# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 19:59:21 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-chloranyl-4-[[4-(ethylamino)-2-oxidanylidene-1~{H}-quinolin-6-yl]amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC1=CC(=O)Nc2ccc(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
 VHK  VHK  "2-chloranyl-4-[[4-(ethylamino)-2-oxidanylidene-1H-quinolin-6-yl]amino]pyridine-3-carbonitrile"
  ligand  38  24  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VHK
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
 VHK  C2   C   CR16  0  -0.319  23.9962   -9.0665  17.8839
 VHK  N3   N   N     0  -0.409  25.7503   -8.8731  11.4566
 VHK  C7   C   CR16  0  -0.602  22.3454  -12.5532  19.4846
 VHK  C8   C   CR6   0   0.508  21.9364  -11.2811  20.0006
 VHK  C10  C   CH3   0  -0.697  23.7264  -16.3182  17.7722
 VHK  C4   C   CR66  0  -0.011  23.8536  -11.4909  17.8909
 VHK  C14  C   CR6   0   0.144  26.8893   -9.3627  11.8512
 VHK  C5   C   CR16  0  -0.361  24.7730  -11.5113  16.8368
 VHK  C6   C   CR6   0   0.521  23.2666  -12.6927  18.4748
 VHK  N1   N   NH1   0  -0.688  23.6301  -13.8968  18.0010
 VHK  C12  C   CR16  0  -0.385  24.8610   -9.3698  13.6322
 VHK  CL   CL  CL    0  -0.066  28.1815   -9.3565  10.7044
 VHK  C13  C   CR16  0  -0.053  24.7548   -8.8852  12.3540
 VHK  C15  C   CR6   0  -0.086  27.1432   -9.8866  13.1205
 VHK  C16  C   CSP   0   0.031  28.4237  -10.3814  13.4688
 VHK  N4   N   NS    0  -0.229  29.4518  -10.7903  13.7942
 VHK  C11  C   CR6   0   0.517  26.0904   -9.8993  14.0663
 VHK  C    C   CR6   0   0.280  25.3094  -10.3452  16.3342
 VHK  O    O   O     0  -0.506  21.1226  -11.1201  20.9067
 VHK  N    N   NR16  0  -0.765  22.5344  -10.1868  19.4124
 VHK  C3   C   CR66  0   0.375  23.4526  -10.2477  18.4048
 VHK  C1   C   CR16  0  -0.269  24.9227   -9.1142  16.8709
 VHK  H1   H   HCR6  0   0.283  23.6903   -8.1121  18.2937
 VHK  H2   H   HCR6  0   0.273  21.8933  -13.4182  19.9478
 VHK  H3   H   HCH3  0   0.248  23.3474  -17.2541  18.1791
 VHK  H4   H   HCH3  0   0.237  23.4567  -16.2757  16.7168
 VHK  H5   H   HCH3  0   0.235  24.8144  -16.3375  17.8483
 VHK  H6   H   HCH2  0   0.237  22.0494  -15.1690  18.4683
 VHK  H7   H   HCH2  0   0.233  23.3906  -15.2318  19.6007
 VHK  H8   H   HCR6  0   0.266  25.0864  -12.4418  16.3814
 VHK  H9   H   HNH1  0   0.408  24.4148  -13.9612  17.3763
 VHK  H10  H   HCR6  0   0.301  23.9987   -9.3523  14.2822
 VHK  H11  H   HCR6  0   0.288  23.8084   -8.4824  12.0141
 VHK  H12  H   HNH1  0   0.421  27.1372  -10.8775  15.5085
 VHK  H13  H   HNR6  0   0.408  22.2674   -9.2778  19.7656
 VHK  H14  H   HCR6  0   0.284  25.3530   -8.1974  16.4885
 VHK  N2   N   NH1   0  -0.779  26.2714  -10.4014  15.2992
 VHK  C9   C   CH2   0  -0.274  23.1407  -15.1473  18.5371

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
 VHK  CL   C14  single    1.728  0.020  1.728
