# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 21:36:22 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: (2~{R})-2-[[6-[(2-chloranyl-3-cyano-pyridin-4-yl)amino]-2-oxidanylidene-1~{H}-quinolin-4-yl]amino]-~{N}-methyl-propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@@H](C)NC1=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
 VHZ  VHZ  "(2R)-2-[[6-[(2-chloranyl-3-cyano-pyridin-4-yl)amino]-2-oxidanylidene-1H-quinolin-4-yl]amino]-N-methyl-propanamide"
  ligand  45  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 OK
;

data_comp_VHZ
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
 VHZ  C10  C   CR66  0  -0.014  91.3218  -11.3888  17.8534
 VHZ  C13  C   CR16  0  -0.579  89.7432  -12.4841  19.3475
 VHZ  C14  C   CR6   0   0.513  89.3743  -11.2275  19.9369
 VHZ  C17  C   CH3   0  -0.511  87.2378  -14.8060  16.3241
 VHZ  C18  C   CH3   0  -0.689  91.3180  -16.1891  17.6893
 VHZ  C    C   CR6   0   0.144  94.4156   -9.1603  11.9225
 VHZ  C4   C   CR6   0  -0.084  94.6772   -9.6978  13.1844
 VHZ  C5   C   CSP   0   0.031  95.9591  -10.1969  13.5204
 VHZ  N1   N   NS    0  -0.229  96.9888  -10.6094  13.8362
 VHZ  C3   C   CR6   0   0.517  93.6293   -9.7220  14.1352
 VHZ  C2   C   CR16  0  -0.385  92.3979   -9.1866  13.7152
 VHZ  C1   C   CR16  0  -0.053  92.2841   -8.6877  12.4430
 VHZ  N    N   N     0  -0.409  93.2742   -8.6672  11.5398
 VHZ  C6   C   CR6   0   0.273  92.8449  -10.2101  16.3900
 VHZ  C11  C   CR16  0  -0.356  92.2569  -11.3826  16.8125
 VHZ  C12  C   CR6   0   0.520  90.6775  -12.5960  18.3532
 VHZ  N4   N   NH1   0  -0.717  91.0066  -13.7869  17.7968
 VHZ  C15  C   CH1   0  -0.195  90.4938  -15.0473  18.2753
 VHZ  C16  C   C     0   0.524  89.0200  -15.2659  17.9199
 VHZ  N5   N   NH1   0  -0.611  88.5882  -14.6585  16.8125
 VHZ  O1   O   O     0  -0.491  88.3238  -16.0028  18.6043
 VHZ  O    O   O     0  -0.498  88.5463  -11.0958  20.8327
 VHZ  N3   N   NR16  0  -0.764  90.0292  -10.1274  19.4316
 VHZ  C9   C   CR66  0   0.377  90.9621  -10.1635  18.4366
 VHZ  C8   C   CR16  0  -0.318  91.5584   -8.9754  17.9967
 VHZ  C7   C   CR16  0  -0.265  92.4961   -8.9989  16.9933
 VHZ  H1   H   HCR6  0   0.274  89.2413  -13.3503  19.7546
 VHZ  H2   H   HCH3  0   0.250  87.1245  -14.1953  15.4333
 VHZ  H3   H   HCH3  0   0.238  87.0143  -15.8407  16.0625
 VHZ  H4   H   HCH3  0   0.238  86.5072  -14.4748  17.0627
 VHZ  H5   H   HCH3  0   0.257  92.3603  -16.1006  17.9959
 VHZ  H6   H   HCH3  0   0.260  90.9436  -17.1465  18.0453
 VHZ  H7   H   HCH3  0   0.243  91.2749  -16.1863  16.5995
 VHZ  H8   H   HCR6  0   0.301  91.5407   -9.1747  14.3722
