# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:48:42 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: methyl 4-[4-[(6-cyanoquinazolin-4-yl)amino]cyclohexyl]piperazine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N1CCN(CC1)[C@@H]2CC[C@H](CC2)Nc3ncnc4ccc(cc34)C#N
#
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
 K1H  K1H  'methyl 4-[4-[(6-cyanoquinazolin-4-yl)amino]cyclohexyl]piperazine-1-carboxylate'  ligand  55  29  .  2022-03-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K1H
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
 K1H  C1   C  CH3   0  -0.410   9.3323  -1.2110  -0.1955
 K1H  C3   C  C     0   0.758   7.3773  -0.0580   0.4154
 K1H  O4   O  O     0  -0.532   7.9537   0.4198   1.3750
 K1H  C7   C  CH2   0  -0.294   4.0190  -0.7850  -0.7895
 K1H  C9   C  CH2   0  -0.292   3.9134   0.5748   1.1342
 K1H  C10  C  CH2   0  -0.299   5.3031   1.1199   0.8666
 K1H  C11  C  CH1   0  -0.000   1.8353  -0.1681   0.1341
 K1H  C12  C  CH2   0  -0.479   1.1678  -0.7019  -1.1370
 K1H  C13  C  CH2   0  -0.459  -0.3066  -1.0283  -0.9283
 K1H  C14  C  CH1   0  -0.041  -1.0791   0.1762  -0.4133
 K1H  C15  C  CH2   0  -0.434  -0.4439   0.6846   0.8749
 K1H  C16  C  CH2   0  -0.468   1.0252   1.0247   0.6546
 K1H  C20  C  CR16  0   0.051  -4.2367   2.8244  -0.3925
 K1H  C22  C  CR66  0   0.262  -5.8316   1.2621  -0.0864
 K1H  C24  C  CR16  0  -0.301  -5.2443  -1.0925   0.0686
 K1H  C27  C  CR16  0  -0.305  -7.1903   0.9107   0.0646
 K1H  O2   O  O2    0  -0.480   7.9701  -0.8867  -0.4483
 K1H  N5   N  NT    0  -0.492   6.0848   0.1682   0.1063
 K1H  C6   C  CH2   0  -0.298   5.4189  -0.2824  -1.0998
 K1H  N8   N  NT    0  -0.445   3.2295   0.2234  -0.1009
 K1H  N17  N  NH1   0  -0.675  -2.4755  -0.1870  -0.2382
 K1H  C18  C  CR6   0   0.556  -3.4846   0.6798  -0.2361
 K1H  N19  N  N     0  -0.480  -3.2150   1.9666  -0.3972
 K1H  N21  N  N     0  -0.466  -5.5088   2.5690  -0.2430
 K1H  C23  C  CR66  0  -0.008  -4.8539   0.2429  -0.0764
 K1H  C25  C  CR6   0   0.007  -6.5798  -1.4086   0.2109
 K1H  C26  C  CR16  0  -0.233  -7.5620  -0.3957   0.2102
 K1H  C28  C  CSP   0   0.056  -6.9717  -2.7711   0.3584
 K1H  H1   H  HCH3  0   0.233   9.9705  -0.3280  -0.2267
 K1H  H2   H  HCH3  0   0.233   9.4584  -1.7105   0.7651
 K1H  H3   H  HCH3  0   0.246   9.6265  -1.8909  -0.9903
 K1H  H4   H  HCH2  0   0.253   3.5652  -1.0349  -1.7468
 K1H  H5   H  HCH2  0   0.198   4.0872  -1.7202  -0.2072
 K1H  H6   H  HCH2  0   0.199   3.9868  -0.2913   1.8145
 K1H  H7   H  HCH2  0   0.249   3.3657   1.3521   1.6645
 K1H  H8   H  HCH2  0   0.233   5.2234   2.0612   0.3105