 VHK  N3   C14  aromatic  1.301  0.020  1.301
 VHK  N3   C13  aromatic  1.340  0.020  1.340
 VHK  C14  C15  aromatic  1.396  0.020  1.396
 VHK  C13  C12  aromatic  1.371  0.020  1.371
 VHK  C15  C16  single    1.416  0.020  1.416
 VHK  C15  C11  aromatic  1.415  0.020  1.415
 VHK  C16  N4   triple    1.153  0.020  1.153
 VHK  C12  C11  aromatic  1.407  0.020  1.407
 VHK  C11  N2   single    1.343  0.020  1.343
 VHK  N2   C    single    1.414  0.020  1.414
 VHK  C    C1   aromatic  1.397  0.020  1.397
 VHK  C    C5   aromatic  1.378  0.020  1.378
 VHK  C1   C2   aromatic  1.374  0.020  1.374
 VHK  C5   C4   aromatic  1.399  0.020  1.399
 VHK  C10  C9   single    1.516  0.020  1.516
 VHK  N1   C9   single    1.446  0.020  1.446
 VHK  N1   C6   single    1.344  0.020  1.344
 VHK  C2   C3   aromatic  1.401  0.020  1.401
 VHK  C4   C3   aromatic  1.404  0.020  1.404
 VHK  C4   C6   single    1.459  0.020  1.459
 VHK  C3   N    single    1.365  0.020  1.365
 VHK  C6   C7   double    1.374  0.020  1.374
 VHK  N    C8   single    1.379  0.020  1.379
 VHK  C7   C8   single    1.432  0.020  1.432
 VHK  C8   O    double    1.229  0.020  1.229
 VHK  C2   H1   single    0.930  0.020  1.080
 VHK  C7   H2   single    0.930  0.020  1.080
 VHK  C10  H3   single    0.970  0.020  1.090
 VHK  C10  H4   single    0.970  0.020  1.090
 VHK  C10  H5   single    0.970  0.020  1.090
 VHK  C9   H6   single    0.970  0.020  1.090
 VHK  C9   H7   single    0.970  0.020  1.090
 VHK  C5   H8   single    0.930  0.020  1.080
 VHK  N1   H9   single    0.860  0.020  1.020
 VHK  C12  H10  single    0.930  0.020  1.080
 VHK  C13  H11  single    0.930  0.020  1.080
 VHK  N2   H12  single    0.860  0.020  1.020
 VHK  N    H13  single    0.860  0.020  1.020
 VHK  C1   H14  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
 VHK  H1   C2   C1   120.02  3.000
 VHK  H1   C2   C3   119.53  3.000
 VHK  C1   C2   C3   120.45  3.000
 VHK  C13  N3   C14  116.35  3.000
 VHK  H2   C7   C6   120.95  3.000
 VHK  H2   C7   C8   115.92  3.000
 VHK  C6   C7   C8   123.12  3.000
 VHK  N    C8   O    119.87  3.000
 VHK  O    C8   C7   124.84  3.000
 VHK  N    C8   C7   115.29  3.000
 VHK  H5   C10  H4   108.36  3.000
 VHK  H5   C10  H3   107.82  3.000
 VHK  H4   C10  H3   108.02  3.000
 VHK  H5   C10  C9   111.33  3.000
 VHK  H4   C10  C9   111.26  3.000
 VHK  H3   C10  C9   109.93  3.000
 VHK  C3   C4   C6   117.90  3.000
 VHK  C6   C4   C5   123.63  3.000
 VHK  C3   C4   C5   118.46  3.000
 VHK  C15  C14  CL   117.95  3.000
 VHK  C15  C14  N3   125.17  3.000
 VHK  CL   C14  N3   116.88  3.000
 VHK  H8   C5   C    117.47  3.000
 VHK  H8   C5   C4   121.33  3.000
 VHK  C    C5   C4   121.20  3.000
 VHK  N1   C6   C4   119.21  3.000
 VHK  C4   C6   C7   118.69  3.000
 VHK  N1   C6   C7   122.10  3.000
 VHK  H9   N1   C6   119.19  3.000
 VHK  H9   N1   C9   116.05  3.000
 VHK  C6   N1   C9   123.55  3.000
