# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 21:58:42 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: (3~{R})-3-[4-[[4-(4-ethanoylpiperazin-1-yl)cyclohexyl]amino]pyrrolo[2,1-f][1,2,4]triazin-5-yl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CC(N)=O)c1ccn2ncnc(N[C@@H]3CC[C@H](CC3)N4CCN(CC4)C(C)=O)c12
#
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
 CKN  CKN  (3~{R})-3-[4-[[4-(4-ethanoylpiperazin-1-yl)cyclohexyl]amino]pyrrolo[2,1-f][1,2,4]triazin-5-yl]butanamide  ligand  64  31  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CKN
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
 CKN  C1   C  CH1   0  -0.398  -4.4141   1.4277   0.4855
 CKN  C2   C  CR5   0   0.048  -4.9456   0.0526   0.2083
 CKN  C3   C  CR56  0   0.326  -4.2051  -1.1251   0.1179
 CKN  N6   N  NH2   0  -0.793  -2.8743   4.2804  -0.9299
 CKN  C7   C  CH2   0  -0.454   0.2661  -0.0373   1.5237
 CKN  C8   C  CH2   0  -0.471   1.7665  -0.3081   1.5290
 CKN  C9   C  CH1   0  -0.002   2.4018  -0.1572   0.1427
 CKN  C10  C  CH2   0  -0.472   1.6500  -1.0658  -0.8354
 CKN  C11  C  CH2   0  -0.430   0.1506  -0.7952  -0.8433
 CKN  C12  C  CH2   0  -0.281   4.5699   0.3615   1.1127
 CKN  C13  C  CH2   0  -0.315   6.0403  -0.0189   1.1719
 CKN  C14  C  CH2   0  -0.308   5.9227  -0.7498  -1.1069
 CKN  C15  C  CH2   0  -0.289   4.4559  -0.3585  -1.1390
 CKN  C16  C  C     0   0.512   7.7214   0.7869  -0.4825
 CKN  C19  C  CR15  0  -0.410  -6.2801  -0.3045  -0.0430
 CKN  C20  C  CH2   0  -0.566  -3.7375   2.0208  -0.7668
 CKN  C21  C  C     0   0.524  -2.7118   3.0673  -0.3930
 CKN  O1   O  O     0  -0.492  -1.7848   2.7856   0.3603
 CKN  C    C  CH3   0  -0.658  -5.4885   2.3783   1.0031
 CKN  C18  C  CR15  0  -0.040  -6.3390  -1.6653  -0.2776
 CKN  N    N  N     0  -0.356  -5.0883  -2.1490  -0.1791
 CKN  N1   N  N     0  -0.291  -4.7494  -3.4448  -0.3411
 CKN  C4   C  CR16  0   0.054  -3.4807  -3.6648  -0.2063
 CKN  N2   N  N     0  -0.504  -2.4986  -2.7887   0.0628
 CKN  C5   C  CR6   0   0.463  -2.8342  -1.5206   0.2375
 CKN  N3   N  NH1   0  -0.689  -1.8792  -0.6346   0.5342
 CKN  C6   C  CH1   0  -0.061  -0.4601  -0.9471   0.5448
 CKN  N4   N  NT    0  -0.443   3.8350  -0.4730   0.1734
 CKN  N5   N  NT    0  -0.439   6.6444   0.0494  -0.1402
 CKN  C17  C  CH3   0  -0.805   8.3737   1.6067   0.6069
 CKN  O    O  O     0  -0.511   8.1649   0.7988  -1.6256
 CKN  H1   H  HCH1  0   0.255  -3.6632   1.3457   1.2772
 CKN  H2   H  HNH2  0   0.402  -2.2261   5.0243  -0.7260
 CKN  H3   H  HNH2  0   0.410  -3.6524   4.4942  -1.5289
 CKN  H4   H  HCH2  0   0.246  -0.1305  -0.1757   2.5321
 CKN  H5   H  HCH2  0   0.231   0.0852   1.0070   1.2488
 CKN  H6   H  HCH2  0   0.247   2.2185   0.3740   2.2486
 CKN  H7   H  HCH2  0   0.222   1.9633  -1.3225   1.8924
 CKN  H8   H  HCH1  0   0.186   2.2578   0.8903  -0.1866
 CKN  H9   H  HCH2  0   0.245   2.0102  -0.9397  -1.8563
 CKN  H10  H  HCH2  0   0.221   1.8396  -2.1090  -0.5582
 CKN  H11  H  HCH2  0   0.217  -0.0414   0.2230  -1.2003
 CKN  H12  H  HCH2  0   0.244  -0.3402  -1.4726  -1.5453