 VHZ  H9   H   HCR6  0   0.288  91.3368   -8.2800  12.1129
 VHZ  H10  H   HNH1  0   0.421  94.6848  -10.7107  15.5656
 VHZ  H11  H   HCR6  0   0.267  92.5391  -12.2942  16.3023
 VHZ  H12  H   HNH1  0   0.415  91.8460  -13.8394  17.2445
 VHZ  H13  H   HCH1  0   0.272  90.5608  -15.0971  19.3679
 VHZ  H14  H   HNH1  0   0.407  89.2234  -14.0583  16.3118
 VHZ  H15  H   HNR6  0   0.411  89.7914   -9.2306  19.8336
 VHZ  H16  H   HCR6  0   0.285  91.2825   -8.0366  18.4599
 VHZ  H17  H   HCR6  0   0.284  92.9642   -8.0783  16.6687
 VHZ  N2   N   NH1   0  -0.779  93.8151  -10.2396  15.3608
 VHZ  CL   CL  CL    0  -0.066  95.7007   -9.1420  10.7681

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
 VHZ  CL   C    single    1.728  0.020  1.728
 VHZ  N    C    aromatic  1.301  0.020  1.301
 VHZ  N    C1   aromatic  1.340  0.020  1.340
 VHZ  C    C4   aromatic  1.396  0.020  1.396
 VHZ  C1   C2   aromatic  1.371  0.020  1.371
 VHZ  C4   C5   single    1.416  0.020  1.416
 VHZ  C4   C3   aromatic  1.415  0.020  1.415
 VHZ  C5   N1   triple    1.153  0.020  1.153
 VHZ  C2   C3   aromatic  1.407  0.020  1.407
 VHZ  C3   N2   single    1.343  0.020  1.343
 VHZ  N2   C6   single    1.415  0.020  1.415
 VHZ  C17  N5   single    1.444  0.020  1.444
 VHZ  C6   C11  aromatic  1.378  0.020  1.378
 VHZ  C6   C7   aromatic  1.397  0.020  1.397
 VHZ  N5   C16  single    1.335  0.020  1.335
 VHZ  C11  C10  aromatic  1.399  0.020  1.399
 VHZ  C7   C8   aromatic  1.374  0.020  1.374
 VHZ  C18  C15  single    1.525  0.020  1.525
 VHZ  C16  O1   double    1.223  0.020  1.223
 VHZ  C16  C15  single    1.532  0.020  1.532
 VHZ  N4   C15  single    1.442  0.020  1.442
 VHZ  N4   C12  single    1.355  0.020  1.355
 VHZ  C10  C12  single    1.457  0.020  1.457
 VHZ  C10  C9   aromatic  1.404  0.020  1.404
 VHZ  C8   C9   aromatic  1.400  0.020  1.400
 VHZ  C12  C13  double    1.369  0.020  1.369
 VHZ  C9   N3   single    1.364  0.020  1.364
 VHZ  C13  C14  single    1.436  0.020  1.436
 VHZ  N3   C14  single    1.376  0.020  1.376
 VHZ  C14  O    double    1.227  0.020  1.227
 VHZ  C13  H1   single    0.930  0.020  1.080
 VHZ  C17  H2   single    0.970  0.020  1.090
 VHZ  C17  H3   single    0.970  0.020  1.090
 VHZ  C17  H4   single    0.970  0.020  1.090
 VHZ  C18  H5   single    0.970  0.020  1.090
 VHZ  C18  H6   single    0.970  0.020  1.090
 VHZ  C18  H7   single    0.970  0.020  1.090
 VHZ  C2   H8   single    0.930  0.020  1.080
 VHZ  C1   H9   single    0.930  0.020  1.080
 VHZ  N2   H10  single    0.860  0.020  1.020
 VHZ  C11  H11  single    0.930  0.020  1.080