 K1H  H9   H  HCH2  0   0.264   5.7947   1.3342   1.8118
 K1H  H10  H  HCH1  0   0.188   1.7887  -0.9732   0.8927
 K1H  H11  H  HCH2  0   0.226   1.2765   0.0400  -1.9362
 K1H  H12  H  HCH2  0   0.251   1.6569  -1.6132  -1.4810
 K1H  H13  H  HCH2  0   0.253  -0.7386  -1.3778  -1.8687
 K1H  H14  H  HCH2  0   0.229  -0.3969  -1.8512  -0.2091
 K1H  H15  H  HCH1  0   0.245  -1.0343   0.9709  -1.1629
 K1H  H16  H  HCH2  0   0.247  -0.9772   1.5684   1.2293
 K1H  H17  H  HCH2  0   0.221  -0.5418  -0.0825   1.6508
 K1H  H18  H  HCH2  0   0.246   1.4278   1.3969   1.5970
 K1H  H19  H  HCH2  0   0.221   1.1098   1.8431  -0.0690
 K1H  H21  H  HCR6  0   0.283  -4.5214  -1.8970   0.0678
 K1H  H22  H  HCR6  0   0.277  -7.9311   1.6986   0.0586
 K1H  H23  H  HCH2  0   0.269   5.9794  -1.0814  -1.5755
 K1H  H24  H  HCH2  0   0.233   5.3517   0.5488  -1.8109
 K1H  H26  H  HNH1  0   0.414  -2.6645  -1.1578  -0.0502
 K1H  H27  H  HCR6  0   0.288  -8.6047  -0.6594   0.3230
 K1H  H20  H  HCR6  0   0.255  -3.9641   3.8667  -0.5261
 K1H  N29  N  NS    0  -0.249  -7.2950  -3.8701   0.4844

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
 K1H  C1   O2   single    1.423  0.020  1.423
 K1H  O2   C3   single    1.336  0.020  1.336
 K1H  C10  C9   single    1.517  0.020  1.517
 K1H  C10  N5   single    1.447  0.020  1.447
 K1H  C9   N8   single    1.455  0.020  1.455
 K1H  C3   N5   single    1.348  0.020  1.348
 K1H  C3   O4   double    1.217  0.020  1.217
 K1H  N5   C6   single    1.450  0.020  1.450
 K1H  N8   C11  single    1.467  0.020  1.467
 K1H  N8   C7   single    1.454  0.020  1.454
 K1H  C11  C12  single    1.532  0.020  1.532
 K1H  C11  C16  single    1.533  0.020  1.533
 K1H  C12  C13  single    1.524  0.020  1.524
 K1H  C6   C7   single    1.519  0.020  1.519
 K1H  C13  C14  single    1.521  0.020  1.521
 K1H  C16  C15  single    1.524  0.020  1.524
 K1H  N29  C28  triple    1.152  0.020  1.152
 K1H  C15  C14  single    1.524  0.020  1.524
 K1H  C14  N17  single    1.453  0.020  1.453
 K1H  C28  C25  single    1.425  0.020  1.425
 K1H  N17  C18  single    1.330  0.020  1.330
 K1H  C24  C25  aromatic  1.380  0.020  1.380
 K1H  C24  C23  aromatic  1.399  0.020  1.399
 K1H  C25  C26  aromatic  1.411  0.020  1.411
 K1H  C18  C23  aromatic  1.446  0.020  1.446
 K1H  C18  N19  aromatic  1.325  0.020  1.325
 K1H  C23  C22  aromatic  1.412  0.020  1.412
 K1H  N19  C20  aromatic  1.334  0.020  1.334
 K1H  C26  C27  aromatic  1.366  0.020  1.366
 K1H  C22  C27  aromatic  1.412  0.020  1.412
 K1H  C22  N21  aromatic  1.355  0.020  1.355
 K1H  C20  N21  aromatic  1.306  0.020  1.306
 K1H  C1   H1   single    0.970  0.020  1.090
