# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 04:09:37 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[2,6-di(propan-2-yl)pyridin-4-yl]amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1cc(Nc2nc(ncc2C(N)=O)N3CCC[C@H](N)C3)cc(n1)C(C)C
#
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
 M92  M92  2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[2,6-di(propan-2-yl)pyridin-4-yl]amino]pyrimidine-5-carboxamide  ligand  60  29  .  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_M92
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
 M92  O    O  O     0  -0.516  -1.2602   3.9121   0.7538
 M92  C15  C  C     0   0.538  -0.0268   3.9611   0.8177
 M92  N4   N  NH2   0  -0.816   0.5932   5.0305   1.3390
 M92  C14  C  CR6   0  -0.309   0.8205   2.8631   0.3192
 M92  C13  C  CR16  0  -0.020   2.1764   3.0157   0.0583
 M92  N3   N  N     0  -0.485   2.9736   2.0658  -0.3785
 M92  C12  C  CR6   0   0.649   2.4055   0.8620  -0.5695
 M92  N5   N  NT    0  -0.473   3.1937  -0.1362  -1.0057
 M92  C20  C  CH2   0  -0.330   4.6366  -0.0127  -1.1013
 M92  C19  C  CH1   0  -0.105   5.3130  -0.7571   0.0587
 M92  N6   N  NH2   0  -0.792   5.0864  -0.1532   1.3638
 M92  C18  C  CH2   0  -0.440   4.8534  -2.2156   0.0558
 M92  C17  C  CH2   0  -0.461   3.3298  -2.3415   0.0334
 M92  C16  C  CH2   0  -0.322   2.7366  -1.5112  -1.0999
 M92  N2   N  N     0  -0.526   1.1083   0.5965  -0.3916
 M92  C11  C  CR6   0   0.574   0.3134   1.5657   0.0194
 M92  N1   N  NH1   0  -0.796  -1.0145   1.3284   0.1458
 M92  C5   C  CR6   0   0.494  -1.7446   0.1667  -0.0415
 M92  C4   C  CR16  0  -0.461  -3.1088   0.3132  -0.2850
 M92  C6   C  CR16  0  -0.402  -1.2327  -1.1294   0.0456
 M92  C7   C  CR6   0   0.256  -2.1006  -2.1994  -0.1185
 M92  C8   C  CH1   0  -0.288  -1.6437  -3.6335   0.0231
 M92  C10  C  CH3   0  -0.682  -0.1602  -3.8534  -0.2424
 M92  C9   C  CH3   0  -0.650  -2.0339  -4.1544   1.4088
 M92  N    N  N     0  -0.459  -3.4026  -2.0439  -0.3636
 M92  C3   C  CR6   0   0.277  -3.9010  -0.8143  -0.4426
 M92  C1   C  CH1   0  -0.332  -5.3826  -0.6868  -0.7058
 M92  C2   C  CH3   0  -0.648  -6.1060  -0.1243   0.5188
 M92  C    C  CH3   0  -0.653  -5.6711   0.1518  -1.9498
 M92  H1   H  HNH2  0   0.408   0.0365   5.7843   1.7073
 M92  H2   H  HNH2  0   0.413   1.5710   5.0408   1.5689
 M92  H3   H  HCR6  0   0.263   2.6514   3.9822   0.1942
 M92  H4   H  HCH2  0   0.241   4.9504  -0.4516  -2.0539
 M92  H5   H  HCH2  0   0.272   4.9198   1.0360  -1.1098
 M92  H6   H  HCH1  0   0.238   6.3905  -0.7322  -0.1320
 M92  H7   H  HNH2  0   0.345   5.3077   0.8344   1.3266
 M92  H8   H  HNH2  0   0.343   4.1056  -0.1997   1.6134
 M92  H10  H  HCH2  0   0.228   5.2599  -2.7043  -0.8348
 M92  H11  H  HCH2  0   0.241   5.2691  -2.7368   0.9208