 VHK  H10  C12  C11  121.19  3.000
 VHK  H10  C12  C13  119.57  3.000
 VHK  C11  C12  C13  119.23  3.000
 VHK  H11  C13  C12  119.45  3.000
 VHK  H11  C13  N3   115.81  3.000
 VHK  C12  C13  N3   124.74  3.000
 VHK  C11  C15  C16  120.34  3.000
 VHK  C11  C15  C14  118.39  3.000
 VHK  C16  C15  C14  121.27  3.000
 VHK  N4   C16  C15  180.00  3.000
 VHK  N2   C11  C15  121.09  3.000
 VHK  N2   C11  C12  122.78  3.000
 VHK  C15  C11  C12  116.13  3.000
 VHK  C1   C    N2   120.29  3.000
 VHK  C1   C    C5   119.83  3.000
 VHK  N2   C    C5   119.86  3.000
 VHK  H13  N    C3   118.41  3.000
 VHK  H13  N    C8   116.74  3.000
 VHK  C3   N    C8   124.86  3.000
 VHK  N    C3   C4   120.13  3.000
 VHK  N    C3   C2   119.88  3.000
 VHK  C4   C3   C2   119.99  3.000
 VHK  H14  C1   C    120.02  3.000
 VHK  H14  C1   C2   119.95  3.000
 VHK  C    C1   C2   120.03  3.000
 VHK  H12  N2   C    116.76  3.000
 VHK  H12  N2   C11  118.80  3.000
 VHK  C    N2   C11  124.41  3.000
 VHK  H7   C9   H6   106.68  3.000
 VHK  H7   C9   N1   110.44  3.000
 VHK  H6   C9   N1   109.36  3.000
 VHK  H7   C9   C10  110.00  3.000
 VHK  H6   C9   C10  109.78  3.000
 VHK  N1   C9   C10  110.50  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
 VHK  CONST_01  C5   C    C1   C2      0.00   0.0  0
 VHK  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 VHK  CONST_03  C11  C15  C14  N3      0.00   0.0  0
 VHK  CONST_04  C11  C12  C13  N3      0.00   0.0  0
 VHK  CONST_05  C1   C    C5   C4      0.00   0.0  0
 VHK  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 VHK  CONST_07  C12  C13  N3   C14     0.00   0.0  0
 VHK  CONST_08  C12  C11  C15  C14     0.00   0.0  0
 VHK  CONST_09  C15  C14  N3   C13     0.00   0.0  0
 VHK  CONST_10  C15  C11  C12  C13     0.00   0.0  0
 VHK  CONST_11  C3   C2   C1   C       0.00   0.0  0
 VHK  CONST_12  C3   C4   C5   C       0.00   0.0  0
 VHK  CONST_13  C3   N    C8   C7      0.00   0.0  0
 VHK  CONST_14  N2   C    C1   C2    180.00   0.0  0
 VHK  CONST_15  C16  C15  C14  N3    180.00   0.0  0
 VHK  CONST_16  N2   C    C5   C4    180.00   0.0  0
 VHK  CONST_17  N2   C11  C15  C14   180.00   0.0  0
 VHK  CONST_18  C16  C15  C11  C12   180.00   0.0  0
 VHK  CONST_19  C13  N3   C14  CL    180.00   0.0  0
 VHK  CONST_20  C11  C15  C14  CL    180.00   0.0  0
 VHK  CONST_21  N2   C11  C12  C13   180.00   0.0  0
 VHK  CONST_22  C3   N    C8   O     180.00   0.0  0
 VHK  CONST_23  H10  C12  C13  N3    180.00   0.0  0
 VHK  CONST_24  H1   C2   C3   C4    180.00   0.0  0
 VHK  CONST_25  H11  C13  N3   C14   180.00   0.0  0
 VHK  CONST_26  H14  C1   C    C5    180.00   0.0  0
 VHK  CONST_27  H8   C5   C4   C6      0.00   0.0  0
 VHK  CONST_28  H10  C12  C11  C15   180.00   0.0  0
 VHK  CONST_29  H11  C13  C12  C11   180.00   0.0  0
 VHK  CONST_30  H1   C2   C1   C     180.00   0.0  0
 VHK  CONST_31  H1   C2   C3   N       0.00   0.0  0
