# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 20:43:30 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: (2~{S})-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
 VHN  VHN  "(2S)-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_VHN
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
 VHN  CL   CL  CL    0  -0.065  95.6111   -9.1466  10.9764
 VHN  C    C   CR6   0   0.146  94.2792   -9.2018  12.0754
 VHN  C4   C   CR6   0  -0.092  94.4993   -9.7406  13.3449
 VHN  C5   C   CSP   0   0.030  95.7777  -10.2150  13.7282
 VHN  N1   N   NS    0  -0.228  96.8028  -10.6088  14.0809
 VHN  C3   C   CR6   0   0.515  93.4150   -9.7920  14.2539
 VHN  C2   C   CR16  0  -0.385  92.1898   -9.2856  13.7829
 VHN  C1   C   CR16  0  -0.052  92.1181   -8.7830  12.5092
 VHN  N    N   N     0  -0.408  93.1443   -8.7312  11.6485
 VHN  N2   N   NH1   0  -0.785  93.5765  -10.3144  15.4831
 VHN  C6   C   CR6   0   0.309  92.6128  -10.3153  16.5129
 VHN  C11  C   CR16  0  -0.367  92.0457   -9.1378  16.9559
 VHN  C10  C   CR66  0  -0.021  91.1038   -9.1344  17.9897
 VHN  C12  C   CR6   0   0.522  90.4488   -7.9258  18.4745
 VHN  N4   N   NH1   0  -0.674  90.7115   -6.7578  17.8457
 VHN  C15  C   CH1   0  -0.233  90.0867   -5.5131  18.2031
 VHN  C18  C   CH3   0  -0.670  90.7675   -4.3694  17.4579
 VHN  C16  C   C     0   0.538  88.5890   -5.5118  17.8641
 VHN  N5   N   NH1   0  -0.622  87.8300   -4.7746  18.6832
 VHN  C17  C   CH3   0  -0.512  86.4151   -4.5806  18.4690
 VHN  O1   O   O     0  -0.479  88.1515   -6.1039  16.8905
 VHN  C13  C   CR16  0  -0.582  89.6270   -8.0145  19.5668
 VHN  C14  C   CR6   0   0.511  89.3509   -9.2521  20.2404
 VHN  O    O   O     0  -0.501  88.6289   -9.3638  21.2266
 VHN  N3   N   NR16  0  -0.764  89.9450  -10.3651  19.6902
 VHN  C9   C   CR66  0   0.373  90.8015  -10.3470  18.6274
 VHN  C8   C   CR16  0  -0.314  91.3899  -11.5360  18.1815
 VHN  C7   C   CR16  0  -0.295  92.2717  -11.5225  17.1277
 VHN  H1   H   HCR6  0   0.304  91.3028   -9.2995  14.3982
 VHN  H2   H   HCR6  0   0.288  91.1747   -8.3989  12.1412
 VHN  H3   H   HNH1  0   0.421  94.4423  -10.7931  15.6873
 VHN  H4   H   HCR6  0   0.281  92.3692   -8.2122  16.4979
 VHN  H5   H   HNH1  0   0.403  91.0709   -6.8017  16.9064
 VHN  H6   H   HCH1  0   0.276  90.2211   -5.3518  19.2772
 VHN  H7   H   HCH3  0   0.253  90.3234   -3.4150  17.7354
 VHN  H8   H   HCH3  0   0.256  91.8279   -4.3349  17.7044
 VHN  H9   H   HCH3  0   0.242  90.6663   -4.4895  16.3783
 VHN  H10  H   HNH1  0   0.407  88.2573   -4.3290  19.4785
 VHN  H11  H   HCH3  0   0.251  86.0311   -3.9438  19.2604
 VHN  H12  H   HCH3  0   0.239  86.2159   -4.0973  17.5122
 VHN  H13  H   HCH3  0   0.239  85.8724   -5.5260  18.4959
 VHN  H14  H   HCR6  0   0.269  89.1245   -7.1463  19.9689
 VHN  H15  H   HNR6  0   0.410  89.7555  -11.2519  20.1375
 VHN  H16  H   HCR6  0   0.284  91.1432  -12.4703  18.6697
 VHN  H17  H   HCR6  0   0.281  92.7134  -12.4479  16.7804

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
 VHN  CL   C    single    1.728  0.020  1.728
 VHN  N    C    aromatic  1.301  0.020  1.301
 VHN  N    C1   aromatic  1.340  0.020  1.340
 VHN  C    C4   aromatic  1.397  0.020  1.397