 M92  H12  H  HCH2  0   0.247   3.0431  -3.3869  -0.1002
 M92  H13  H  HCH2  0   0.227   2.8927  -2.0243   0.9854
 M92  H14  H  HCH2  0   0.271   1.6515  -1.5398  -1.0955
 M92  H15  H  HCH2  0   0.244   3.0709  -1.9116  -2.0626
 M92  H16  H  HNH1  0   0.430  -1.5470   2.1785   0.3269
 M92  H17  H  HCR6  0   0.262  -3.5424   1.3032  -0.3651
 M92  H18  H  HCR6  0   0.270  -0.1876  -1.2923   0.2467
 M92  H19  H  HCH1  0   0.239  -2.2095  -4.2067  -0.7176
 M92  H20  H  HCH3  0   0.220   0.4671  -3.3893   0.5214
 M92  H21  H  HCH3  0   0.243   0.0664  -4.9200  -0.2362
 M92  H22  H  HCH3  0   0.235   0.1405  -3.4563  -1.2131
 M92  H23  H  HCH3  0   0.233  -3.1032  -4.0404   1.5870
 M92  H24  H  HCH3  0   0.231  -1.7892  -5.2132   1.5065
 M92  H25  H  HCH3  0   0.221  -1.5007  -3.6131   2.1932
 M92  H26  H  HCH1  0   0.242  -5.7486  -1.7013  -0.8843
 M92  H27  H  HCH3  0   0.221  -5.7858   0.8968   0.7352
 M92  H28  H  HCH3  0   0.232  -7.1840  -0.1038   0.3511
 M92  H29  H  HCH3  0   0.232  -5.9180  -0.7311   1.4055
 M92  H30  H  HCH3  0   0.234  -6.7411   0.1600  -2.1619
 M92  H31  H  HCH3  0   0.220  -5.3563   1.1890  -1.8196
 M92  H32  H  HCH3  0   0.234  -5.1597  -0.2452  -2.8274

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
 M92  C10  C8   single    1.523  0.020  1.523
 M92  C8   C7   single    1.512  0.020  1.512
 M92  C8   C9   single    1.531  0.020  1.531
 M92  N    C7   aromatic  1.334  0.020  1.334
 M92  N    C3   aromatic  1.329  0.020  1.329
 M92  C7   C6   aromatic  1.387  0.020  1.387
 M92  C    C1   single    1.528  0.020  1.528
 M92  C1   C3   single    1.510  0.020  1.510
 M92  C1   C2   single    1.530  0.020  1.530
 M92  C3   C4   aromatic  1.387  0.020  1.387
 M92  C6   C5   aromatic  1.396  0.020  1.396
 M92  C17  C18  single    1.529  0.020  1.529
 M92  C17  C16  single    1.525  0.020  1.525
 M92  C4   C5   aromatic  1.394  0.020  1.394
 M92  C5   N1   single    1.385  0.020  1.385
 M92  C18  C19  single    1.529  0.020  1.529
 M92  N1   C11  single    1.355  0.020  1.355
 M92  C16  N5   single    1.452  0.020  1.452
 M92  C11  N2   aromatic  1.319  0.020  1.319
 M92  C11  C14  aromatic  1.425  0.020  1.425
 M92  N2   C12  aromatic  1.336  0.020  1.336
 M92  C19  N6   single    1.456  0.020  1.456
 M92  C19  C20  single    1.535  0.020  1.535
 M92  O    C15  double    1.236  0.020  1.236
 M92  C14  C15  single    1.474  0.020  1.474
 M92  C14  C13  aromatic  1.389  0.020  1.389
 M92  N5   C12  single    1.345  0.020  1.345
 M92  N5   C20  single    1.451  0.020  1.451
 M92  C15  N4   single    1.342  0.020  1.342
 M92  C12  N3   aromatic  1.345  0.020  1.345
 M92  C13  N3   aromatic  1.315  0.020  1.315
 M92  N4   H1   single    0.860  0.020  1.020
 M92  N4   H2   single    0.860  0.020  1.020