 CKN  H13  H  HCH2  0   0.250   4.1765   0.2373   2.1200
 CKN  H14  H  HCH2  0   0.196   4.4851   1.4325   0.8575
 CKN  H15  H  HCH2  0   0.275   6.5463   0.6376   1.8739
 CKN  H16  H  HCH2  0   0.241   6.1346  -1.0407   1.5548
 CKN  H17  H  HCH2  0   0.238   6.0133  -1.8075  -0.8366
 CKN  H18  H  HCH2  0   0.263   6.3569  -0.6189  -2.0941
 CKN  H19  H  HCH2  0   0.196   4.3647   0.6655  -1.5409
 CKN  H20  H  HCH2  0   0.249   3.9678  -1.0256  -1.8469
 CKN  H21  H  HCR5  0   0.254  -7.1287   0.3611  -0.0531
 CKN  H22  H  HCH2  0   0.279  -3.2006   1.2479  -1.3234
 CKN  H23  H  HCH2  0   0.268  -4.5011   2.4094  -1.4438
 CKN  H24  H  HCH3  0   0.229  -6.2866   2.5144   0.2723
 CKN  H25  H  HCH3  0   0.242  -5.9338   2.0086   1.9267
 CKN  H26  H  HCH3  0   0.241  -5.0646   3.3614   1.2118
 CKN  H27  H  HCR5  0   0.285  -7.1702  -2.3132  -0.5007
 CKN  H28  H  HCR6  0   0.268  -3.1807  -4.6983  -0.3329
 CKN  H29  H  HNH1  0   0.408  -2.1089   0.3464   0.5886
 CKN  H30  H  HCH1  0   0.248  -0.3525  -1.9832   0.8720
 CKN  H32  H  HCH3  0   0.265   8.7244   0.9843   1.4310
 CKN  H33  H  HCH3  0   0.267   9.2282   2.1323   0.1887
 CKN  H34  H  HCH3  0   0.263   7.6888   2.3459   1.0245

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
 CKN  C17  C16  single    1.511  0.020  1.511
 CKN  C14  C15  single    1.518  0.020  1.518
 CKN  C14  N5   single    1.447  0.020  1.447
 CKN  C15  N4   single    1.456  0.020  1.456
 CKN  C16  N5   single    1.349  0.020  1.349
 CKN  C16  O    double    1.226  0.020  1.226
 CKN  N6   C21  single    1.336  0.020  1.336
 CKN  N5   C13  single    1.446  0.020  1.446
 CKN  C21  O1   double    1.227  0.020  1.227
 CKN  C21  C20  single    1.512  0.020  1.512
 CKN  N4   C9   single    1.468  0.020  1.468
 CKN  N4   C12  single    1.456  0.020  1.456
 CKN  C9   C8   single    1.532  0.020  1.532
 CKN  C9   C10  single    1.532  0.020  1.532
 CKN  C20  C1   single    1.542  0.020  1.542
 CKN  C8   C7   single    1.525  0.020  1.525
 CKN  C13  C12  single    1.520  0.020  1.520
 CKN  C7   C6   single    1.521  0.020  1.521
 CKN  C    C1   single    1.525  0.020  1.525
 CKN  C10  C11  single    1.524  0.020  1.524
 CKN  C1   C2   single    1.500  0.020  1.500
 CKN  C11  C6   single    1.524  0.020  1.524
 CKN  C6   N3   single    1.453  0.020  1.453
 CKN  N3   C5   single    1.336  0.020  1.336
 CKN  C2   C3   aromatic  1.394  0.020  1.394
 CKN  C2   C19  aromatic  1.404  0.020  1.404
 CKN  C5   C3   aromatic  1.432  0.020  1.432
 CKN  C5   N2   aromatic  1.323  0.020  1.323
 CKN  C3   N    aromatic  1.384  0.020  1.384
 CKN  C19  C18  aromatic  1.382  0.020  1.382
 CKN  N2   C4   aromatic  1.343  0.020  1.343
 CKN  N    C18  aromatic  1.345  0.020  1.345
 CKN  N    N1   aromatic  1.349  0.020  1.349
 CKN  C4   N1   aromatic  1.295  0.020  1.295
 CKN  C1   H1   single    0.970  0.020  1.090
 CKN  N6   H2   single    0.860  0.020  1.020
 CKN  N6   H3   single    0.860  0.020  1.020
 CKN  C7   H4   single    0.970  0.020  1.090
 CKN  C7   H5   single    0.970  0.020  1.090