 K1H  C1   H2   single    0.970  0.020  1.090
 K1H  C1   H3   single    0.970  0.020  1.090
 K1H  C7   H4   single    0.970  0.020  1.090
 K1H  C7   H5   single    0.970  0.020  1.090
 K1H  C9   H6   single    0.970  0.020  1.090
 K1H  C9   H7   single    0.970  0.020  1.090
 K1H  C10  H8   single    0.970  0.020  1.090
 K1H  C10  H9   single    0.970  0.020  1.090
 K1H  C11  H10  single    0.970  0.020  1.090
 K1H  C12  H11  single    0.970  0.020  1.090
 K1H  C12  H12  single    0.970  0.020  1.090
 K1H  C13  H13  single    0.970  0.020  1.090
 K1H  C13  H14  single    0.970  0.020  1.090
 K1H  C14  H15  single    0.970  0.020  1.090
 K1H  C15  H16  single    0.970  0.020  1.090
 K1H  C15  H17  single    0.970  0.020  1.090
 K1H  C16  H18  single    0.970  0.020  1.090
 K1H  C16  H19  single    0.970  0.020  1.090
 K1H  C20  H20  single    0.930  0.020  1.080
 K1H  C24  H21  single    0.930  0.020  1.080
 K1H  C27  H22  single    0.930  0.020  1.080
 K1H  C6   H23  single    0.970  0.020  1.090
 K1H  C6   H24  single    0.970  0.020  1.090
 K1H  N17  H26  single    0.860  0.020  1.020
 K1H  C26  H27  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
 K1H  H3   C1   H2   109.06  3.000
 K1H  H3   C1   H1   109.11  3.000
 K1H  H2   C1   H1   109.19  3.000
 K1H  H3   C1   O2   105.78  3.000
 K1H  H2   C1   O2   111.83  3.000
 K1H  H1   C1   O2   111.77  3.000
 K1H  N5   C3   O2   112.42  3.000
 K1H  N5   C3   O4   124.68  3.000
 K1H  O2   C3   O4   122.90  3.000
 K1H  H5   C7   H4   107.18  3.000
 K1H  H5   C7   N8   111.79  3.000
 K1H  H4   C7   N8   110.45  3.000
 K1H  H5   C7   C6   109.33  3.000
 K1H  H4   C7   C6   106.29  3.000
 K1H  N8   C7   C6   111.56  3.000
 K1H  H7   C9   H6   107.06  3.000
 K1H  H7   C9   N8   110.46  3.000
 K1H  H6   C9   N8   111.41  3.000
 K1H  H7   C9   C10  106.87  3.000
 K1H  H6   C9   C10  109.26  3.000
 K1H  N8   C9   C10  111.58  3.000
 K1H  H9   C10  H8   107.75  3.000
 K1H  H9   C10  N5   110.02  3.000
 K1H  H8   C10  N5   109.72  3.000
 K1H  H9   C10  C9   109.39  3.000
 K1H  H8   C10  C9   109.36  3.000
 K1H  N5   C10  C9   110.56  3.000
 K1H  H10  C11  N8   110.11  3.000
 K1H  H10  C11  C16  108.11  3.000
 K1H  N8   C11  C16  110.43  3.000
 K1H  H10  C11  C12  107.26  3.000
 K1H  C16  C11  C12  108.82  3.000
 K1H  N8   C11  C12  111.97  3.000
 K1H  H12  C12  H11  106.94  3.000
 K1H  H12  C12  C13  107.35  3.000
 K1H  H11  C12  C13  109.92  3.000
 K1H  H12  C12  C11  110.96  3.000
 K1H  H11  C12  C11  109.03  3.000
 K1H  C13  C12  C11  112.48  3.000
 K1H  H14  C13  H13  106.97  3.000
 K1H  H14  C13  C14  109.29  3.000
