# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 15:35:43 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 5-[[(1R,2S)-2-azanylcyclohexyl]amino]-3-[(3,5-dimethoxyphenyl)amino]pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2nc(N[C@@H]3CCCC[C@@H]3N)cnc2C(N)=O)cc(OC)c1
#
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
 KZI  KZI  5-[[(1R,2S)-2-azanylcyclohexyl]amino]-3-[(3,5-dimethoxyphenyl)amino]pyrazine-2-carboxamide  ligand  54  28  .  2022-07-25  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_KZI
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
 KZI  O1    O  O     0  -0.518   1.8559  -3.9758  -0.4949
 KZI  O2    O  O2    0  -0.475   2.1155   3.3665   0.6012
 KZI  O3    O  O2    0  -0.476   5.8918   0.5089  -0.2690
 KZI  N4    N  N     0  -0.498  -0.5693  -0.5239   0.0152
 KZI  N5    N  NH1   0  -0.648  -2.6740   0.3253   0.1644
 KZI  N6    N  NH2   0  -0.804  -0.0193  -5.2271  -0.5063
 KZI  N8    N  N     0  -0.369  -1.5488  -3.0695  -0.1970
 KZI  C10   C  CR16  0  -0.558   4.0797   2.0406   0.1721
 KZI  C11   C  CH2   0  -0.448  -4.8302  -0.0200  -1.0105
 KZI  C12   C  CR16  0  -0.510   3.7325  -0.3253  -0.2036
 KZI  C13   C  CR6   0   0.525   0.2634  -1.5427  -0.1283
 KZI  C14   C  C     0   0.528   0.6238  -4.0587  -0.4264
 KZI  C15   C  CR16  0  -0.218  -2.3803  -2.0717  -0.0548
 KZI  C16   C  CR16  0  -0.464   1.8329   1.1023   0.2255
 KZI  C17   C  CR6   0  -0.067  -0.2365  -2.8678  -0.2510
 KZI  C18   C  CR6   0   0.414   2.3523  -0.1621  -0.0436
 KZI  C19   C  CR6   0   0.448   2.7042   2.1850   0.3325
 KZI  C20   C  CH1   0  -0.096  -4.1171   0.3038   0.3054
 KZI  C21   C  CH3   0  -0.438   2.9253   4.5127   0.7671
 KZI  C22   C  CR6   0   0.500  -1.8822  -0.7466   0.0414
 KZI  C23   C  CR6   0   0.437   4.5815   0.7663  -0.0970
 KZI  C24   C  CH1   0  -0.100  -4.5846   1.6684   0.8323
 KZI  C25   C  CH2   0  -0.430  -4.6545   1.0755  -2.0537
 KZI  C26   C  CH2   0  -0.437  -5.1340   2.4181  -1.5186
 KZI  C27   C  CH3   0  -0.439   6.8162   1.5750  -0.1862
 KZI  C28   C  CH2   0  -0.439  -4.4255   2.7682  -0.2157
 KZI  N42   N  NH2   0  -0.799  -3.8336   2.0170   2.0269
 KZI  HN5   H  HNH1  0   0.389  -2.2055   1.1853   0.4113
 KZI  HN6   H  HNH2  0   0.404   0.4952  -6.0826  -0.6298
 KZI  HN6A  H  HNH2  0   0.408  -1.0228  -5.2659  -0.4501
 KZI  HN9   H  HNH1  0   0.431   2.1283  -2.1839  -0.3016
 KZI  H10   H  HCR6  0   0.298   4.7414   2.8901   0.2498
 KZI  H11   H  HCH2  0   0.242  -4.4881  -0.9779  -1.4077
 KZI  H11A  H  HCH2  0   0.229  -5.8942  -0.1507  -0.7896
 KZI  H12   H  HCR6  0   0.263   4.1491  -1.3026  -0.4176
 KZI  H15   H  HCR6  0   0.274  -3.4366  -2.2988  -0.0062