 M92  C13  H3   single    0.930  0.020  1.080
 M92  C20  H4   single    0.970  0.020  1.090
 M92  C20  H5   single    0.970  0.020  1.090
 M92  C19  H6   single    0.970  0.020  1.090
 M92  N6   H7   single    0.890  0.020  1.040
 M92  N6   H8   single    0.890  0.020  1.040
 M92  C18  H10  single    0.970  0.020  1.090
 M92  C18  H11  single    0.970  0.020  1.090
 M92  C17  H12  single    0.970  0.020  1.090
 M92  C17  H13  single    0.970  0.020  1.090
 M92  C16  H14  single    0.970  0.020  1.090
 M92  C16  H15  single    0.970  0.020  1.090
 M92  N1   H16  single    0.860  0.020  1.020
 M92  C4   H17  single    0.930  0.020  1.080
 M92  C6   H18  single    0.930  0.020  1.080
 M92  C8   H19  single    0.970  0.020  1.090
 M92  C10  H20  single    0.970  0.020  1.090
 M92  C10  H21  single    0.970  0.020  1.090
 M92  C10  H22  single    0.970  0.020  1.090
 M92  C9   H23  single    0.970  0.020  1.090
 M92  C9   H24  single    0.970  0.020  1.090
 M92  C9   H25  single    0.970  0.020  1.090
 M92  C1   H26  single    0.970  0.020  1.090
 M92  C2   H27  single    0.970  0.020  1.090
 M92  C2   H28  single    0.970  0.020  1.090
 M92  C2   H29  single    0.970  0.020  1.090
 M92  C    H30  single    0.970  0.020  1.090
 M92  C    H31  single    0.970  0.020  1.090
 M92  C    H32  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
 M92  C14  C15  N4   117.36  3.000
 M92  N4   C15  O    120.85  3.000
 M92  C14  C15  O    121.79  3.000
 M92  H2   N4   H1   116.54  3.000
 M92  H2   N4   C15  123.16  3.000
 M92  H1   N4   C15  118.91  3.000
 M92  C11  C14  C13  114.07  3.000
 M92  C13  C14  C15  122.88  3.000
 M92  C11  C14  C15  123.01  3.000
 M92  H3   C13  N3   114.81  3.000
 M92  H3   C13  C14  120.09  3.000
 M92  N3   C13  C14  125.09  3.000
 M92  C12  N3   C13  115.96  3.000
 M92  N2   C12  N5   117.70  3.000
 M92  N5   C12  N3   117.58  3.000
 M92  N2   C12  N3   124.69  3.000
 M92  C16  N5   C20  112.91  3.000
 M92  C20  N5   C12  122.75  3.000
 M92  C16  N5   C12  122.65  3.000
 M92  H5   C20  H4   107.78  3.000
 M92  H5   C20  C19  111.04  3.000
 M92  H4   C20  C19  109.68  3.000
 M92  H5   C20  N5   109.99  3.000
 M92  H4   C20  N5   107.95  3.000
 M92  C19  C20  N5   110.31  3.000
 M92  H6   C19  C18  108.49  3.000
 M92  H6   C19  N6   107.46  3.000
 M92  C18  C19  N6   110.52  3.000
 M92  H6   C19  C20  106.92  3.000
 M92  N6   C19  C20  114.06  3.000
 M92  C18  C19  C20  109.18  3.000
 M92  H8   N6   H7   105.38  3.000
 M92  H8   N6   C19  110.64  3.000
 M92  H7   N6   C19  109.73  3.000
 M92  H11  C18  H10  106.86  3.000
 M92  H11  C18  C17  110.59  3.000
 M92  H10  C18  C17  108.75  3.000
 M92  H11  C18  C19  109.84  3.000
 M92  H10  C18  C19  108.42  3.000
 M92  C17  C18  C19  112.21  3.000
 M92  H13  C17  H12  106.19  3.000
