# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 05:37:09 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3,5-bis(2-cyanopropan-2-yl)phenyl]amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C#N)c1cc(Nc2nc(ncc2C(N)=O)N3CCC[C@H](N)C3)cc(c1)C(C)(C)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
 M8Z  M8Z  2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3,5-bis(2-cyanopropan-2-yl)phenyl]amino]pyrimidine-5-carboxamide  ligand  63  33  .  2021-08-14  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M8Z
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
 M8Z  C1   C  CT    0  -0.295   4.9424  -0.8984  -0.4288
 M8Z  C2   C  CH3   0  -0.663   5.0444  -2.3879  -0.7725
 M8Z  C3   C  CSP   0   0.157   5.5049  -0.1465  -1.5585
 M8Z  C4   C  CR6   0   0.235   3.5119  -0.4103  -0.2094
 M8Z  C5   C  CR16  0  -0.374   3.2743   0.9507  -0.0570
 M8Z  C6   C  CR6   0   0.230   1.9948   1.4259   0.1981
 M8Z  C8   C  CR6   0   0.461   1.1541  -0.8292   0.1300
 M8Z  C9   C  CR6   0   0.575  -1.1604  -1.7497   0.0649
 M8Z  C10  C  CR6   0  -0.308  -1.9515  -2.9202   0.2761
 M8Z  C11  C  CR16  0  -0.017  -3.3151  -2.7144   0.1102
 M8Z  C12  C  CR6   0   0.652  -3.0281  -0.5695  -0.5222
 M8Z  C13  C  CH2   0  -0.315  -2.7668   1.7461  -1.3065
 M8Z  C14  C  CH2   0  -0.467  -3.1350   2.8859  -0.3639
 M8Z  C15  C  CH2   0  -0.432  -4.6402   3.1432  -0.3872
 M8Z  C16  C  CH1   0  -0.112  -5.4419   1.8659  -0.1359
 M8Z  C17  C  CH2   0  -0.323  -4.9886   0.7844  -1.1267
 M8Z  C18  C  C     0   0.545  -1.3721  -4.2216   0.6490
 M8Z  C19  C  CR16  0  -0.465   2.4484  -1.2912  -0.1200
 M8Z  C20  C  CT    0  -0.290   1.7920   2.9332   0.3492
 M8Z  C21  C  CH3   0  -0.612   2.0823   3.6375  -0.9883
 M8Z  C22  C  CH3   0  -0.675   0.3927   3.3262   0.8318
 M8Z  C23  C  CSP   0   0.155   2.7517   3.4172   1.3505
 M8Z  N7   N  NS    0  -0.263   3.4944   3.8116   2.1360
 M8Z  C7   C  CR16  0  -0.398   0.9311   0.5376   0.2938
 M8Z  N    N  NS    0  -0.263   5.9568   0.4337  -2.4435
 M8Z  C    C  CH3   0  -0.613   5.7874  -0.6019   0.8230
 M8Z  N1   N  NH1   0  -0.801   0.1729  -1.8077   0.2669
 M8Z  N3   N  N     0  -0.534  -1.7070  -0.6144  -0.3345
 M8Z  N2   N  N     0  -0.488  -3.8721  -1.5862  -0.2679
 M8Z  O    O  O     0  -0.521  -0.1683  -4.3474   0.9056
 M8Z  N6   N  NH2   0  -0.822  -2.1909  -5.2830   0.7078
 M8Z  N4   N  NT    0  -0.479  -3.5582   0.5656  -1.0083
 M8Z  H1   H  HCH3  0   0.269   6.0845  -2.6546  -0.9548
 M8Z  H2   H  HCH3  0   0.258   4.6908  -2.9881   0.0651
 M8Z  H3   H  HCH3  0   0.260   4.4648  -2.6467  -1.6579
 M8Z  H4   H  HCR6  0   0.259   4.1005   1.6499  -0.1274
 M8Z  H5   H  HCR6  0   0.255  -4.0195  -3.5158   0.3080
 M8Z  H6   H  HCH2  0   0.243  -2.9797   2.0423  -2.3396
 M8Z  H7   H  HCH2  0   0.268  -1.7106   1.4988  -1.2501
 M8Z  H8   H  HCH2  0   0.228  -2.7932   2.6495   0.6482
 M8Z  H9   H  HCH2  0   0.245  -2.5988   3.7879  -0.6667