 VHZ  N4   H12  single    0.890  0.020  1.040
 VHZ  C15  H13  single    0.970  0.020  1.090
 VHZ  N5   H14  single    0.860  0.020  1.020
 VHZ  N3   H15  single    0.860  0.020  1.020
 VHZ  C8   H16  single    0.930  0.020  1.080
 VHZ  C7   H17  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
 VHZ  C9   C10  C12  117.87  3.000
 VHZ  C9   C10  C11  118.45  3.000
 VHZ  C12  C10  C11  123.67  3.000
 VHZ  H1   C13  C12  121.67  3.000
 VHZ  H1   C13  C14  115.30  3.000
 VHZ  C12  C13  C14  123.02  3.000
 VHZ  N3   C14  O    120.22  3.000
 VHZ  O    C14  C13  124.53  3.000
 VHZ  N3   C14  C13  115.24  3.000
 VHZ  H4   C17  H3   108.26  3.000
 VHZ  H4   C17  H2   108.35  3.000
 VHZ  H3   C17  H2   108.39  3.000
 VHZ  H4   C17  N5   111.51  3.000
 VHZ  H3   C17  N5   111.70  3.000
 VHZ  H2   C17  N5   108.52  3.000
 VHZ  H7   C18  H6   108.40  3.000
 VHZ  H7   C18  H5   108.58  3.000
 VHZ  H6   C18  H5   107.97  3.000
 VHZ  H7   C18  C15  111.14  3.000
 VHZ  H6   C18  C15  110.31  3.000
 VHZ  H5   C18  C15  110.36  3.000
 VHZ  N    C    C4   125.18  3.000
 VHZ  C4   C    CL   117.94  3.000
 VHZ  N    C    CL   116.88  3.000
 VHZ  C3   C4   C5   120.33  3.000
 VHZ  C3   C4   C    118.36  3.000
 VHZ  C5   C4   C    121.31  3.000
 VHZ  N1   C5   C4   180.00  3.000
 VHZ  N2   C3   C2   122.69  3.000
 VHZ  N2   C3   C4   121.14  3.000
 VHZ  C2   C3   C4   116.17  3.000
 VHZ  H8   C2   C1   119.64  3.000
 VHZ  H8   C2   C3   121.14  3.000
 VHZ  C1   C2   C3   119.21  3.000
 VHZ  H9   C1   N    115.79  3.000
 VHZ  H9   C1   C2   119.50  3.000
 VHZ  N    C1   C2   124.71  3.000
 VHZ  C1   N    C    116.36  3.000
 VHZ  C7   C6   C11  119.91  3.000
 VHZ  C7   C6   N2   120.22  3.000
 VHZ  C11  C6   N2   119.86  3.000
 VHZ  H11  C11  C6   117.45  3.000
 VHZ  H11  C11  C10  121.42  3.000
 VHZ  C6   C11  C10  121.13  3.000
 VHZ  N4   C12  C13  122.40  3.000
 VHZ  C13  C12  C10  118.90  3.000
 VHZ  N4   C12  C10  118.69  3.000
 VHZ  H12  N4   C15  115.67  3.000
 VHZ  H12  N4   C12  118.28  3.000
 VHZ  C15  N4   C12  123.05  3.000
 VHZ  H13  C15  C16  106.48  3.000
 VHZ  H13  C15  N4   110.41  3.000
 VHZ  C16  C15  N4   112.94  3.000
 VHZ  H13  C15  C18  108.43  3.000
 VHZ  N4   C15  C18  109.54  3.000
 VHZ  C16  C15  C18  108.90  3.000
 VHZ  O1   C16  N5   123.66  3.000
 VHZ  O1   C16  C15  120.25  3.000
 VHZ  N5   C16  C15  116.03  3.000
 VHZ  H14  N5   C16  118.66  3.000
 VHZ  H14  N5   C17  118.86  3.000
 VHZ  C16  N5   C17  122.47  3.000
 VHZ  H15  N3   C9   118.30  3.000
 VHZ  H15  N3   C14  116.81  3.000
 VHZ  C9   N3   C14  124.88  3.000
 VHZ  C8   C9   N3   119.86  3.000
 VHZ  N3   C9   C10  120.08  3.000