 VHN  C1   C2   aromatic  1.371  0.020  1.371
 VHN  C4   C5   single    1.416  0.020  1.416
 VHN  C4   C3   aromatic  1.416  0.020  1.416
 VHN  C5   N1   triple    1.153  0.020  1.153
 VHN  C2   C3   aromatic  1.407  0.020  1.407
 VHN  C3   N2   single    1.345  0.020  1.345
 VHN  N2   C6   single    1.410  0.020  1.410
 VHN  C6   C11  aromatic  1.380  0.020  1.380
 VHN  C6   C7   aromatic  1.397  0.020  1.397
 VHN  O1   C16  double    1.221  0.020  1.221
 VHN  C11  C10  aromatic  1.399  0.020  1.399
 VHN  C7   C8   aromatic  1.374  0.020  1.374
 VHN  C18  C15  single    1.525  0.020  1.525
 VHN  N4   C15  single    1.438  0.020  1.438
 VHN  N4   C12  single    1.352  0.020  1.352
 VHN  C16  C15  single    1.536  0.020  1.536
 VHN  C16  N5   single    1.338  0.020  1.338
 VHN  C10  C12  single    1.458  0.020  1.458
 VHN  C10  C9   aromatic  1.403  0.020  1.403
 VHN  C8   C9   aromatic  1.400  0.020  1.400
 VHN  C12  C13  double    1.370  0.020  1.370
 VHN  C17  N5   single    1.444  0.020  1.444
 VHN  C9   N3   single    1.365  0.020  1.365
 VHN  C13  C14  single    1.436  0.020  1.436
 VHN  N3   C14  single    1.376  0.020  1.376
 VHN  C14  O    double    1.227  0.020  1.227
 VHN  C2   H1   single    0.930  0.020  1.080
 VHN  C1   H2   single    0.930  0.020  1.080
 VHN  N2   H3   single    0.860  0.020  1.020
 VHN  C11  H4   single    0.930  0.020  1.080
 VHN  N4   H5   single    0.890  0.020  1.040
 VHN  C15  H6   single    0.970  0.020  1.090
 VHN  C18  H7   single    0.970  0.020  1.090
 VHN  C18  H8   single    0.970  0.020  1.090
 VHN  C18  H9   single    0.970  0.020  1.090
 VHN  N5   H10  single    0.860  0.020  1.020
 VHN  C17  H11  single    0.970  0.020  1.090
 VHN  C17  H12  single    0.970  0.020  1.090
 VHN  C17  H13  single    0.970  0.020  1.090
 VHN  C13  H14  single    0.930  0.020  1.080
 VHN  N3   H15  single    0.860  0.020  1.020
 VHN  C8   H16  single    0.930  0.020  1.080
 VHN  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
 VHN  N    C    C4   125.14  3.000
 VHN  C4   C    CL   117.97  3.000
 VHN  N    C    CL   116.89  3.000
 VHN  C3   C4   C5   120.35  3.000
 VHN  C3   C4   C    118.48  3.000
 VHN  C5   C4   C    121.17  3.000
 VHN  N1   C5   C4   180.00  3.000
 VHN  N2   C3   C2   123.38  3.000
 VHN  N2   C3   C4   120.59  3.000
 VHN  C2   C3   C4   116.04  3.000
 VHN  H1   C2   C1   119.41  3.000
 VHN  H1   C2   C3   121.34  3.000
 VHN  C1   C2   C3   119.24  3.000
 VHN  H2   C1   N    115.78  3.000
 VHN  H2   C1   C2   119.42  3.000
 VHN  N    C1   C2   124.79  3.000
 VHN  C1   N    C    116.31  3.000
 VHN  H3   N2   C6   115.96  3.000
 VHN  H3   N2   C3   118.13  3.000
 VHN  C6   N2   C3   125.83  3.000
 VHN  C7   C6   C11  119.72  3.000
 VHN  C7   C6   N2   119.26  3.000
 VHN  C11  C6   N2   120.97  3.000
 VHN  H4   C11  C10  120.80  3.000
 VHN  H4   C11  C6   118.10  3.000
 VHN  C10  C11  C6   121.08  3.000
 VHN  C9   C10  C12  117.95  3.000
 VHN  C9   C10  C11  118.62  3.000
 VHN  C12  C10  C11  123.40  3.000
 VHN  C13  C12  N4   122.91  3.000
 VHN  C13  C12  C10  118.76  3.000
 VHN  N4   C12  C10  118.31  3.000
 VHN  H5   N4   C15  115.14  3.000
 VHN  H5   N4   C12  117.74  3.000