 M8Z  H10  H  HCH2  0   0.240  -4.9109   3.9032   0.3484
 M8Z  H11  H  HCH2  0   0.227  -4.9138   3.5378  -1.3706
 M8Z  H12  H  HCH1  0   0.241  -6.4954   2.0711  -0.3473
 M8Z  H13  H  HCH2  0   0.274  -5.5197  -0.1465  -0.9530
 M8Z  H14  H  HCH2  0   0.238  -5.2032   1.1089  -2.1506
 M8Z  H15  H  HCR6  0   0.277   2.6021  -2.3550  -0.2443
 M8Z  H16  H  HCH3  0   0.254   1.3805   3.2724  -1.7380
 M8Z  H17  H  HCH3  0   0.256   1.9517   4.7150  -0.8907
 M8Z  H18  H  HCH3  0   0.253   3.0927   3.4420  -1.3439
 M8Z  H19  H  HCH3  0   0.262   0.1175   2.8240   1.7581
 M8Z  H20  H  HCH3  0   0.273   0.3411   4.4016   0.9942
 M8Z  H21  H  HCH3  0   0.255  -0.3416   3.0779   0.0667
 M8Z  H22  H  HCR6  0   0.276  -0.0641   0.8844   0.5164
 M8Z  H23  H  HCH3  0   0.255   6.8182  -0.9233   0.6764
 M8Z  H24  H  HCH3  0   0.252   5.7874   0.4585   1.0699
 M8Z  H25  H  HCH3  0   0.256   5.3714  -1.1496   1.6683
 M8Z  H26  H  HNH1  0   0.432   0.4871  -2.7446   0.5216
 M8Z  H27  H  HNH2  0   0.412  -3.1415  -5.2740   0.3856
 M8Z  H28  H  HNH2  0   0.407  -1.7978  -6.1850   0.9206
 M8Z  N5   N  NH2   0  -0.791  -5.3472   1.4703   1.2612
 M8Z  H29  H  HNH2  0   0.347  -5.9028   0.6386   1.4196
 M8Z  H30  H  HNH2  0   0.341  -4.3962   1.2120   1.4954

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
 M8Z  N7   C23  triple    1.151  0.020  1.151
 M8Z  C23  C20  single    1.469  0.020  1.469
 M8Z  C21  C20  single    1.539  0.020  1.539
 M8Z  C20  C6   single    1.528  0.020  1.528
 M8Z  C20  C22  single    1.531  0.020  1.531
 M8Z  C    C1   single    1.539  0.020  1.539
 M8Z  C6   C5   aromatic  1.389  0.020  1.389
 M8Z  C6   C7   aromatic  1.389  0.020  1.389
 M8Z  C5   C4   aromatic  1.390  0.020  1.390
 M8Z  C14  C15  single    1.527  0.020  1.527
 M8Z  C14  C13  single    1.524  0.020  1.524
 M8Z  C7   C8   aromatic  1.394  0.020  1.394
 M8Z  N    C3   triple    1.151  0.020  1.151
 M8Z  C4   C1   single    1.527  0.020  1.527
 M8Z  C4   C19  aromatic  1.384  0.020  1.384
 M8Z  C3   C1   single    1.469  0.020  1.469
 M8Z  C15  C16  single    1.529  0.020  1.529
 M8Z  C1   C2   single    1.532  0.020  1.532
 M8Z  C8   C19  aromatic  1.397  0.020  1.397
 M8Z  C8   N1   single    1.392  0.020  1.392
 M8Z  C13  N4   single    1.452  0.020  1.452
 M8Z  N1   C9   single    1.350  0.020  1.350
 M8Z  C16  N5   single    1.455  0.020  1.455
 M8Z  C16  C17  single    1.535  0.020  1.535
 M8Z  N3   C9   aromatic  1.322  0.020  1.322
 M8Z  N3   C12  aromatic  1.335  0.020  1.335
 M8Z  C9   C10  aromatic  1.428  0.020  1.428
 M8Z  N4   C12  single    1.344  0.020  1.344
 M8Z  N4   C17  single    1.452  0.020  1.452
 M8Z  O    C18  double    1.237  0.020  1.237
 M8Z  C12  N2   aromatic  1.346  0.020  1.346
 M8Z  C10  C18  single    1.473  0.020  1.473
 M8Z  C10  C11  aromatic  1.389  0.020  1.389
 M8Z  C18  N6   single    1.342  0.020  1.342