 VHZ  C8   C9   C10  120.07  3.000
 VHZ  H16  C8   C7   120.09  3.000
 VHZ  H16  C8   C9   119.53  3.000
 VHZ  C7   C8   C9   120.38  3.000
 VHZ  H17  C7   C8   119.98  3.000
 VHZ  H17  C7   C6   119.98  3.000
 VHZ  C8   C7   C6   120.04  3.000
 VHZ  H10  N2   C6   116.91  3.000
 VHZ  H10  N2   C3   118.94  3.000
 VHZ  C6   N2   C3   124.11  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
 VHZ  CONST_01  C7   C6   C11  C10     0.00   0.0  0
 VHZ  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 VHZ  CONST_03  C2   C1   N    C       0.00   0.0  0
 VHZ  CONST_04  C2   C3   C4   C       0.00   0.0  0
 VHZ  CONST_05  C1   N    C    C4      0.00   0.0  0
 VHZ  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 VHZ  CONST_07  N    C    C4   C3      0.00   0.0  0
 VHZ  CONST_08  N    C1   C2   C3      0.00   0.0  0
 VHZ  CONST_09  C9   C10  C11  C6      0.00   0.0  0
 VHZ  CONST_10  C9   C8   C7   C6      0.00   0.0  0
 VHZ  CONST_11  C8   C7   C6   C11     0.00   0.0  0
 VHZ  CONST_12  C8   C9   C10  C11     0.00   0.0  0
 VHZ  CONST_13  C9   N3   C14  C13     0.00   0.0  0
 VHZ  CONST_14  N2   C6   C11  C10   180.00   0.0  0
 VHZ  CONST_15  C1   N    C    CL    180.00   0.0  0
 VHZ  CONST_16  C3   C4   C    CL    180.00   0.0  0
 VHZ  CONST_17  N2   C3   C4   C     180.00   0.0  0
 VHZ  CONST_18  N    C    C4   C5    180.00   0.0  0
 VHZ  CONST_19  C2   C3   C4   C5    180.00   0.0  0
 VHZ  CONST_20  N2   C3   C2   C1    180.00   0.0  0
 VHZ  CONST_21  C8   C7   C6   N2    180.00   0.0  0
 VHZ  CONST_22  C9   N3   C14  O     180.00   0.0  0
 VHZ  CONST_23  H16  C8   C9   C10   180.00   0.0  0
 VHZ  CONST_24  H9   C1   N    C     180.00   0.0  0
 VHZ  CONST_25  H8   C2   C3   C4    180.00   0.0  0
 VHZ  CONST_26  H9   C1   C2   C3    180.00   0.0  0
 VHZ  CONST_27  H8   C2   C1   N     180.00   0.0  0
 VHZ  CONST_28  H16  C8   C7   C6    180.00   0.0  0
 VHZ  CONST_29  H17  C7   C6   C11   180.00   0.0  0
 VHZ  CONST_30  H11  C11  C10  C12     0.00   0.0  0
 VHZ  CONST_31  H16  C8   C9   N3      0.00   0.0  0
 VHZ  CONST_32  H11  C11  C10  C9    180.00   0.0  0
 VHZ  CONST_33  H17  C7   C8   C9    180.00   0.0  0
 VHZ  CONST_34  H11  C11  C6   C7    180.00   0.0  0
 VHZ  CONST_35  H15  N3   C14  C13   180.00   0.0  0
 VHZ  CONST_36  H15  N3   C14  O       0.00   0.0  0
 VHZ  CONST_37  O1   C16  N5   C17     0.00   0.0  0
 VHZ  CONST_38  C15  C16  N5   C17   180.00   0.0  0
 VHZ  CONST_39  H14  N5   C16  C15     0.00   0.0  0
 VHZ  CONST_40  H14  N5   C16  O1    180.00   0.0  0
 VHZ  Var_01    C14  C13  C12  C10    -0.70  30.0  1
