# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 08:50:58 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: 2-chloranyl-4-[[1-methyl-2-oxidanylidene-4-[[(1~{R})-1-pyrimidin-2-ylethyl]amino]quinolin-6-yl]amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC1=CC(=O)N(C)c2ccc(Nc3ccnc(Cl)c3C#N)cc12)c4ncccn4
#
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
 VJ5  VJ5  "2-chloranyl-4-[[1-methyl-2-oxidanylidene-4-[[(1R)-1-pyrimidin-2-ylethyl]amino]quinolin-6-yl]amino]pyridine-3-carbonitrile"
  ligand  49  31  .  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_VJ5
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
 VJ5  C1   C   CH1   0  -0.178  23.2202  -15.0117  18.5401
 VJ5  C2   C   CR6   0   0.528  23.4297  -12.5640  18.5846
 VJ5  C3   C   CR16  0  -0.570  22.5301  -12.4193  19.6017
 VJ5  C4   C   CR6   0   0.542  22.1169  -11.1482  20.1189
 VJ5  C6   C   CR66  0   0.370  23.6070  -10.1104  18.5180
 VJ5  C10  C   CR6   0   0.517  26.5206   -9.7907  14.2974
 VJ5  C12  C   CR16  0  -0.052  25.4237   -8.5984  12.5318
 VJ5  C14  C   CR6   0  -0.089  27.6392   -9.8523  13.4325
 VJ5  C18  C   CR6   0   0.373  21.7644  -15.1418  18.1357
 VJ5  N4   N   NS    0  -0.228  29.7877  -11.0146  14.2288
 VJ5  C15  C   CSP   0   0.030  28.8336  -10.4882  13.8509
 VJ5  C13  C   CR6   0   0.145  27.5354   -9.2660  12.1691
 VJ5  CL   CL  CL    0  -0.065  28.9062   -9.3502  11.1204
 VJ5  N3   N   N     0  -0.408  26.4828   -8.6537  11.7120
 VJ5  C11  C   CR16  0  -0.386  25.3835   -9.1325  13.7940
 VJ5  C9   C   CR6   0   0.302  25.5485  -10.2545  16.4965
 VJ5  C8   C   CR16  0  -0.270  25.1357   -9.0181  16.9898
 VJ5  C7   C   CR16  0  -0.333  24.1752   -8.9486  17.9725
 VJ5  C16  C   CR16  0  -0.375  24.9913  -11.4052  17.0132
 VJ5  C17  C   CR66  0  -0.015  24.0231  -11.3614  18.0205
 VJ5  N1   N   NR6   0  -0.615  22.6740  -10.0220  19.5256
 VJ5  O    O   O     0  -0.506  21.3012  -11.0390  21.0300
 VJ5  N    N   NH1   0  -0.684  23.8137  -13.7711  18.1107
 VJ5  C    C   CH3   0  -0.676  24.0159  -16.1771  17.9601
 VJ5  N6   N   N     0  -0.395  21.4118  -14.6655  16.9502
 VJ5  C21  C   CR16  0  -0.028  20.1434  -14.8238  16.5946
 VJ5  C20  C   CR16  0  -0.343  19.2225  -15.4586  17.4108
 VJ5  C19  C   CR16  0  -0.028  19.6997  -15.9252  18.6231
 VJ5  N5   N   N     0  -0.405  20.9658  -15.7683  18.9896
 VJ5  H1   H   HCH1  0   0.275  23.2687  -15.0730  19.6307
 VJ5  H2   H   HCR6  0   0.273  22.0601  -13.2737  20.0674
 VJ5  H3   H   HCH3  0   0.283  21.5158   -8.8403  20.7732
 VJ5  H4   H   HCH3  0   0.253  23.1093   -8.1674  20.4235
 VJ5  H5   H   HCH3  0   0.254  21.8338   -8.1230  19.1923
 VJ5  H6   H   HCR6  0   0.288  24.5490   -8.0952  12.1385
 VJ5  H7   H   HCR6  0   0.303  24.4778   -9.0550  14.3773
 VJ5  H8   H   HNH1  0   0.422  27.3593  -10.9242  15.7580
 VJ5  H9   H   HCR6  0   0.288  25.5767   -8.1039  16.6133
 VJ5  H10  H   HCR6  0   0.295  23.8863   -7.9724  18.3310