 M8Z  N2   C11  aromatic  1.314  0.020  1.314
 M8Z  C2   H1   single    0.970  0.020  1.090
 M8Z  C2   H2   single    0.970  0.020  1.090
 M8Z  C2   H3   single    0.970  0.020  1.090
 M8Z  C5   H4   single    0.930  0.020  1.080
 M8Z  C11  H5   single    0.930  0.020  1.080
 M8Z  C13  H6   single    0.970  0.020  1.090
 M8Z  C13  H7   single    0.970  0.020  1.090
 M8Z  C14  H8   single    0.970  0.020  1.090
 M8Z  C14  H9   single    0.970  0.020  1.090
 M8Z  C15  H10  single    0.970  0.020  1.090
 M8Z  C15  H11  single    0.970  0.020  1.090
 M8Z  C16  H12  single    0.970  0.020  1.090
 M8Z  C17  H13  single    0.970  0.020  1.090
 M8Z  C17  H14  single    0.970  0.020  1.090
 M8Z  C19  H15  single    0.930  0.020  1.080
 M8Z  C21  H16  single    0.970  0.020  1.090
 M8Z  C21  H17  single    0.970  0.020  1.090
 M8Z  C21  H18  single    0.970  0.020  1.090
 M8Z  C22  H19  single    0.970  0.020  1.090
 M8Z  C22  H20  single    0.970  0.020  1.090
 M8Z  C22  H21  single    0.970  0.020  1.090
 M8Z  C7   H22  single    0.930  0.020  1.080
 M8Z  C    H23  single    0.970  0.020  1.090
 M8Z  C    H24  single    0.970  0.020  1.090
 M8Z  C    H25  single    0.970  0.020  1.090
 M8Z  N1   H26  single    0.860  0.020  1.020
 M8Z  N6   H27  single    0.860  0.020  1.020
 M8Z  N6   H28  single    0.860  0.020  1.020
 M8Z  N5   H29  single    0.890  0.020  1.040
 M8Z  N5   H30  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
 M8Z  C    C1   C4   109.62  3.000
 M8Z  C4   C1   C3   107.79  3.000
 M8Z  C    C1   C3   108.46  3.000
 M8Z  C3   C1   C2   107.44  3.000
 M8Z  C4   C1   C2   113.91  3.000
 M8Z  C    C1   C2   109.46  3.000
 M8Z  H3   C2   H2   108.74  3.000
 M8Z  H3   C2   H1   108.30  3.000
 M8Z  H2   C2   H1   107.68  3.000
 M8Z  H3   C2   C1   112.20  3.000
 M8Z  H2   C2   C1   109.97  3.000
 M8Z  H1   C2   C1   109.82  3.000
 M8Z  N    C3   C1   180.00  3.000
 M8Z  C19  C4   C5   119.00  3.000
 M8Z  C19  C4   C1   121.71  3.000
 M8Z  C5   C4   C1   119.26  3.000
 M8Z  H4   C5   C6   119.55  3.000
 M8Z  H4   C5   C4   119.60  3.000
 M8Z  C6   C5   C4   120.85  3.000
 M8Z  C7   C6   C20  121.49  3.000
 M8Z  C7   C6   C5   119.96  3.000
 M8Z  C20  C6   C5   118.55  3.000
 M8Z  N1   C8   C7   124.37  3.000
 M8Z  N1   C8   C19  115.98  3.000
 M8Z  C7   C8   C19  119.56  3.000
 M8Z  N3   C9   N1   119.38  3.000
 M8Z  N3   C9   C10  121.29  3.000
 M8Z  N1   C9   C10  119.33  3.000
 M8Z  C18  C10  C11  123.20  3.000
 M8Z  C11  C10  C9   113.87  3.000
 M8Z  C18  C10  C9   122.93  3.000
 M8Z  H5   C11  N2   114.30  3.000
 M8Z  H5   C11  C10  120.40  3.000
 M8Z  N2   C11  C10  125.29  3.000
 M8Z  N4   C12  N2   117.33  3.000
 M8Z  N2   C12  N3   124.66  3.000
 M8Z  N4   C12  N3   118.01  3.000
 M8Z  H7   C13  H6   107.43  3.000
 M8Z  H7   C13  N4   109.52  3.000
 M8Z  H6   C13  N4   107.91  3.000
 M8Z  H7   C13  C14  111.90  3.000