 M92  H13  C17  C16  109.47  3.000
 M92  H12  C17  C16  109.16  3.000
 M92  H13  C17  C18  111.18  3.000
 M92  H12  C17  C18  110.01  3.000
 M92  C16  C17  C18  110.72  3.000
 M92  H15  C16  H14  107.40  3.000
 M92  H15  C16  C17  109.60  3.000
 M92  H14  C16  C17  111.81  3.000
 M92  H15  C16  N5   107.89  3.000
 M92  H14  C16  N5   109.84  3.000
 M92  C17  C16  N5   110.17  3.000
 M92  C11  N2   C12  118.73  3.000
 M92  N1   C11  N2   119.40  3.000
 M92  N2   C11  C14  121.33  3.000
 M92  N1   C11  C14  119.26  3.000
 M92  H16  N1   C5   116.63  3.000
 M92  H16  N1   C11  112.49  3.000
 M92  C5   N1   C11  130.63  3.000
 M92  C6   C5   C4   117.86  3.000
 M92  C4   C5   N1   116.85  3.000
 M92  C6   C5   N1   125.24  3.000
 M92  H17  C4   C3   120.38  3.000
 M92  H17  C4   C5   120.04  3.000
 M92  C3   C4   C5   119.58  3.000
 M92  H18  C6   C7   120.84  3.000
 M92  H18  C6   C5   120.53  3.000
 M92  C7   C6   C5   118.63  3.000
 M92  N    C7   C8   115.00  3.000
 M92  N    C7   C6   122.85  3.000
 M92  C8   C7   C6   122.10  3.000
 M92  H19  C8   C9   107.62  3.000
 M92  H19  C8   C10  108.06  3.000
 M92  C9   C8   C10  110.91  3.000
 M92  H19  C8   C7   106.10  3.000
 M92  C9   C8   C7   109.30  3.000
 M92  C10  C8   C7   114.52  3.000
 M92  H22  C10  H21  107.68  3.000
 M92  H22  C10  H20  108.02  3.000
 M92  H21  C10  H20  107.00  3.000
 M92  H22  C10  C8   111.78  3.000
 M92  H21  C10  C8   110.04  3.000
 M92  H20  C10  C8   112.10  3.000
 M92  H25  C9   H24  107.90  3.000
 M92  H25  C9   H23  108.04  3.000
 M92  H24  C9   H23  107.87  3.000
 M92  H25  C9   C8   110.92  3.000
 M92  H24  C9   C8   110.74  3.000
 M92  H23  C9   C8   111.24  3.000
 M92  C3   N    C7   118.99  3.000
 M92  C1   C3   N    117.15  3.000
 M92  C1   C3   C4   120.76  3.000
 M92  N    C3   C4   122.08  3.000
 M92  H26  C1   C    108.26  3.000
 M92  H26  C1   C2   108.28  3.000
 M92  C    C1   C2   111.15  3.000
 M92  H26  C1   C3   106.18  3.000
 M92  C2   C1   C3   110.82  3.000
 M92  C    C1   C3   111.93  3.000
 M92  H29  C2   H28  107.79  3.000
 M92  H29  C2   H27  107.97  3.000
 M92  H28  C2   H27  107.62  3.000
 M92  H29  C2   C1   111.39  3.000
 M92  H28  C2   C1   110.55  3.000
 M92  H27  C2   C1   111.35  3.000
 M92  H32  C    H31  107.86  3.000
 M92  H32  C    H30  107.83  3.000
 M92  H31  C    H30  107.39  3.000
 M92  H32  C    C1   111.52  3.000
 M92  H31  C    C1   111.71  3.000
 M92  H30  C    C1   110.34  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
 M92  CONST_01  C12  N2   C11  C14     0.00   0.0  0
 M92  CONST_02  C12  N3   C13  C14     0.00   0.0  0
 M92  CONST_03  N2   C11  C14  C13     0.00   0.0  0
 M92  CONST_04  N2   C12  N3   C13     0.00   0.0  0
 M92  CONST_05  C11  N2   C12  N3      0.00   0.0  0
 M92  CONST_06  C11  C14  C13  N3      0.00   0.0  0
