  N4   C15  -177.30  30.0  3
 VH5  Var_68    H4   C12  C13  O      -2.20  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
 VH5  plan-1  C1   0.020
 VH5  plan-1  C2   0.020
 VH5  plan-1  C3   0.020
 VH5  plan-1  C4   0.020
 VH5  plan-1  C19  0.020
 VH5  plan-1  N5   0.020
 VH5  plan-1  N    0.020
 VH5  plan-1  C    0.020
 VH5  plan-1  CL   0.020
 VH5  plan-1  N1   0.020
 VH5  plan-1  H1   0.020
 VH5  plan-1  H2   0.020
 VH5  plan-2  C5   0.020
 VH5  plan-2  C6   0.020
 VH5  plan-2  C8   0.020
 VH5  plan-2  C9   0.020
 VH5  plan-2  N1   0.020
 VH5  plan-2  C10  0.020
 VH5  plan-2  C11  0.020
 VH5  plan-2  N2   0.020
 VH5  plan-2  C7   0.020
 VH5  plan-2  H3   0.020
 VH5  plan-2  H6   0.020
 VH5  plan-2  H20  0.020
 VH5  plan-3  C11  0.020
 VH5  plan-3  N3   0.020
 VH5  plan-3  C17  0.020
 VH5  plan-3  C14  0.020
 VH5  plan-4  C8   0.020
 VH5  plan-4  C12  0.020
 VH5  plan-4  C13  0.020
 VH5  plan-4  O    0.020
 VH5  plan-4  N2   0.020
 VH5  plan-4  H19  0.020