 CKN  C8   H6   single    0.970  0.020  1.090
 CKN  C8   H7   single    0.970  0.020  1.090
 CKN  C9   H8   single    0.970  0.020  1.090
 CKN  C10  H9   single    0.970  0.020  1.090
 CKN  C10  H10  single    0.970  0.020  1.090
 CKN  C11  H11  single    0.970  0.020  1.090
 CKN  C11  H12  single    0.970  0.020  1.090
 CKN  C12  H13  single    0.970  0.020  1.090
 CKN  C12  H14  single    0.970  0.020  1.090
 CKN  C13  H15  single    0.970  0.020  1.090
 CKN  C13  H16  single    0.970  0.020  1.090
 CKN  C14  H17  single    0.970  0.020  1.090
 CKN  C14  H18  single    0.970  0.020  1.090
 CKN  C15  H19  single    0.970  0.020  1.090
 CKN  C15  H20  single    0.970  0.020  1.090
 CKN  C19  H21  single    0.930  0.020  1.080
 CKN  C20  H22  single    0.970  0.020  1.090
 CKN  C20  H23  single    0.970  0.020  1.090
 CKN  C    H24  single    0.970  0.020  1.090
 CKN  C    H25  single    0.970  0.020  1.090
 CKN  C    H26  single    0.970  0.020  1.090
 CKN  C18  H27  single    0.930  0.020  1.080
 CKN  C4   H28  single    0.930  0.020  1.080
 CKN  N3   H29  single    0.860  0.020  1.020
 CKN  C6   H30  single    0.970  0.020  1.090
 CKN  C17  H32  single    0.970  0.020  1.090
 CKN  C17  H33  single    0.970  0.020  1.090
 CKN  C17  H34  single    0.970  0.020  1.090

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
 CKN  H1   C1   C    106.53  3.000
 CKN  H1   C1   C20  108.38  3.000
 CKN  C    C1   C20  110.18  3.000
 CKN  H1   C1   C2   107.95  3.000
 CKN  C    C1   C2   112.61  3.000
 CKN  C20  C1   C2   110.98  3.000
 CKN  C19  C2   C3   106.17  3.000
 CKN  C19  C2   C1   127.08  3.000
 CKN  C3   C2   C1   126.74  3.000
 CKN  C5   C3   N    115.12  3.000
 CKN  N    C3   C2   107.45  3.000
 CKN  C5   C3   C2   137.43  3.000
 CKN  H3   N6   H2   117.49  3.000
 CKN  H3   N6   C21  121.78  3.000
 CKN  H2   N6   C21  120.71  3.000
 CKN  H5   C7   H4   107.01  3.000
 CKN  H5   C7   C6   109.28  3.000
 CKN  H4   C7   C6   110.19  3.000
 CKN  H5   C7   C8   109.44  3.000
 CKN  H4   C7   C8   109.36  3.000
 CKN  C6   C7   C8   111.46  3.000
 CKN  H7   C8   H6   106.62  3.000
 CKN  H7   C8   C9   108.47  3.000
 CKN  H6   C8   C9   111.34  3.000
 CKN  H7   C8   C7   110.02  3.000
 CKN  H6   C8   C7   107.42  3.000
 CKN  C9   C8   C7   112.79  3.000
 CKN  H8   C9   N4   109.67  3.000
 CKN  H8   C9   C10  107.90  3.000
 CKN  N4   C9   C10  111.40  3.000
 CKN  H8   C9   C8   107.95  3.000
 CKN  C10  C9   C8   108.41  3.000
 CKN  N4   C9   C8   111.38  3.000
 CKN  H10  C10  H9   106.85  3.000
 CKN  H10  C10  C11  109.92  3.000
 CKN  H9   C10  C11  107.45  3.000
 CKN  H10  C10  C9   108.55  3.000
 CKN  H9   C10  C9   111.54  3.000
 CKN  C11  C10  C9   112.39  3.000
 CKN  H12  C11  H11  106.75  3.000
 CKN  H12  C11  C6   110.09  3.000
 CKN  H11  C11  C6   108.61  3.000
 CKN  H12  C11  C10  109.60  3.000
 CKN  H11  C11  C10  109.82  3.000
 CKN  C6   C11  C10  111.83  3.000
 CKN  H14  C12  H13  107.26  3.000
 CKN  H14  C12  N4   111.60  3.000
 CKN  H13  C12  N4   110.44  3.000