 VJ5  H11  H   HCR6  0   0.265  25.3435  -12.3490  16.6177
 VJ5  H12  H   HNH1  0   0.404  24.2590  -13.8016  17.2092
 VJ5  H13  H   HCH3  0   0.255  25.0546  -16.1273  18.2854
 VJ5  H14  H   HCH3  0   0.255  23.5986  -17.1251  18.2954
 VJ5  H15  H   HCH3  0   0.239  23.9902  -16.1619  16.8693
 VJ5  H16  H   HCR6  0   0.279  19.8535  -14.4319  15.6260
 VJ5  H17  H   HCR6  0   0.284  18.1906  -15.5827  17.1176
 VJ5  H18  H   HCR6  0   0.279  19.0470  -16.4362  19.3221
 VJ5  C5   C   CH3   0  -0.567  22.2646   -8.7118  20.0017
 VJ5  N2   N   NH1   0  -0.784  26.5645  -10.3478  15.5205

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
 VJ5  CL   C13  single    1.728  0.020  1.728
 VJ5  N3   C13  aromatic  1.301  0.020  1.301
 VJ5  N3   C12  aromatic  1.340  0.020  1.340
 VJ5  C13  C14  aromatic  1.397  0.020  1.397
 VJ5  C12  C11  aromatic  1.371  0.020  1.371
 VJ5  C14  C15  single    1.416  0.020  1.416
 VJ5  C14  C10  aromatic  1.415  0.020  1.415
 VJ5  C15  N4   triple    1.153  0.020  1.153
 VJ5  C11  C10  aromatic  1.407  0.020  1.407
 VJ5  C10  N2   single    1.345  0.020  1.345
 VJ5  N2   C9   single    1.412  0.020  1.412
 VJ5  C21  N6   aromatic  1.327  0.020  1.327
 VJ5  C21  C20  aromatic  1.385  0.020  1.385
 VJ5  C9   C8   aromatic  1.394  0.020  1.394
 VJ5  C9   C16  aromatic  1.379  0.020  1.379
 VJ5  N6   C18  aromatic  1.325  0.020  1.325
 VJ5  C8   C7   aromatic  1.376  0.020  1.376
 VJ5  C20  C19  aromatic  1.384  0.020  1.384
 VJ5  C16  C17  aromatic  1.398  0.020  1.398
 VJ5  C    C1   single    1.526  0.020  1.526
 VJ5  C18  C1   single    1.517  0.020  1.517
 VJ5  C18  N5   aromatic  1.326  0.020  1.326
 VJ5  C7   C6   aromatic  1.404  0.020  1.404
 VJ5  N    C1   single    1.441  0.020  1.441
 VJ5  N    C2   single    1.352  0.020  1.352
 VJ5  C17  C6   aromatic  1.409  0.020  1.409
 VJ5  C17  C2   single    1.455  0.020  1.455
 VJ5  C19  N5   aromatic  1.327  0.020  1.327
 VJ5  C6   N1   single    1.376  0.020  1.376
 VJ5  C2   C3   double    1.365  0.020  1.365
 VJ5  N1   C5   single    1.453  0.020  1.453
 VJ5  N1   C4   single    1.389  0.020  1.389
 VJ5  C3   C4   single    1.433  0.020  1.433
 VJ5  C4   O    double    1.228  0.020  1.228
 VJ5  C1   H1   single    0.970  0.020  1.090
 VJ5  C3   H2   single    0.930  0.020  1.080
 VJ5  C5   H3   single    0.970  0.020  1.090
 VJ5  C5   H4   single    0.970  0.020  1.090
 VJ5  C5   H5   single    0.970  0.020  1.090
 VJ5  C12  H6   single    0.930  0.020  1.080
 VJ5  C11  H7   single    0.930  0.020  1.080
 VJ5  N2   H8   single    0.860  0.020  1.020
 VJ5  C8   H9   single    0.930  0.020  1.080
 VJ5  C7   H10  single    0.930  0.020  1.080
 VJ5  C16  H11  single    0.930  0.020  1.080
 VJ5  N    H12  single    0.890  0.020  1.040
 VJ5  C    H13  single    0.970  0.020  1.090
 VJ5  C    H14  single    0.970  0.020  1.090
 VJ5  C    H15  single    0.970  0.020  1.090