 KZI  H16   H  HCR6  0   0.288   0.7743   1.2565   0.3511
 KZI  H20   H  HCH1  0   0.257  -4.3924  -0.4526   1.0521
 KZI  H21   H  HCH3  0   0.228   3.6446   4.3907   1.5811
 KZI  H21A  H  HCH3  0   0.228   3.4678   4.7673  -0.1472
 KZI  H21B  H  HCH3  0   0.261   2.2538   5.3318   1.0129
 KZI  H24   H  HCH1  0   0.223  -5.6622   1.5521   1.0243
 KZI  H25   H  HCH2  0   0.218  -3.6007   1.1470  -2.3409
 KZI  H25A  H  HCH2  0   0.234  -5.2022   0.8066  -2.9597
 KZI  H26   H  HCH2  0   0.233  -4.9697   3.2069  -2.2560
 KZI  H26A  H  HCH2  0   0.213  -6.2149   2.3743  -1.3480
 KZI  H27   H  HCH3  0   0.229   6.6274   2.3404  -0.9432
 KZI  H27A  H  HCH3  0   0.229   6.8118   2.0463   0.8000
 KZI  H27B  H  HCH3  0   0.261   7.7989   1.1442  -0.3614
 KZI  H28   H  HCH2  0   0.238  -4.8207   3.7034   0.1911
 KZI  H28A  H  HCH2  0   0.216  -3.3624   2.9472  -0.4104
 KZI  HN42  H  HNH2  0   0.350  -4.1509   2.9122   2.3782
 KZI  HN4A  H  HNH2  0   0.347  -4.0231   1.3463   2.7627
 KZI  N9    N  NH1   0  -0.811   1.6017  -1.3242  -0.1605

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
 KZI  O1   C14   double    1.237  0.020  1.237
 KZI  O2   C19   single    1.347  0.020  1.347
 KZI  O2   C21   single    1.413  0.020  1.413
 KZI  O3   C23   single    1.346  0.020  1.346
 KZI  O3   C27   single    1.414  0.020  1.414
 KZI  N4   C13   aromatic  1.324  0.020  1.324
 KZI  N4   C22   aromatic  1.332  0.020  1.332
 KZI  N5   C20   single    1.450  0.020  1.450
 KZI  N5   C22   single    1.338  0.020  1.338
 KZI  N6   C14   single    1.336  0.020  1.336
 KZI  N8   C15   aromatic  1.307  0.020  1.307
 KZI  N8   C17   aromatic  1.329  0.020  1.329
 KZI  N9   C13   single    1.356  0.020  1.356
 KZI  N9   C18   single    1.388  0.020  1.388
 KZI  C10  C19   aromatic  1.392  0.020  1.392
 KZI  C10  C23   aromatic  1.396  0.020  1.396
 KZI  C11  C20   single    1.531  0.020  1.531
 KZI  C11  C25   single    1.523  0.020  1.523
 KZI  C12  C18   aromatic  1.399  0.020  1.399
 KZI  C12  C23   aromatic  1.387  0.020  1.387
 KZI  C13  C17   aromatic  1.422  0.020  1.422
 KZI  C14  C17   single    1.480  0.020  1.480
 KZI  C15  C22   aromatic  1.419  0.020  1.419
 KZI  C16  C18   aromatic  1.393  0.020  1.393
 KZI  C16  C19   aromatic  1.394  0.020  1.394
 KZI  C20  C24   single    1.536  0.020  1.536
 KZI  C24  C28   single    1.527  0.020  1.527
 KZI  C24  N42   single    1.453  0.020  1.453
 KZI  C25  C26   single    1.523  0.020  1.523
 KZI  C26  C28   single    1.524  0.020  1.524
 KZI  N5   HN5   single    0.860  0.020  1.020
 KZI  N6   HN6   single    0.860  0.020  1.020
 KZI  N6   HN6A  single    0.860  0.020  1.020