 CKN  H14  C12  C13  109.03  3.000
 CKN  H13  C12  C13  106.56  3.000
 CKN  N4   C12  C13  111.72  3.000
 CKN  H16  C13  H15  107.33  3.000
 CKN  H16  C13  N5   108.99  3.000
 CKN  H15  C13  N5   111.30  3.000
 CKN  H16  C13  C12  109.29  3.000
 CKN  H15  C13  C12  108.93  3.000
 CKN  N5   C13  C12  110.91  3.000
 CKN  H18  C14  H17  107.91  3.000
 CKN  H18  C14  N5   109.95  3.000
 CKN  H17  C14  N5   109.10  3.000
 CKN  H18  C14  C15  109.62  3.000
 CKN  H17  C14  C15  109.51  3.000
 CKN  N5   C14  C15  110.70  3.000
 CKN  H20  C15  H19  107.14  3.000
 CKN  H20  C15  N4   110.29  3.000
 CKN  H19  C15  N4   111.46  3.000
 CKN  H20  C15  C14  106.80  3.000
 CKN  H19  C15  C14  109.06  3.000
 CKN  N4   C15  C14  111.87  3.000
 CKN  O    C16  C17  120.70  3.000
 CKN  O    C16  N5   122.04  3.000
 CKN  C17  C16  N5   117.26  3.000
 CKN  H21  C19  C18  124.92  3.000
 CKN  H21  C19  C2   126.34  3.000
 CKN  C18  C19  C2   108.74  3.000
 CKN  H23  C20  H22  106.22  3.000
 CKN  H23  C20  C21  112.41  3.000
 CKN  H22  C20  C21  106.38  3.000
 CKN  H23  C20  C1   109.48  3.000
 CKN  H22  C20  C1   110.91  3.000
 CKN  C21  C20  C1   111.29  3.000
 CKN  O1   C21  C20  120.34  3.000
 CKN  C20  C21  N6   116.51  3.000
 CKN  O1   C21  N6   123.15  3.000
 CKN  H26  C    H25  107.60  3.000
 CKN  H26  C    H24  107.46  3.000
 CKN  H25  C    H24  108.13  3.000
 CKN  H26  C    C1   110.67  3.000
 CKN  H25  C    C1   111.35  3.000
 CKN  H24  C    C1   111.46  3.000
 CKN  H27  C18  N    121.10  3.000
 CKN  H27  C18  C19  131.31  3.000
 CKN  N    C18  C19  107.59  3.000
 CKN  N1   N    C18  124.78  3.000
 CKN  N1   N    C3   125.16  3.000
 CKN  C18  N    C3   110.06  3.000
 CKN  C4   N1   N    113.38  3.000
 CKN  H28  C4   N2   116.29  3.000
 CKN  H28  C4   N1   114.91  3.000
 CKN  N2   C4   N1   128.79  3.000
 CKN  C5   N2   C4   117.77  3.000
 CKN  N3   C5   N2   118.91  3.000
 CKN  N2   C5   C3   119.77  3.000
 CKN  N3   C5   C3   121.32  3.000
 CKN  H29  N3   C6   115.53  3.000
 CKN  H29  N3   C5   119.60  3.000
 CKN  C6   N3   C5   123.85  3.000
 CKN  H30  C6   N3   107.61  3.000
 CKN  H30  C6   C11  109.16  3.000
 CKN  N3   C6   C11  111.30  3.000
 CKN  H30  C6   C7   109.13  3.000
 CKN  N3   C6   C7   110.02  3.000
 CKN  C11  C6   C7   109.59  3.000
 CKN  C15  N4   C12  108.73  3.000
 CKN  C12  N4   C9   112.53  3.000
 CKN  C15  N4   C9   112.36  3.000
 CKN  C16  N5   C14  122.03  3.000
 CKN  C16  N5   C13  126.11  3.000
 CKN  C14  N5   C13  111.82  3.000
 CKN  H34  C17  H33  108.26  3.000
 CKN  H34  C17  H32  107.42  3.000
 CKN  H33  C17  H32  108.29  3.000
 CKN  H34  C17  C16  111.87  3.000
 CKN  H33  C17  C16  108.92  3.000
 CKN  H32  C17  C16  111.96  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
 CKN  CONST_01  N2   C5   C3   C2    180.00   0.0  0
 CKN  CONST_02  C18  N    C3   C2      0.00   0.0  0
 CKN  CONST_03  N1   N    C3   C2    180.00   0.0  0
 CKN  CONST_04  N    C18  C19  C2      0.00   0.0  0
 CKN  CONST_05  C18  C19  C2   C3      0.00   0.0  0
 CKN  CONST_06  C4   N2   C5   C3      0.00   0.0  0