 VJ5  C21  H16  single    0.930  0.020  1.080
 VJ5  C20  H17  single    0.930  0.020  1.080
 VJ5  C19  H18  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
 VJ5  H1   C1   C    108.25  3.000
 VJ5  H1   C1   N    109.10  3.000
 VJ5  C    C1   N    109.25  3.000
 VJ5  H1   C1   C18  107.68  3.000
 VJ5  N    C1   C18  112.95  3.000
 VJ5  C    C1   C18  109.49  3.000
 VJ5  N    C2   C17  119.08  3.000
 VJ5  C17  C2   C3   118.03  3.000
 VJ5  N    C2   C3   122.86  3.000
 VJ5  H2   C3   C4   114.85  3.000
 VJ5  H2   C3   C2   121.59  3.000
 VJ5  C4   C3   C2   123.55  3.000
 VJ5  O    C4   N1   120.74  3.000
 VJ5  O    C4   C3   122.56  3.000
 VJ5  N1   C4   C3   116.69  3.000
 VJ5  N1   C6   C17  121.04  3.000
 VJ5  N1   C6   C7   120.39  3.000
 VJ5  C17  C6   C7   118.56  3.000
 VJ5  N2   C10  C11  123.07  3.000
 VJ5  N2   C10  C14  120.79  3.000
 VJ5  C11  C10  C14  116.13  3.000
 VJ5  H6   C12  C11  119.45  3.000
 VJ5  H6   C12  N3   115.79  3.000
 VJ5  C11  C12  N3   124.76  3.000
 VJ5  C13  C14  C15  121.23  3.000
 VJ5  C15  C14  C10  120.36  3.000
 VJ5  C13  C14  C10  118.41  3.000
 VJ5  N5   C18  N6   125.83  3.000
 VJ5  N5   C18  C1   116.54  3.000
 VJ5  N6   C18  C1   117.59  3.000
 VJ5  N4   C15  C14  180.00  3.000
 VJ5  N3   C13  CL   116.85  3.000
 VJ5  N3   C13  C14  125.15  3.000
 VJ5  CL   C13  C14  118.00  3.000
 VJ5  C13  N3   C12  116.35  3.000
 VJ5  H7   C11  C12  119.59  3.000
 VJ5  H7   C11  C10  121.20  3.000
 VJ5  C12  C11  C10  119.21  3.000
 VJ5  C16  C9   C8   119.20  3.000
 VJ5  C16  C9   N2   119.65  3.000
 VJ5  C8   C9   N2   121.09  3.000
 VJ5  H9   C8   C7   119.35  3.000
 VJ5  H9   C8   C9   120.35  3.000
 VJ5  C7   C8   C9   120.29  3.000
 VJ5  H10  C7   C8   118.02  3.000
 VJ5  H10  C7   C6   120.74  3.000
 VJ5  C8   C7   C6   121.22  3.000
 VJ5  H11  C16  C17  121.07  3.000
 VJ5  H11  C16  C9   117.34  3.000
 VJ5  C17  C16  C9   121.59  3.000
 VJ5  C16  C17  C6   119.13  3.000
 VJ5  C6   C17  C2   118.46  3.000
 VJ5  C16  C17  C2   122.42  3.000
 VJ5  C6   N1   C5   119.27  3.000
 VJ5  C5   N1   C4   118.56  3.000
 VJ5  C6   N1   C4   122.17  3.000
 VJ5  H12  N    C2   117.83  3.000
 VJ5  H12  N    C1   115.04  3.000
 VJ5  C2   N    C1   123.17  3.000
 VJ5  H15  C    H14  108.12  3.000
 VJ5  H15  C    H13  108.68  3.000
 VJ5  H14  C    H13  108.25  3.000
 VJ5  H15  C    C1   110.92  3.000
 VJ5  H14  C    C1   110.38  3.000
 VJ5  H13  C    C1   110.41  3.000
 VJ5  C21  N6   C18  116.82  3.000
 VJ5  H16  C21  C20  120.96  3.000
 VJ5  H16  C21  N6   116.87  3.000
 VJ5  C20  C21  N6   122.18  3.000
 VJ5  H17  C20  C19  121.91  3.000
 VJ5  H17  C20  C21  121.89  3.000
 VJ5  C19  C20  C21  116.21  3.000
 VJ5  H18  C19  N5   116.87  3.000
 VJ5  H18  C19  C20  121.07  3.000
 VJ5  N5   C19  C20  122.07  3.000
 VJ5  C19  N5   C18  116.90  3.000
 VJ5  H5   C5   H4   108.91  3.000
 VJ5  H5   C5   H3   108.67  3.000
 VJ5  H4   C5   H3   108.63  3.000