 VHN  C15  N4   C12  123.21  3.000
 VHN  H6   C15  C16  109.65  3.000
 VHN  H6   C15  C18  108.31  3.000
 VHN  C16  C15  C18  109.08  3.000
 VHN  H6   C15  N4   108.55  3.000
 VHN  C16  C15  N4   111.69  3.000
 VHN  C18  C15  N4   109.49  3.000
 VHN  H9   C18  H8   108.53  3.000
 VHN  H9   C18  H7   108.11  3.000
 VHN  H8   C18  H7   108.16  3.000
 VHN  H9   C18  C15  111.07  3.000
 VHN  H8   C18  C15  110.35  3.000
 VHN  H7   C18  C15  110.53  3.000
 VHN  O1   C16  N5   123.52  3.000
 VHN  N5   C16  C15  114.74  3.000
 VHN  O1   C16  C15  121.69  3.000
 VHN  H10  N5   C17  118.26  3.000
 VHN  H10  N5   C16  119.12  3.000
 VHN  C17  N5   C16  122.61  3.000
 VHN  H13  C17  H12  108.36  3.000
 VHN  H13  C17  H11  108.32  3.000
 VHN  H12  C17  H11  108.36  3.000
 VHN  H13  C17  N5   111.57  3.000
 VHN  H12  C17  N5   111.64  3.000
 VHN  H11  C17  N5   108.49  3.000
 VHN  H14  C13  C14  115.37  3.000
 VHN  H14  C13  C12  121.58  3.000
 VHN  C14  C13  C12  123.04  3.000
 VHN  N3   C14  O    120.10  3.000
 VHN  O    C14  C13  124.65  3.000
 VHN  N3   C14  C13  115.24  3.000
 VHN  H15  N3   C9   118.27  3.000
 VHN  H15  N3   C14  116.84  3.000
 VHN  C9   N3   C14  124.84  3.000
 VHN  C8   C9   N3   120.04  3.000
 VHN  N3   C9   C10  120.03  3.000
 VHN  C8   C9   C10  119.93  3.000
 VHN  H16  C8   C7   120.03  3.000
 VHN  H16  C8   C9   119.58  3.000
 VHN  C7   C8   C9   120.39  3.000
 VHN  H17  C7   C8   119.97  3.000
 VHN  H17  C7   C6   119.86  3.000
 VHN  C8   C7   C6   120.17  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
 VHN  CONST_01  C2   C1   N    C       0.00   0.0  0
 VHN  CONST_02  C2   C3   C4   C       0.00   0.0  0
 VHN  CONST_03  C1   N    C    C4      0.00   0.0  0
 VHN  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 VHN  CONST_05  N    C    C4   C3      0.00   0.0  0
 VHN  CONST_06  N    C1   C2   C3      0.00   0.0  0
 VHN  CONST_07  C9   C10  C11  C6      0.00   0.0  0
 VHN  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 VHN  CONST_09  C8   C7   C6   C11     0.00   0.0  0
 VHN  CONST_10  C8   C9   C10  C11     0.00   0.0  0
 VHN  CONST_11  C7   C6   C11  C10     0.00   0.0  0
 VHN  CONST_12  C7   C8   C9   C10     0.00   0.0  0
 VHN  CONST_13  C9   N3   C14  C13     0.00   0.0  0
 VHN  CONST_14  C1   N    C    CL    180.00   0.0  0
 VHN  CONST_15  C3   C4   C    CL    180.00   0.0  0
 VHN  CONST_16  N2   C3   C4   C     180.00   0.0  0
 VHN  CONST_17  N    C    C4   C5    180.00   0.0  0
 VHN  CONST_18  C2   C3   C4   C5    180.00   0.0  0
 VHN  CONST_19  N2   C3   C2   C1    180.00   0.0  0
 VHN  CONST_20  C10  C11  C6   N2    180.00   0.0  0
 VHN  CONST_21  C8   C7   C6   N2    180.00   0.0  0
 VHN  CONST_22  C9   N3   C14  O     180.00   0.0  0
 VHN  CONST_23  H2   C1   N    C     180.00   0.0  0
 VHN  CONST_24  H1   C2   C3   C4    180.00   0.0  0
 VHN  CONST_25  H2   C1   C2   C3    180.00   0.0  0
 VHN  CONST_26  H1   C2   C1   N     180.00   0.0  0
 VHN  CONST_27  H16  C8   C7   C6    180.00   0.0  0
 VHN  CONST_28  H17  C7   C6   C11   180.00   0.0  0
 VHN  CONST_29  H16  C8   C9   C10   180.00   0.0  0
 VHN  CONST_30  H4   C11  C10  C12     0.00   0.0  0
