# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:09:30 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-[(3~{R})-3-(4-azanylpyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCC[C@H](C1)n2ncc3c(N)ncnc23
#
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
 J3H  J3H  1-[(3~{R})-3-(4-azanylpyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]propan-1-one  ligand  38  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J3H
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
 J3H  C1   C  CR56  0   0.590  -1.8981  -0.1760   0.2125
 J3H  C2   C  CR56  0  -0.249  -3.0622   0.2513  -0.4275
 J3H  C3   C  CR6   0   0.469  -4.2135  -0.5362  -0.2023
 J3H  N    N  N     0  -0.483  -4.1091  -1.6096   0.5853
 J3H  C    C  CR16  0   0.060  -2.9250  -1.8941   1.1280
 J3H  O    O  O     0  -0.500   2.9709  -1.7115  -0.9720
 J3H  C10  C  C     0   0.566   3.4406  -0.6872  -0.4956
 J3H  C11  C  CH2   0  -0.596   4.8339  -0.6733   0.1058
 J3H  C12  C  CH3   0  -0.650   5.5288  -2.0212   0.0262
 J3H  C4   C  CR15  0  -0.085  -2.6721   1.4107  -1.1366
 J3H  C5   C  CH1   0  -0.094   0.4565   0.6811   0.2834
 J3H  C6   C  CH2   0  -0.441   0.8278   1.9294   1.0797
 J3H  C7   C  CH2   0  -0.441   2.3122   1.9179   1.4304
 J3H  C8   C  CH2   0  -0.326   3.1661   1.6954   0.1887
 J3H  C9   C  CH2   0  -0.308   1.3718   0.5169  -0.9339
 J3H  N1   N  N     0  -0.464  -1.7841  -1.2480   1.0036
 J3H  N2   N  NR5   0  -0.382  -0.9312   0.6991  -0.1246
 J3H  N3   N  N     0  -0.255  -1.4017   1.6575  -0.9414
 J3H  N4   N  NH2   0  -0.813  -5.3965  -0.2557  -0.7444
 J3H  N5   N  NT    0  -0.459   2.7522   0.4814  -0.4963
 J3H  H1   H  HCR6  0   0.254  -2.9062  -2.7782   1.7566
 J3H  H2   H  HCH2  0   0.268   5.4376   0.0853  -0.3997
 J3H  H3   H  HCH2  0   0.264   4.7703  -0.3518   1.1492
 J3H  H4   H  HCH3  0   0.227   5.6537  -2.3525  -1.0039
 J3H  H5   H  HCH3  0   0.231   6.5199  -1.9479   0.4734
 J3H  H6   H  HCH3  0   0.227   4.9791  -2.7928   0.5634
 J3H  H7   H  HCR5  0   0.274  -3.2625   2.0566  -1.7685
 J3H  H8   H  HCH1  0   0.272   0.5651  -0.2008   0.9197
 J3H  H9   H  HCH2  0   0.236   0.5966   2.8176   0.4849
 J3H  H10  H  HCH2  0   0.254   0.2204   1.9826   1.9852
 J3H  H11  H  HCH2  0   0.249   2.5923   2.8639   1.8968
 J3H  H12  H  HCH2  0   0.233   2.5211   1.1267   2.1569
 J3H  H13  H  HCH2  0   0.249   3.0453   2.5349  -0.5026
 J3H  H14  H  HCH2  0   0.278   4.2198   1.6535   0.4478
 J3H  H15  H  HCH2  0   0.274   1.1300  -0.3940  -1.4747
 J3H  H16  H  HCH2  0   0.254   1.2350   1.3616  -1.6156
 J3H  H17  H  HNH2  0   0.414  -5.5379   0.5537  -1.3223
 J3H  H18  H  HNH2  0   0.407  -6.1933  -0.8346  -0.5404

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
 J3H  C    N1   aromatic  1.317  0.020  1.317
 J3H  C    N    aromatic  1.333  0.020  1.333
 J3H  N1   C1   aromatic  1.337  0.020  1.337