 VJ5  H5   C5   N1   110.81  3.000
 VJ5  H4   C5   N1   111.03  3.000
 VJ5  H3   C5   N1   108.74  3.000
 VJ5  H8   N2   C9   116.19  3.000
 VJ5  H8   N2   C10  118.43  3.000
 VJ5  C9   N2   C10  125.30  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
 VJ5  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 VJ5  CONST_02  C9   C16  C17  C6      0.00   0.0  0
 VJ5  CONST_03  N3   C13  C14  C10     0.00   0.0  0
 VJ5  CONST_04  N3   C12  C11  C10     0.00   0.0  0
 VJ5  CONST_05  C14  C13  N3   C12     0.00   0.0  0
 VJ5  CONST_06  C14  C10  C11  C12     0.00   0.0  0
 VJ5  CONST_07  C20  C21  N6   C18     0.00   0.0  0
 VJ5  CONST_08  C20  C19  N5   C18     0.00   0.0  0
 VJ5  CONST_09  C11  C12  N3   C13     0.00   0.0  0
 VJ5  CONST_10  C11  C10  C14  C13     0.00   0.0  0
 VJ5  CONST_11  C17  C16  C9   C8      0.00   0.0  0
 VJ5  CONST_12  C17  C6   C7   C8      0.00   0.0  0
 VJ5  CONST_13  C16  C9   C8   C7      0.00   0.0  0
 VJ5  CONST_14  C16  C17  C6   C7      0.00   0.0  0
 VJ5  CONST_15  C19  C20  C21  N6      0.00   0.0  0
 VJ5  CONST_16  C19  N5   C18  N6      0.00   0.0  0
 VJ5  CONST_17  N5   C18  N6   C21     0.00   0.0  0
 VJ5  CONST_18  N5   C19  C20  C21     0.00   0.0  0
 VJ5  CONST_19  C6   N1   C4   C3      0.00   0.0  0
 VJ5  CONST_20  C21  N6   C18  C1    180.00   0.0  0
 VJ5  CONST_21  C19  N5   C18  C1    180.00   0.0  0
 VJ5  CONST_22  CL   C13  C14  C10   180.00   0.0  0
 VJ5  CONST_23  CL   C13  N3   C12   180.00   0.0  0
 VJ5  CONST_24  N2   C10  C11  C12   180.00   0.0  0
 VJ5  CONST_25  N3   C13  C14  C15   180.00   0.0  0
 VJ5  CONST_26  C11  C10  C14  C15   180.00   0.0  0
 VJ5  CONST_27  N2   C10  C14  C13   180.00   0.0  0
 VJ5  CONST_28  C7   C8   C9   N2    180.00   0.0  0
 VJ5  CONST_29  C17  C16  C9   N2    180.00   0.0  0
 VJ5  CONST_30  C5   N1   C4   C3    180.00   0.0  0
 VJ5  CONST_31  O    C4   N1   C6    180.00   0.0  0
 VJ5  CONST_32  H11  C16  C17  C2      0.00   0.0  0
 VJ5  CONST_33  H9   C8   C7   C6    180.00   0.0  0
 VJ5  CONST_34  H11  C16  C17  C6    180.00   0.0  0
 VJ5  CONST_35  H6   C12  C11  C10   180.00   0.0  0
 VJ5  CONST_36  H7   C11  C10  C14   180.00   0.0  0
 VJ5  CONST_37  H16  C21  N6   C18   180.00   0.0  0
 VJ5  CONST_38  H18  C19  N5   C18   180.00   0.0  0
 VJ5  CONST_39  H6   C12  N3   C13   180.00   0.0  0
 VJ5  CONST_40  H7   C11  C12  N3    180.00   0.0  0
 VJ5  CONST_41  H10  C7   C8   C9    180.00   0.0  0
 VJ5  CONST_42  H11  C16  C9   C8    180.00   0.0  0
 VJ5  CONST_43  H9   C8   C9   C16   180.00   0.0  0
 VJ5  CONST_44  H10  C7   C6   C17   180.00   0.0  0
 VJ5  CONST_45  H10  C7   C6   N1      0.00   0.0  0
 VJ5  CONST_46  H17  C20  C21  N6    180.00   0.0  0
 VJ5  CONST_47  H18  C19  C20  C21   180.00   0.0  0
 VJ5  CONST_48  H16  C21  C20  C19   180.00   0.0  0
 VJ5  CONST_49  H17  C20  C19  N5    180.00   0.0  0
 VJ5  CONST_50  O    C4   N1   C5      0.00   0.0  0