 M8Z  H6   C13  C14  109.52  3.000
 M8Z  N4   C13  C14  110.44  3.000
 M8Z  H9   C14  H8   106.35  3.000
 M8Z  H9   C14  C15  109.91  3.000
 M8Z  H8   C14  C15  111.00  3.000
 M8Z  H9   C14  C13  109.12  3.000
 M8Z  H8   C14  C13  109.58  3.000
 M8Z  C15  C14  C13  110.77  3.000
 M8Z  H11  C15  H10  107.00  3.000
 M8Z  H11  C15  C16  108.54  3.000
 M8Z  H10  C15  C16  109.93  3.000
 M8Z  H11  C15  C14  108.72  3.000
 M8Z  H10  C15  C14  110.57  3.000
 M8Z  C16  C15  C14  111.93  3.000
 M8Z  H12  C16  N5   107.41  3.000
 M8Z  H12  C16  C17  106.96  3.000
 M8Z  N5   C16  C17  114.14  3.000
 M8Z  H12  C16  C15  108.45  3.000
 M8Z  C17  C16  C15  109.13  3.000
 M8Z  N5   C16  C15  110.54  3.000
 M8Z  H14  C17  H13  107.92  3.000
 M8Z  H14  C17  N4   108.29  3.000
 M8Z  H13  C17  N4   109.85  3.000
 M8Z  H14  C17  C16  109.68  3.000
 M8Z  H13  C17  C16  110.88  3.000
 M8Z  N4   C17  C16  110.15  3.000
 M8Z  N6   C18  O    120.28  3.000
 M8Z  N6   C18  C10  118.04  3.000
 M8Z  O    C18  C10  121.68  3.000
 M8Z  H15  C19  C8   118.52  3.000
 M8Z  H15  C19  C4   120.61  3.000
 M8Z  C8   C19  C4   120.87  3.000
 M8Z  C23  C20  C22  107.31  3.000
 M8Z  C22  C20  C21  109.19  3.000
 M8Z  C23  C20  C21  108.56  3.000
 M8Z  C22  C20  C6   113.92  3.000
 M8Z  C21  C20  C6   109.90  3.000
 M8Z  C23  C20  C6   107.80  3.000
 M8Z  H18  C21  H17  108.54  3.000
 M8Z  H18  C21  H16  108.22  3.000
 M8Z  H17  C21  H16  108.40  3.000
 M8Z  H18  C21  C20  112.13  3.000
 M8Z  H17  C21  C20  110.61  3.000
 M8Z  H16  C21  C20  108.84  3.000
 M8Z  H21  C22  H20  107.33  3.000
 M8Z  H21  C22  H19  108.79  3.000
 M8Z  H20  C22  H19  108.46  3.000
 M8Z  H21  C22  C20  109.64  3.000
 M8Z  H20  C22  C20  110.10  3.000
 M8Z  H19  C22  C20  112.37  3.000
 M8Z  N7   C23  C20  180.00  3.000
 M8Z  H22  C7   C8   119.18  3.000
 M8Z  H22  C7   C6   121.05  3.000
 M8Z  C8   C7   C6   119.75  3.000
 M8Z  H25  C    H24  108.28  3.000
 M8Z  H25  C    H23  108.49  3.000
 M8Z  H24  C    H23  108.53  3.000
 M8Z  H25  C    C1   108.93  3.000
 M8Z  H24  C    C1   111.84  3.000
 M8Z  H23  C    C1   110.68  3.000
 M8Z  H26  N1   C9   112.39  3.000
 M8Z  H26  N1   C8   116.92  3.000
 M8Z  C9   N1   C8   130.63  3.000
 M8Z  C12  N3   C9   118.72  3.000
 M8Z  C12  N2   C11  115.94  3.000
 M8Z  H28  N6   H27  116.47  3.000
 M8Z  H28  N6   C18  118.67  3.000
 M8Z  H27  N6   C18  123.83  3.000
 M8Z  C17  N4   C13  113.43  3.000
 M8Z  C17  N4   C12  123.05  3.000
 M8Z  C13  N4   C12  123.09  3.000
 M8Z  H30  N5   H29  105.63  3.000
 M8Z  H30  N5   C16  110.63  3.000
 M8Z  H29  N5   C16  109.74  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
 M8Z  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 M8Z  CONST_02  C7   C8   C19  C4      0.00   0.0  0
 M8Z  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 M8Z  CONST_04  C8   C19  C4   C5      0.00   0.0  0
 M8Z  CONST_05  C19  C4   C5   C6      0.00   0.0  0