 VHK  CONST_32  H14  C1   C2   C3    180.00   0.0  0
 VHK  CONST_33  H8   C5   C4   C3    180.00   0.0  0
 VHK  CONST_34  H8   C5   C    C1    180.00   0.0  0
 VHK  CONST_35  H13  N    C8   C7    180.00   0.0  0
 VHK  CONST_36  H13  N    C8   O       0.00   0.0  0
 VHK  Var_01    C8   N    C3   C2   -179.91  30.0  1
 VHK  Var_02    C5   C4   C6   C7   -178.28  30.0  1
 VHK  Var_03    C3   C4   C6   C7      0.61  30.0  1
 VHK  Var_04    C4   C3   N    C8      0.03  30.0  1
 VHK  Var_05    C4   C6   C7   C8     -0.38  30.0  1
 VHK  Var_06    N    C8   C7   C6     -0.03  30.0  1
 VHK  Var_07    N1   C6   C7   C8   -179.63  30.0  1
 VHK  Var_08    C11  N2   C    C5    116.29  30.0  1
 VHK  Var_09    N1   C6   C4   C5      0.99  30.0  1
 VHK  Var_10    O    C8   C7   C6   -179.55  30.0  1
 VHK  Var_11    C3   C4   C6   N1    179.88  30.0  1
 VHK  Var_12    C    N2   C11  C12    -6.26  30.0  2
 VHK  Var_13    C    N2   C11  C15   174.25  30.0  2
 VHK  Var_14    C1   C    N2   C11   -65.18  30.0  2
 VHK  Var_15    H13  N    C3   C2     -0.21  30.0  1
 VHK  Var_16    H13  N    C3   C4    179.73  30.0  1
 VHK  Var_17    H2   C7   C6   C4   -179.55  30.0  1
 VHK  Var_18    H2   C7   C8   N     179.18  30.0  1
 VHK  Var_19    C9   N1   C6   C7     -2.78  30.0  1
 VHK  Var_20    C4   C6   N1   C9    177.98  30.0  2
 VHK  Var_21    H9   N1   C6   C7   -169.69  30.0  1
 VHK  Var_22    H9   N1   C6   C4     11.07  30.0  1
 VHK  Var_23    H12  N2   C    C5    -61.88  30.0  1
 VHK  Var_24    H2   C7   C6   N1      1.21  30.0  1
 VHK  Var_25    H12  N2   C11  C12   171.88  30.0  2
 VHK  Var_26    H12  N2   C11  C15    -7.61  30.0  2
 VHK  Var_27    H2   C7   C8   O      -0.34  30.0  1
 VHK  Var_28    H12  N2   C    C1    116.65  30.0  1
 VHK  Var_29    C6   N1   C9   C10   179.26  30.0  1
 VHK  Var_30    H6   C9   N1   C6     58.30  30.0  3
 VHK  Var_31    H7   C9   N1   C6    -58.81  30.0  3
 VHK  Var_32    H9   N1   C9   C10   -13.46  30.0  1
 VHK  Var_33    H3   C10  C9   N1   -179.65  30.0  3
 VHK  Var_34    H4   C10  C9   N1    -60.04  30.0  3
 VHK  Var_35    H5   C10  C9   N1     60.94  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
 VHK  plan-1  N3   0.020
 VHK  plan-1  C14  0.020
 VHK  plan-1  C12  0.020
 VHK  plan-1  CL   0.020
 VHK  plan-1  C13  0.020
 VHK  plan-1  C15  0.020
 VHK  plan-1  C16  0.020
 VHK  plan-1  N4   0.020
 VHK  plan-1  C11  0.020
 VHK  plan-1  H10  0.020
 VHK  plan-1  H11  0.020
 VHK  plan-1  N2   0.020
 VHK  plan-2  C2   0.020
 VHK  plan-2  C4   0.020
 VHK  plan-2  C5   0.020
 VHK  plan-2  C6   0.020
 VHK  plan-2  C    0.020
 VHK  plan-2  N    0.020
 VHK  plan-2  C3   0.020
 VHK  plan-2  C1   0.020
 VHK  plan-2  H1   0.020
 VHK  plan-2  H8   0.020
 VHK  plan-2  H14  0.020
 VHK  plan-2  N2   0.020
 VHK  plan-3  C7   0.020
 VHK  plan-3  C8   0.020
 VHK  plan-3  O    0.020
 VHK  plan-3  N    0.020
 VHK  plan-3  C3   0.020
 VHK  plan-3  H13  0.020