 CKN  CONST_07  C19  C18  N    C3      0.00   0.0  0
 CKN  CONST_08  C4   N1   N    C3      0.00   0.0  0
 CKN  CONST_09  C5   C3   C2   C19   180.00   0.0  0
 CKN  CONST_10  N    C3   C2   C19     0.00   0.0  0
 CKN  CONST_11  N1   N    C18  C19   180.00   0.0  0
 CKN  CONST_12  C5   C3   N    C18   180.00   0.0  0
 CKN  CONST_13  C4   N1   N    C18   180.00   0.0  0
 CKN  CONST_14  N2   C5   C3   N       0.00   0.0  0
 CKN  CONST_15  N2   C4   N1   N       0.00   0.0  0
 CKN  CONST_16  C5   C3   N    N1      0.00   0.0  0
 CKN  CONST_17  C5   N2   C4   N1      0.00   0.0  0
 CKN  CONST_18  C5   C3   C2   C1      0.00   0.0  0
 CKN  CONST_19  N    C3   C2   C1    180.00   0.0  0
 CKN  CONST_20  C18  C19  C2   C1    180.00   0.0  0
 CKN  CONST_21  N3   C5   C3   C2      0.00   0.0  0
 CKN  CONST_22  N3   C5   C3   N     180.00   0.0  0
 CKN  CONST_23  N3   C5   N2   C4    180.00   0.0  0
 CKN  CONST_24  C6   N3   C5   C3    180.00   0.0  0
 CKN  CONST_25  C6   N3   C5   N2      0.00   0.0  0
 CKN  CONST_26  H27  C18  C19  C2    180.00   0.0  0
 CKN  CONST_27  H21  C19  C2   C3    180.00   0.0  0
 CKN  CONST_28  H28  C4   N1   N     180.00   0.0  0
 CKN  CONST_29  C17  C16  N5   C13     0.00   0.0  0
 CKN  CONST_30  O    C16  N5   C13   180.00   0.0  0
 CKN  CONST_31  C17  C16  N5   C14   180.00   0.0  0
 CKN  CONST_32  O    C16  N5   C14     0.00   0.0  0
 CKN  CONST_33  H29  N3   C5   C3      0.00   0.0  0
 CKN  CONST_34  H2   N6   C21  C20   180.00   0.0  0
 CKN  CONST_35  H3   N6   C21  C20     0.00   0.0  0
 CKN  Var_01    C14  C15  N4   C9   -177.34  30.0  1
 CKN  Var_02    C13  C12  N4   C9    177.65  30.0  1
 CKN  Var_03    C6   C7   C8   C9     57.01  30.0  1
 CKN  Var_04    C6   C11  C10  C9    -57.01  30.0  1
 CKN  Var_05    C14  N5   C13  C12   -54.55  30.0  1
 CKN  Var_06    C15  C14  N5   C13    54.56  30.0  1
 CKN  Var_07    N5   C14  C15  N4    -56.62  30.0  1
 CKN  Var_08    N5   C13  C12  N4     56.45  30.0  1
 CKN  Var_09    H32  C17  C16  N5     59.53  30.0  3
 CKN  Var_10    N6   C21  C20  C1   -123.48  30.0  2

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
 CKN  chir_01  C1  C20  C   C2   negativ
 CKN  chir_02  C9  N4   C8  C10  positiv
 CKN  chir_03  C6  N3   C7  C11  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
 CKN  plan-1  C13  0.020
 CKN  plan-1  C14  0.020
 CKN  plan-1  C16  0.020
 CKN  plan-1  N5   0.020
 CKN  plan-1  C17  0.020
 CKN  plan-1  O    0.020
 CKN  plan-2  C1   0.020
 CKN  plan-2  C2   0.020
 CKN  plan-2  C3   0.020
 CKN  plan-2  C19  0.020
 CKN  plan-2  C18  0.020
 CKN  plan-2  N    0.020
 CKN  plan-2  N1   0.020
 CKN  plan-2  C4   0.020
 CKN  plan-2  N2   0.020
 CKN  plan-2  C5   0.020
 CKN  plan-2  N3   0.020
 CKN  plan-2  H21  0.020
 CKN  plan-2  H27  0.020
 CKN  plan-2  H28  0.020
 CKN  plan-3  C5   0.020
 CKN  plan-3  N3   0.020
 CKN  plan-3  C6   0.020
 CKN  plan-3  H29  0.020
 CKN  plan-4  N6   0.020
 CKN  plan-4  C20  0.020
 CKN  plan-4  C21  0.020
 CKN  plan-4  O1   0.020
 CKN  plan-4  H2   0.020
 CKN  plan-4  H3   0.020