 VHN  CONST_31  H16  C8   C9   N3      0.00   0.0  0
 VHN  CONST_32  H4   C11  C10  C9    180.00   0.0  0
 VHN  CONST_33  H17  C7   C8   C9    180.00   0.0  0
 VHN  CONST_34  H4   C11  C6   C7    180.00   0.0  0
 VHN  CONST_35  H15  N3   C14  C13   180.00   0.0  0
 VHN  CONST_36  H15  N3   C14  O       0.00   0.0  0
 VHN  CONST_37  C17  N5   C16  C15   180.00   0.0  0
 VHN  CONST_38  O1   C16  N5   C17     0.00   0.0  0
 VHN  CONST_39  H10  N5   C16  C15     0.00   0.0  0
 VHN  CONST_40  H10  N5   C16  O1    180.00   0.0  0
 VHN  Var_01    C13  C12  C10  C11  -174.49  30.0  1
 VHN  Var_02    C14  C13  C12  C10    -1.66  30.0  1
 VHN  Var_03    C14  N3   C9   C10    -1.84  30.0  1
 VHN  Var_04    N3   C14  C13  C12    -1.64  30.0  1
 VHN  Var_05    C9   C10  C12  C13     3.34  30.0  1
 VHN  Var_06    C8   C9   N3   C14   177.49  30.0  1
 VHN  Var_07    C6   N2   C3   C4    174.07  30.0  2
 VHN  Var_08    C11  C6   N2   C3    -56.02  30.0  2
 VHN  Var_09    C7   C6   N2   C3    126.65  30.0  2
 VHN  Var_10    C6   N2   C3   C2     -6.70  30.0  2
 VHN  Var_11    N4   C12  C10  C11     3.65  30.0  1
 VHN  Var_12    O    C14  C13  C12   179.39  30.0  1
 VHN  Var_13    C9   C10  C12  N4   -178.52  30.0  1
 VHN  Var_14    C14  C13  C12  N4   -179.71  30.0  1
 VHN  Var_15    H14  C13  C12  C10   179.54  30.0  1
 VHN  Var_16    H15  N3   C9   C10  -179.20  30.0  1
 VHN  Var_17    H14  C13  C14  N3    177.23  30.0  1
 VHN  Var_18    H15  N3   C9   C8      0.14  30.0  1
 VHN  Var_19    C15  N4   C12  C10   177.60  30.0  2
 VHN  Var_20    C13  C12  N4   C15    -4.34  30.0  2
 VHN  Var_21    H3   N2   C3   C4     -9.24  30.0  2
 VHN  Var_22    H3   N2   C3   C2    170.00  30.0  2
 VHN  Var_23    H3   N2   C6   C11   127.23  30.0  2
 VHN  Var_24    H5   N4   C12  C10    20.95  30.0  2
 VHN  Var_25    H14  C13  C12  N4      1.49  30.0  1
 VHN  Var_26    H5   N4   C12  C13  -161.00  30.0  2
 VHN  Var_27    H14  C13  C14  O      -1.74  30.0  1
 VHN  Var_28    H3   N2   C6   C7    -50.10  30.0  2
 VHN  Var_29    H11  C17  N5   C16  -179.63  30.0  3
 VHN  Var_30    H12  C17  N5   C16   -60.29  30.0  3
 VHN  Var_31    H13  C17  N5   C16    61.13  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
 VHN  chir_01  C15  C18  N4  C16  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
 VHN  plan-1  CL   0.020
 VHN  plan-1  C    0.020
 VHN  plan-1  C4   0.020
 VHN  plan-1  C5   0.020
 VHN  plan-1  N1   0.020
 VHN  plan-1  C3   0.020
 VHN  plan-1  C2   0.020
 VHN  plan-1  C1   0.020
 VHN  plan-1  N    0.020
 VHN  plan-1  N2   0.020
 VHN  plan-1  H1   0.020
 VHN  plan-1  H2   0.020
 VHN  plan-2  N2   0.020
 VHN  plan-2  C6   0.020
 VHN  plan-2  C11  0.020
 VHN  plan-2  C10  0.020
 VHN  plan-2  C12  0.020
 VHN  plan-2  N3   0.020
 VHN  plan-2  C9   0.020
 VHN  plan-2  C8   0.020
 VHN  plan-2  C7   0.020
 VHN  plan-2  H4   0.020
 VHN  plan-2  H16  0.020
 VHN  plan-2  H17  0.020
 VHN  plan-3  C15  0.020
 VHN  plan-3  C16  0.020
 VHN  plan-3  N5   0.020
 VHN  plan-3  C17  0.020
 VHN  plan-3  O1   0.020
 VHN  plan-3  H10  0.020
 VHN  plan-4  C13  0.020
 VHN  plan-4  C14  0.020
 VHN  plan-4  O    0.020
 VHN  plan-4  N3   0.020
 VHN  plan-4  C9   0.020
 VHN  plan-4  H15  0.020