 K1H  H13  C13  C14  110.13  3.000
 K1H  H14  C13  C12  109.28  3.000
 K1H  H13  C13  C12  109.46  3.000
 K1H  C14  C13  C12  111.60  3.000
 K1H  H15  C14  N17  107.68  3.000
 K1H  H15  C14  C15  108.67  3.000
 K1H  N17  C14  C15  112.46  3.000
 K1H  H15  C14  C13  108.82  3.000
 K1H  N17  C14  C13  109.33  3.000
 K1H  C15  C14  C13  109.80  3.000
 K1H  H17  C15  H16  107.07  3.000
 K1H  H17  C15  C16  110.17  3.000
 K1H  H16  C15  C16  109.72  3.000
 K1H  H17  C15  C14  109.14  3.000
 K1H  H16  C15  C14  109.93  3.000
 K1H  C16  C15  C14  110.74  3.000
 K1H  H19  C16  H18  106.70  3.000
 K1H  H19  C16  C15  109.67  3.000
 K1H  H18  C16  C15  107.89  3.000
 K1H  H19  C16  C11  108.43  3.000
 K1H  H18  C16  C11  111.34  3.000
 K1H  C15  C16  C11  112.64  3.000
 K1H  H20  C20  N21  116.52  3.000
 K1H  H20  C20  N19  115.12  3.000
 K1H  N21  C20  N19  128.36  3.000
 K1H  C23  C22  N21  122.13  3.000
 K1H  N21  C22  C27  118.80  3.000
 K1H  C23  C22  C27  119.07  3.000
 K1H  H21  C24  C25  118.47  3.000
 K1H  H21  C24  C23  121.56  3.000
 K1H  C25  C24  C23  119.97  3.000
 K1H  H22  C27  C26  120.73  3.000
 K1H  H22  C27  C22  118.51  3.000
 K1H  C26  C27  C22  120.76  3.000
 K1H  C3   O2   C1   116.83  3.000
 K1H  C6   N5   C10  113.17  3.000
 K1H  C6   N5   C3   125.39  3.000
 K1H  C10  N5   C3   120.51  3.000
 K1H  H24  C6   H23  107.79  3.000
 K1H  H24  C6   N5   109.40  3.000
 K1H  H23  C6   N5   110.86  3.000
 K1H  H24  C6   C7   109.08  3.000
 K1H  H23  C6   C7   108.77  3.000
 K1H  N5   C6   C7   110.87  3.000
 K1H  C11  N8   C9   112.04  3.000
 K1H  C11  N8   C7   114.00  3.000
 K1H  C9   N8   C7   108.32  3.000
 K1H  H26  N17  C18  119.06  3.000
 K1H  H26  N17  C14  116.34  3.000
 K1H  C18  N17  C14  124.48  3.000
 K1H  C23  C18  N19  119.97  3.000
 K1H  N19  C18  N17  118.59  3.000
 K1H  C23  C18  N17  121.44  3.000
 K1H  C18  N19  C20  117.93  3.000
 K1H  C22  N21  C20  115.71  3.000
 K1H  C18  C23  C24  124.34  3.000
 K1H  C18  C23  C22  115.89  3.000
 K1H  C24  C23  C22  119.77  3.000
 K1H  C28  C25  C26  119.66  3.000
 K1H  C26  C25  C24  120.62  3.000
 K1H  C28  C25  C24  119.72  3.000
 K1H  H27  C26  C25  119.74  3.000
 K1H  H27  C26  C27  120.45  3.000
 K1H  C25  C26  C27  119.81  3.000
 K1H  C25  C28  N29  180.00  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
 K1H  CONST_01  C23  C18  N19  C20     0.00   0.0  0
 K1H  CONST_02  C23  C22  N21  C20     0.00   0.0  0
 K1H  CONST_03  C27  C22  N21  C20   180.00   0.0  0
 K1H  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 K1H  CONST_05  N19  C18  C23  C22     0.00   0.0  0
 K1H  CONST_06  C25  C26  C27  C22     0.00   0.0  0