 KZI  N9   HN9   single    0.860  0.020  1.020
 KZI  C10  H10   single    0.930  0.020  1.080
 KZI  C11  H11   single    0.970  0.020  1.090
 KZI  C11  H11A  single    0.970  0.020  1.090
 KZI  C12  H12   single    0.930  0.020  1.080
 KZI  C15  H15   single    0.930  0.020  1.080
 KZI  C16  H16   single    0.930  0.020  1.080
 KZI  C20  H20   single    0.970  0.020  1.090
 KZI  C21  H21   single    0.970  0.020  1.090
 KZI  C21  H21A  single    0.970  0.020  1.090
 KZI  C21  H21B  single    0.970  0.020  1.090
 KZI  C24  H24   single    0.970  0.020  1.090
 KZI  C25  H25   single    0.970  0.020  1.090
 KZI  C25  H25A  single    0.970  0.020  1.090
 KZI  C26  H26   single    0.970  0.020  1.090
 KZI  C26  H26A  single    0.970  0.020  1.090
 KZI  C27  H27   single    0.970  0.020  1.090
 KZI  C27  H27A  single    0.970  0.020  1.090
 KZI  C27  H27B  single    0.970  0.020  1.090
 KZI  C28  H28   single    0.970  0.020  1.090
 KZI  C28  H28A  single    0.970  0.020  1.090
 KZI  N42  HN42  single    0.890  0.020  1.040
 KZI  N42  HN4A  single    0.890  0.020  1.040

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
 KZI  C21   O2   C19   118.97  3.000
 KZI  C27   O3   C23   119.00  3.000
 KZI  C22   N4   C13   119.58  3.000
 KZI  HN5   N5   C22   115.47  3.000
 KZI  HN5   N5   C20   116.77  3.000
 KZI  C22   N5   C20   125.86  3.000
 KZI  HN6A  N6   HN6   118.98  3.000
 KZI  HN6A  N6   C14   120.70  3.000
 KZI  HN6   N6   C14   120.32  3.000
 KZI  C17   N8   C15   121.13  3.000
 KZI  H10   C10  C23   120.79  3.000
 KZI  H10   C10  C19   121.04  3.000
 KZI  C23   C10  C19   118.17  3.000
 KZI  H11A  C11  H11   105.85  3.000
 KZI  H11A  C11  C25   109.65  3.000
 KZI  H11   C11  C25   110.22  3.000
 KZI  H11A  C11  C20   107.73  3.000
 KZI  H11   C11  C20   110.62  3.000
 KZI  C25   C11  C20   112.51  3.000
 KZI  H12   C12  C23   119.32  3.000
 KZI  H12   C12  C18   120.46  3.000
 KZI  C23   C12  C18   120.22  3.000
 KZI  C17   C13  N9    119.68  3.000
 KZI  C17   C13  N4    120.37  3.000
 KZI  N9    C13  N4    119.95  3.000
 KZI  C17   C14  N6    115.54  3.000
 KZI  C17   C14  O1    122.13  3.000
 KZI  N6    C14  O1    122.33  3.000
 KZI  H15   C15  C22   122.40  3.000
 KZI  H15   C15  N8    117.78  3.000
 KZI  C22   C15  N8    119.82  3.000
 KZI  H16   C16  C19   119.62  3.000
 KZI  H16   C16  C18   121.25  3.000
 KZI  C19   C16  C18   119.12  3.000
 KZI  C14   C17  C13   123.78  3.000
 KZI  C14   C17  N8    117.18  3.000
 KZI  C13   C17  N8    119.03  3.000
 KZI  C16   C18  C12   119.72  3.000
 KZI  C16   C18  N9    125.05  3.000
 KZI  C12   C18  N9    115.22  3.000
 KZI  C16   C19  C10   121.88  3.000
 KZI  C16   C19  O2    115.04  3.000