 VJ5  Var_01    N1   C4   C3   C2      0.43  30.0  1
 VJ5  Var_02    C16  C17  C2   C3    177.47  30.0  1
 VJ5  Var_03    C6   C17  C2   C3     -2.16  30.0  1
 VJ5  Var_04    C7   C6   N1   C4   -178.09  30.0  1
 VJ5  Var_05    C17  C6   N1   C4      1.28  30.0  1
 VJ5  Var_06    C17  C2   C3   C4      1.56  30.0  1
 VJ5  Var_07    O    C4   C3   C2    179.63  30.0  1
 VJ5  Var_08    N    C2   C3   C4    179.74  30.0  1
 VJ5  Var_09    C7   C6   N1   C5      1.15  30.0  1
 VJ5  Var_10    C17  C6   N1   C5   -179.49  30.0  1
 VJ5  Var_11    N    C2   C17  C6    179.59  30.0  1
 VJ5  Var_12    C8   C9   N2   C10   -59.60  30.0  2
 VJ5  Var_13    C16  C9   N2   C10   123.11  30.0  2
 VJ5  Var_14    C9   N2   C10  C14   174.80  30.0  2
 VJ5  Var_15    C9   N2   C10  C11    -5.80  30.0  2
 VJ5  Var_16    N    C2   C17  C16    -0.77  30.0  1
 VJ5  Var_17    H2   C3   C2   C17  -179.55  30.0  1
 VJ5  Var_18    H2   C3   C4   N1   -178.53  30.0  1
 VJ5  Var_19    C17  C2   N    C1   -175.67  30.0  2
 VJ5  Var_20    C3   C2   N    C1      6.17  30.0  2
 VJ5  Var_21    H12  N    C2   C3    162.65  30.0  1
 VJ5  Var_22    H3   C5   N1   C4     -1.94  30.0  3
 VJ5  Var_23    H4   C5   N1   C4    117.52  30.0  3
 VJ5  Var_24    H5   C5   N1   C4   -121.32  30.0  3
 VJ5  Var_25    H3   C5   N1   C6    178.79  30.0  3
 VJ5  Var_26    H4   C5   N1   C6    -61.75  30.0  3
 VJ5  Var_27    H5   C5   N1   C6     59.42  30.0  3
 VJ5  Var_28    H8   N2   C10  C14    -8.73  30.0  2
 VJ5  Var_29    H8   N2   C10  C11   170.67  30.0  2
 VJ5  Var_30    H8   N2   C9   C8    123.86  30.0  2
 VJ5  Var_31    H8   N2   C9   C16   -53.43  30.0  2
 VJ5  Var_32    H12  N    C2   C17   -19.20  30.0  1
 VJ5  Var_33    H2   C3   C4   O       0.67  30.0  1
 VJ5  Var_34    H2   C3   C2   N      -1.37  30.0  1

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
 VJ5  chir_01  C1  C  C18  N  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
 VJ5  plan-1  C10  0.020
 VJ5  plan-1  C12  0.020
 VJ5  plan-1  C14  0.020
 VJ5  plan-1  N4   0.020
 VJ5  plan-1  C15  0.020
 VJ5  plan-1  C13  0.020
 VJ5  plan-1  CL   0.020
 VJ5  plan-1  N3   0.020
 VJ5  plan-1  C11  0.020
 VJ5  plan-1  H6   0.020
 VJ5  plan-1  H7   0.020
 VJ5  plan-1  N2   0.020
 VJ5  plan-2  C1   0.020
 VJ5  plan-2  C18  0.020
 VJ5  plan-2  N6   0.020
 VJ5  plan-2  C21  0.020
 VJ5  plan-2  C20  0.020
 VJ5  plan-2  C19  0.020
 VJ5  plan-2  N5   0.020
 VJ5  plan-2  H16  0.020
 VJ5  plan-2  H17  0.020
 VJ5  plan-2  H18  0.020
 VJ5  plan-3  C2   0.020
 VJ5  plan-3  C6   0.020
 VJ5  plan-3  C9   0.020
 VJ5  plan-3  C8   0.020
 VJ5  plan-3  C7   0.020
 VJ5  plan-3  C16  0.020
 VJ5  plan-3  C17  0.020
 VJ5  plan-3  N1   0.020
 VJ5  plan-3  H9   0.020
 VJ5  plan-3  H10  0.020
 VJ5  plan-3  H11  0.020
 VJ5  plan-3  N2   0.020
 VJ5  plan-4  C3   0.020
 VJ5  plan-4  C4   0.020
 VJ5  plan-4  C6   0.020
 VJ5  plan-4  N1   0.020
 VJ5  plan-4  O    0.020
 VJ5  plan-4  C5   0.020