 K1H  CONST_07  N19  C20  N21  C22     0.00   0.0  0
 K1H  CONST_08  C27  C26  C25  C24     0.00   0.0  0
 K1H  CONST_09  N19  C18  C23  C24   180.00   0.0  0
 K1H  CONST_10  C27  C22  C23  C24     0.00   0.0  0
 K1H  CONST_11  N21  C22  C23  C24   180.00   0.0  0
 K1H  CONST_12  C18  C23  C22  C27   180.00   0.0  0
 K1H  CONST_13  C25  C24  C23  C18   180.00   0.0  0
 K1H  CONST_14  N21  C22  C23  C18     0.00   0.0  0
 K1H  CONST_15  N21  C20  N19  C18     0.00   0.0  0
 K1H  CONST_16  C26  C27  C22  N21   180.00   0.0  0
 K1H  CONST_17  C26  C25  C24  C23     0.00   0.0  0
 K1H  CONST_18  C26  C27  C22  C23     0.00   0.0  0
 K1H  CONST_19  N17  C18  N19  C20   180.00   0.0  0
 K1H  CONST_20  N17  C18  C23  C22   180.00   0.0  0
 K1H  CONST_21  N17  C18  C23  C24     0.00   0.0  0
 K1H  CONST_22  C28  C25  C26  C27   180.00   0.0  0
 K1H  CONST_23  C28  C25  C24  C23   180.00   0.0  0
 K1H  CONST_24  C23  C18  N17  C14   180.00   0.0  0
 K1H  CONST_25  N19  C18  N17  C14     0.00   0.0  0
 K1H  CONST_26  H21  C24  C23  C22   180.00   0.0  0
 K1H  CONST_27  H27  C26  C27  C22   180.00   0.0  0
 K1H  CONST_28  H20  C20  N21  C22   180.00   0.0  0
 K1H  CONST_29  H22  C27  C22  N21     0.00   0.0  0
 K1H  CONST_30  H26  N17  C18  N19   180.00   0.0  0
 K1H  Var_01    C10  C9   N8   C7     59.55  30.0  1
 K1H  Var_02    C10  N5   C6   C7    -52.12  30.0  1
 K1H  Var_03    C6   N5   C10  C9     52.49  30.0  1
 K1H  Var_04    C6   C7   N8   C9    -58.97  30.0  1
 K1H  Var_05    C14  C13  C12  C11    56.32  30.0  1
 K1H  Var_06    C14  C15  C16  C11   -57.59  30.0  1
 K1H  Var_07    N8   C9   C10  N5    -56.54  30.0  1
 K1H  Var_08    N8   C7   C6   N5     55.59  30.0  1
 K1H  Var_09    N5   C3   O2   C1   -178.83  30.0  3
 K1H  Var_10    H1   C1   O2   C3    -61.80  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
 K1H  chir_01  C11  N8   C12  C16  positiv
 K1H  chir_02  C14  N17  C13  C15  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
 K1H  plan-1  C14  0.020
 K1H  plan-1  N17  0.020
 K1H  plan-1  C18  0.020
 K1H  plan-1  H26  0.020
 K1H  plan-2  C20  0.020
 K1H  plan-2  C22  0.020
 K1H  plan-2  C24  0.020
 K1H  plan-2  C27  0.020
 K1H  plan-2  N17  0.020
 K1H  plan-2  C18  0.020
 K1H  plan-2  N19  0.020
 K1H  plan-2  N21  0.020
 K1H  plan-2  C23  0.020
 K1H  plan-2  C25  0.020
 K1H  plan-2  C26  0.020
 K1H  plan-2  C28  0.020
 K1H  plan-2  H21  0.020
 K1H  plan-2  H22  0.020
 K1H  plan-2  H27  0.020
 K1H  plan-2  H20  0.020
 K1H  plan-2  N29  0.020
 K1H  plan-3  C3   0.020
 K1H  plan-3  O4   0.020
 K1H  plan-3  O2   0.020
 K1H  plan-3  N5   0.020