 KZI  C10   C19  O2    123.07  3.000
 KZI  H20   C20  C24   107.61  3.000
 KZI  H20   C20  C11   108.78  3.000
 KZI  C24   C20  C11   109.93  3.000
 KZI  H20   C20  N5    109.02  3.000
 KZI  C24   C20  N5    108.85  3.000
 KZI  C11   C20  N5    112.52  3.000
 KZI  H21B  C21  H21A  108.67  3.000
 KZI  H21B  C21  H21   108.79  3.000
 KZI  H21A  C21  H21   108.80  3.000
 KZI  H21B  C21  O2    106.48  3.000
 KZI  H21A  C21  O2    112.03  3.000
 KZI  H21   C21  O2    111.96  3.000
 KZI  C15   C22  N5    123.13  3.000
 KZI  C15   C22  N4    120.06  3.000
 KZI  N5    C22  N4    116.81  3.000
 KZI  C12   C23  C10   120.88  3.000
 KZI  C12   C23  O3    115.81  3.000
 KZI  C10   C23  O3    123.31  3.000
 KZI  H24   C24  N42   112.82  3.000
 KZI  H24   C24  C28   107.32  3.000
 KZI  N42   C24  C28   109.72  3.000
 KZI  H24   C24  C20   105.30  3.000
 KZI  N42   C24  C20   109.74  3.000
 KZI  C28   C24  C20   111.88  3.000
 KZI  H25A  C25  H25   106.33  3.000
 KZI  H25A  C25  C26   110.53  3.000
 KZI  H25   C25  C26   109.74  3.000
 KZI  H25A  C25  C11   109.47  3.000
 KZI  H25   C25  C11   109.74  3.000
 KZI  C26   C25  C11   110.93  3.000
 KZI  H26A  C26  H26   106.42  3.000
 KZI  H26A  C26  C28   109.56  3.000
 KZI  H26   C26  C28   109.96  3.000
 KZI  H26A  C26  C25   109.28  3.000
 KZI  H26   C26  C25   110.62  3.000
 KZI  C28   C26  C25   110.89  3.000
 KZI  H27B  C27  H27A  108.66  3.000
 KZI  H27B  C27  H27   108.78  3.000
 KZI  H27A  C27  H27   108.80  3.000
 KZI  H27B  C27  O3    106.43  3.000
 KZI  H27A  C27  O3    112.05  3.000
 KZI  H27   C27  O3    112.00  3.000
 KZI  H28A  C28  H28   106.09  3.000
 KZI  H28A  C28  C26   109.68  3.000
 KZI  H28   C28  C26   110.27  3.000
 KZI  H28A  C28  C24   109.92  3.000
 KZI  H28   C28  C24   108.83  3.000
 KZI  C26   C28  C24   111.89  3.000
 KZI  HN4A  N42  HN42  105.93  3.000
 KZI  HN4A  N42  C24   109.96  3.000
 KZI  HN42  N42  C24   109.58  3.000
 KZI  HN9   N9   C18   116.03  3.000
 KZI  HN9   N9   C13   112.19  3.000
 KZI  C18   N9   C13   131.78  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
 KZI  CONST_01  N8    C17  C13  N4      0.00   0.0  0
 KZI  CONST_02  N8    C15  C22  N4      0.00   0.0  0
 KZI  CONST_03  C18   C16  C19  C10     0.00   0.0  0
 KZI  CONST_04  C18   C12  C23  C10     0.00   0.0  0
 KZI  CONST_05  C19   C16  C18  C12     0.00   0.0  0
 KZI  CONST_06  C19   C10  C23  C12     0.00   0.0  0
 KZI  CONST_07  C15   C22  N4   C13     0.00   0.0  0
 KZI  CONST_08  C15   N8   C17  C13     0.00   0.0  0
 KZI  CONST_09  C23   C12  C18  C16     0.00   0.0  0
 KZI  CONST_10  C23   C10  C19  C16     0.00   0.0  0
 KZI  CONST_11  C22   C15  N8   C17     0.00   0.0  0