 M92  CONST_07  N    C7   C6   C5      0.00   0.0  0
 M92  CONST_08  N    C3   C4   C5      0.00   0.0  0
 M92  CONST_09  C7   N    C3   C4      0.00   0.0  0
 M92  CONST_10  C7   C6   C5   C4      0.00   0.0  0
 M92  CONST_11  C3   N    C7   C6      0.00   0.0  0
 M92  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 M92  CONST_13  N5   C12  N3   C13   180.00   0.0  0
 M92  CONST_14  C11  N2   C12  N5    180.00   0.0  0
 M92  CONST_15  N2   C11  C14  C15   180.00   0.0  0
 M92  CONST_16  N3   C13  C14  C15   180.00   0.0  0
 M92  CONST_17  N1   C11  C14  C13   180.00   0.0  0
 M92  CONST_18  N1   C11  N2   C12   180.00   0.0  0
 M92  CONST_19  C7   C6   C5   N1    180.00   0.0  0
 M92  CONST_20  C3   C4   C5   N1    180.00   0.0  0
 M92  CONST_21  C8   C7   C6   C5    180.00   0.0  0
 M92  CONST_22  C1   C3   C4   C5    180.00   0.0  0
 M92  CONST_23  C1   C3   N    C7    180.00   0.0  0
 M92  CONST_24  C3   N    C7   C8    180.00   0.0  0
 M92  CONST_25  H3   C13  N3   C12   180.00   0.0  0
 M92  CONST_26  H18  C6   C5   C4    180.00   0.0  0
 M92  CONST_27  H17  C4   C5   C6    180.00   0.0  0
 M92  CONST_28  H1   N4   C15  C14   180.00   0.0  0
 M92  CONST_29  H2   N4   C15  C14     0.00   0.0  0
 M92  Var_01    C16  N5   C12  N3    172.61  30.0  1
 M92  Var_02    C17  C16  N5   C12  -105.04  30.0  1
 M92  Var_03    C19  C20  N5   C12   103.59  30.0  1
 M92  Var_04    C18  C17  C16  N5    -54.11  30.0  1
 M92  Var_05    C16  C17  C18  C19    51.87  30.0  1
 M92  Var_06    C5   N1   C11  C14  -177.90  30.0  3
 M92  Var_07    C6   C5   N1   C11    23.96  30.0  2
 M92  Var_08    C11  C14  C15  O     -14.80  30.0  2
 M92  Var_09    C    C1   C3   C4     56.76  30.0  2
 M92  Var_10    C10  C8   C7   C6    -25.11  30.0  3
 M92  Var_11    H20  C10  C8   C7     67.68  30.0  3
 M92  Var_12    H23  C9   C8   C7     55.35  30.0  3
 M92  Var_13    H30  C    C1   C3    175.42  30.0  3
 M92  Var_14    H27  C2   C1   C3     64.65  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
 M92  chir_01  C19  C18  N6  C20  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
 M92  plan-1  C15  0.020
 M92  plan-1  C14  0.020
 M92  plan-1  C13  0.020
 M92  plan-1  N3   0.020
 M92  plan-1  C12  0.020
 M92  plan-1  N5   0.020
 M92  plan-1  N2   0.020
 M92  plan-1  C11  0.020
 M92  plan-1  N1   0.020
 M92  plan-1  H3   0.020
 M92  plan-2  N1   0.020
 M92  plan-2  C5   0.020
 M92  plan-2  C4   0.020
 M92  plan-2  C6   0.020
 M92  plan-2  C7   0.020
 M92  plan-2  C8   0.020
 M92  plan-2  N    0.020
 M92  plan-2  C3   0.020
 M92  plan-2  C1   0.020
 M92  plan-2  H17  0.020
 M92  plan-2  H18  0.020
 M92  plan-3  O    0.020
 M92  plan-3  C15  0.020
 M92  plan-3  N4   0.020
 M92  plan-3  C14  0.020
 M92  plan-3  H1   0.020
 M92  plan-3  H2   0.020