 VHZ  Var_02    C14  N3   C9   C10    -0.27  30.0  1
 VHZ  Var_03    C11  C10  C12  C13  -177.87  30.0  1
 VHZ  Var_04    C9   C10  C12  C13     0.93  30.0  1
 VHZ  Var_05    C8   C9   N3   C14   179.62  30.0  1
 VHZ  Var_06    N3   C14  C13  C12    -0.01  30.0  1
 VHZ  Var_07    N4   C12  C13  C14  -179.34  30.0  1
 VHZ  Var_08    C6   N2   C3   C4    175.26  30.0  2
 VHZ  Var_09    C11  C6   N2   C3    112.03  30.0  2
 VHZ  Var_10    C7   C6   N2   C3    -68.95  30.0  2
 VHZ  Var_11    C6   N2   C3   C2     -5.24  30.0  2
 VHZ  Var_12    N4   C12  C10  C11     0.82  30.0  1
 VHZ  Var_13    O    C14  C13  C12  -179.63  30.0  1
 VHZ  Var_14    C9   C10  C12  N4    179.62  30.0  1
 VHZ  Var_15    H1   C13  C12  C10  -179.70  30.0  1
 VHZ  Var_16    H15  N3   C9   C10   179.91  30.0  1
 VHZ  Var_17    H1   C13  C14  N3    179.05  30.0  1
 VHZ  Var_18    H15  N3   C9   C8     -0.21  30.0  1
 VHZ  Var_19    C15  N4   C12  C10   175.83  30.0  2
 VHZ  Var_20    C15  N4   C12  C13    -5.52  30.0  2
 VHZ  Var_21    H12  N4   C12  C10    16.29  30.0  2
 VHZ  Var_22    H12  N4   C12  C13  -165.07  30.0  2
 VHZ  Var_23    H10  N2   C3   C4     -6.95  30.0  2
 VHZ  Var_24    H10  N2   C3   C2    172.55  30.0  2
 VHZ  Var_25    H10  N2   C6   C11   -65.80  30.0  2
 VHZ  Var_26    H1   C13  C12  N4      1.66  30.0  1
 VHZ  Var_27    H1   C13  C14  O      -0.57  30.0  1
 VHZ  Var_28    H10  N2   C6   C7    113.22  30.0  2
 VHZ  Var_29    H2   C17  N5   C16   178.32  30.0  3
 VHZ  Var_30    H3   C17  N5   C16   -62.25  30.0  3
 VHZ  Var_31    H4   C17  N5   C16    59.04  30.0  3

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
 VHZ  chir_01  C15  C18  C16  N4  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
 VHZ  plan-1  C    0.020
 VHZ  plan-1  C4   0.020
 VHZ  plan-1  C5   0.020
 VHZ  plan-1  N1   0.020
 VHZ  plan-1  C3   0.020
 VHZ  plan-1  C2   0.020
 VHZ  plan-1  C1   0.020
 VHZ  plan-1  N    0.020
 VHZ  plan-1  H8   0.020
 VHZ  plan-1  H9   0.020
 VHZ  plan-1  N2   0.020
 VHZ  plan-1  CL   0.020
 VHZ  plan-2  C10  0.020
 VHZ  plan-2  C6   0.020
 VHZ  plan-2  C11  0.020
 VHZ  plan-2  C12  0.020
 VHZ  plan-2  N3   0.020
 VHZ  plan-2  C9   0.020
 VHZ  plan-2  C8   0.020
 VHZ  plan-2  C7   0.020
 VHZ  plan-2  H11  0.020
 VHZ  plan-2  H16  0.020
 VHZ  plan-2  H17  0.020
 VHZ  plan-2  N2   0.020
 VHZ  plan-3  C17  0.020
 VHZ  plan-3  C15  0.020
 VHZ  plan-3  C16  0.020
 VHZ  plan-3  N5   0.020
 VHZ  plan-3  O1   0.020
 VHZ  plan-3  H14  0.020
 VHZ  plan-4  C13  0.020
 VHZ  plan-4  C14  0.020
 VHZ  plan-4  O    0.020
 VHZ  plan-4  N3   0.020
 VHZ  plan-4  C9   0.020
 VHZ  plan-4  H15  0.020