 KZI  CONST_12  C22   N4   C13  C17     0.00   0.0  0
 KZI  CONST_13  C23   C10  C19  O2    180.00   0.0  0
 KZI  CONST_14  C18   C16  C19  O2    180.00   0.0  0
 KZI  CONST_15  C19   C10  C23  O3    180.00   0.0  0
 KZI  CONST_16  C18   C12  C23  O3    180.00   0.0  0
 KZI  CONST_17  C14   C17  C13  N4    180.00   0.0  0
 KZI  CONST_18  C13   N4   C22  N5    180.00   0.0  0
 KZI  CONST_19  N8    C15  C22  N5    180.00   0.0  0
 KZI  CONST_20  N9    C13  C17  N8    180.00   0.0  0
 KZI  CONST_21  C22   N4   C13  N9    180.00   0.0  0
 KZI  CONST_22  C23   C12  C18  N9    180.00   0.0  0
 KZI  CONST_23  C19   C16  C18  N9    180.00   0.0  0
 KZI  CONST_24  C15   N8   C17  C14   180.00   0.0  0
 KZI  CONST_25  C20   N5   C22  N4    180.00   0.0  0
 KZI  CONST_26  C20   N5   C22  C15     0.00   0.0  0
 KZI  CONST_27  H15   C15  C22  N4    180.00   0.0  0
 KZI  CONST_28  H16   C16  C19  C10   180.00   0.0  0
 KZI  CONST_29  H12   C12  C23  C10   180.00   0.0  0
 KZI  CONST_30  H10   C10  C23  C12   180.00   0.0  0
 KZI  CONST_31  HN5   N5   C22  N4      0.00   0.0  0
 KZI  CONST_32  HN6   N6   C14  C17   180.00   0.0  0
 KZI  CONST_33  HN6A  N6   C14  C17     0.00   0.0  0
 KZI  Var_01    C28   C26  C25  C11    55.50  30.0  1
 KZI  Var_02    C26   C25  C11  C20   -56.32  30.0  1
 KZI  Var_03    C25   C26  C28  C24   -55.27  30.0  1
 KZI  Var_04    C18   N9   C13  N4      1.30  30.0  2
 KZI  Var_05    C13   N9   C18  C12  -176.57  30.0  1
 KZI  Var_06    N8    C17  C14  O1    179.65  30.0  2
 KZI  Var_07    H21   C21  O2   C19   -58.98  30.0  3
 KZI  Var_08    H27   C27  O3   C23   -60.83  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
 KZI  chir_01  C20  N5   C11  C24  positiv
 KZI  chir_02  C24  N42  C28  C20  negativ

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
 KZI  plan-1  N4    0.020
 KZI  plan-1  N5    0.020
 KZI  plan-1  N8    0.020
 KZI  plan-1  C13   0.020
 KZI  plan-1  C14   0.020
 KZI  plan-1  C15   0.020
 KZI  plan-1  C17   0.020
 KZI  plan-1  C22   0.020
 KZI  plan-1  H15   0.020
 KZI  plan-1  N9    0.020
 KZI  plan-2  O2    0.020
 KZI  plan-2  O3    0.020
 KZI  plan-2  C10   0.020
 KZI  plan-2  C12   0.020
 KZI  plan-2  C16   0.020
 KZI  plan-2  C18   0.020
 KZI  plan-2  C19   0.020
 KZI  plan-2  C23   0.020
 KZI  plan-2  H10   0.020
 KZI  plan-2  H12   0.020
 KZI  plan-2  H16   0.020
 KZI  plan-2  N9    0.020
 KZI  plan-3  O1    0.020
 KZI  plan-3  N6    0.020
 KZI  plan-3  C14   0.020
 KZI  plan-3  C17   0.020
 KZI  plan-3  HN6   0.020
 KZI  plan-3  HN6A  0.020
 KZI  plan-4  N5    0.020
 KZI  plan-4  C20   0.020
 KZI  plan-4  C22   0.020
 KZI  plan-4  HN5   0.020