 M8Z  CONST_06  C19  C8   C7   C6      0.00   0.0  0
 M8Z  CONST_07  N2   C12  N3   C9      0.00   0.0  0
 M8Z  CONST_08  N2   C11  C10  C9      0.00   0.0  0
 M8Z  CONST_09  C12  N3   C9   C10     0.00   0.0  0
 M8Z  CONST_10  C12  N2   C11  C10     0.00   0.0  0
 M8Z  CONST_11  N3   C9   C10  C11     0.00   0.0  0
 M8Z  CONST_12  N3   C12  N2   C11     0.00   0.0  0
 M8Z  CONST_13  N4   C12  N3   C9    180.00   0.0  0
 M8Z  CONST_14  N4   C12  N2   C11   180.00   0.0  0
 M8Z  CONST_15  C6   C5   C4   C1    180.00   0.0  0
 M8Z  CONST_16  C8   C19  C4   C1    180.00   0.0  0
 M8Z  CONST_17  C20  C6   C5   C4    180.00   0.0  0
 M8Z  CONST_18  N1   C8   C19  C4    180.00   0.0  0
 M8Z  CONST_19  N1   C8   C7   C6    180.00   0.0  0
 M8Z  CONST_20  C20  C6   C7   C8    180.00   0.0  0
 M8Z  CONST_21  N1   C9   C10  C11   180.00   0.0  0
 M8Z  CONST_22  N1   C9   N3   C12   180.00   0.0  0
 M8Z  CONST_23  N3   C9   C10  C18   180.00   0.0  0
 M8Z  CONST_24  N2   C11  C10  C18   180.00   0.0  0
 M8Z  CONST_25  H22  C7   C6   C5    180.00   0.0  0
 M8Z  CONST_26  H15  C19  C4   C5    180.00   0.0  0
 M8Z  CONST_27  H5   C11  C10  C9    180.00   0.0  0
 M8Z  CONST_28  H4   C5   C4   C19   180.00   0.0  0
 M8Z  CONST_29  H27  N6   C18  C10     0.00   0.0  0
 M8Z  CONST_30  H28  N6   C18  C10   180.00   0.0  0
 M8Z  Var_01    C14  C13  N4   C12  -113.46  30.0  1
 M8Z  Var_02    C16  C17  N4   C12   111.64  30.0  1
 M8Z  Var_03    C16  C15  C14  C13    52.43  30.0  1
 M8Z  Var_04    N3   C12  N4   C13    -1.46  30.0  2
 M8Z  Var_05    N4   C13  C14  C15   -53.52  30.0  1
 M8Z  Var_06    N3   C9   N1   C8      0.28  30.0  2
 M8Z  Var_07    C7   C8   N1   C9     28.59  30.0  1
 M8Z  Var_08    C5   C4   C1   C2   -172.04  30.0  3
 M8Z  Var_09    C23  C20  C6   C5    -52.42  30.0  3
 M8Z  Var_10    O    C18  C10  C9      5.89  30.0  2
 M8Z  Var_11    H23  C    C1   C4   -178.73  30.0  3
 M8Z  Var_12    H1   C2   C1   C4    177.68  30.0  3
 M8Z  Var_13    H16  C21  C20  C6     61.62  30.0  3
 M8Z  Var_14    H19  C22  C20  C6     54.45  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
 M8Z  chir_01  C16  C15  N5  C17  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
 M8Z  plan-1  C1   0.020
 M8Z  plan-1  C4   0.020
 M8Z  plan-1  C5   0.020
 M8Z  plan-1  C6   0.020
 M8Z  plan-1  C8   0.020
 M8Z  plan-1  C19  0.020
 M8Z  plan-1  C20  0.020
 M8Z  plan-1  C7   0.020
 M8Z  plan-1  N1   0.020
 M8Z  plan-1  H4   0.020
 M8Z  plan-1  H15  0.020
 M8Z  plan-1  H22  0.020
 M8Z  plan-2  C9   0.020
 M8Z  plan-2  C10  0.020
 M8Z  plan-2  C11  0.020
 M8Z  plan-2  C12  0.020
 M8Z  plan-2  C18  0.020
 M8Z  plan-2  N1   0.020
 M8Z  plan-2  N3   0.020
 M8Z  plan-2  N2   0.020
 M8Z  plan-2  N4   0.020
 M8Z  plan-2  H5   0.020
 M8Z  plan-3  C10  0.020
 M8Z  plan-3  C18  0.020
 M8Z  plan-3  O    0.020
 M8Z  plan-3  N6   0.020
 M8Z  plan-3  H27  0.020
 M8Z  plan-3  H28  0.020