 J3H  N    C3   aromatic  1.335  0.020  1.335
 J3H  C1   C2   aromatic  1.395  0.020  1.395
 J3H  C1   N2   aromatic  1.347  0.020  1.347
 J3H  C3   N4   single    1.331  0.020  1.331
 J3H  C3   C2   aromatic  1.413  0.020  1.413
 J3H  O    C10  double    1.223  0.020  1.223
 J3H  C2   C4   aromatic  1.414  0.020  1.414
 J3H  C5   N2   single    1.447  0.020  1.447
 J3H  C5   C6   single    1.526  0.020  1.526
 J3H  C5   C9   single    1.532  0.020  1.532
 J3H  N2   N3   aromatic  1.344  0.020  1.344
 J3H  C7   C6   single    1.525  0.020  1.525
 J3H  C7   C8   single    1.523  0.020  1.523
 J3H  C10  C11  single    1.518  0.020  1.518
 J3H  C10  N5   single    1.356  0.020  1.356
 J3H  C11  C12  single    1.519  0.020  1.519
 J3H  N5   C9   single    1.449  0.020  1.449
 J3H  N5   C8   single    1.454  0.020  1.454
 J3H  C4   N3   aromatic  1.309  0.020  1.309
 J3H  C    H1   single    0.930  0.020  1.080
 J3H  C11  H2   single    0.970  0.020  1.090
 J3H  C11  H3   single    0.970  0.020  1.090
 J3H  C12  H4   single    0.970  0.020  1.090
 J3H  C12  H5   single    0.970  0.020  1.090
 J3H  C12  H6   single    0.970  0.020  1.090
 J3H  C4   H7   single    0.930  0.020  1.080
 J3H  C5   H8   single    0.970  0.020  1.090
 J3H  C6   H9   single    0.970  0.020  1.090
 J3H  C6   H10  single    0.970  0.020  1.090
 J3H  C7   H11  single    0.970  0.020  1.090
 J3H  C7   H12  single    0.970  0.020  1.090
 J3H  C8   H13  single    0.970  0.020  1.090
 J3H  C8   H14  single    0.970  0.020  1.090
 J3H  C9   H15  single    0.970  0.020  1.090
 J3H  C9   H16  single    0.970  0.020  1.090
 J3H  N4   H17  single    0.860  0.020  1.020
 J3H  N4   H18  single    0.860  0.020  1.020

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
 J3H  N2   C1   N1   127.42  3.000
 J3H  N2   C1   C2   106.57  3.000
 J3H  N1   C1   C2   126.01  3.000
 J3H  C4   C2   C3   139.61  3.000
 J3H  C4   C2   C1   104.53  3.000
 J3H  C3   C2   C1   115.85  3.000
 J3H  N4   C3   N    118.62  3.000
 J3H  N4   C3   C2   122.81  3.000
 J3H  N    C3   C2   118.57  3.000
 J3H  C    N    C3   118.76  3.000
 J3H  H1   C    N1   116.07  3.000
 J3H  H1   C    N    115.16  3.000
 J3H  N1   C    N    128.77  3.000
 J3H  N5   C10  C11  117.28  3.000
 J3H  N5   C10  O    121.75  3.000
 J3H  C11  C10  O    120.97  3.000
 J3H  H3   C11  H2   105.62  3.000
 J3H  H3   C11  C12  109.72  3.000
 J3H  H2   C11  C12  109.82  3.000
 J3H  H3   C11  C10  109.11  3.000
 J3H  H2   C11  C10  109.27  3.000
 J3H  C12  C11  C10  113.03  3.000
 J3H  H6   C12  H5   107.71  3.000
 J3H  H6   C12  H4   107.99  3.000
 J3H  H5   C12  H4   107.72  3.000
 J3H  H6   C12  C11  111.85  3.000
 J3H  H5   C12  C11  109.57  3.000
 J3H  H4   C12  C11  111.84  3.000
 J3H  H7   C4   N3   120.36  3.000
 J3H  H7   C4   C2   129.30  3.000
 J3H  N3   C4   C2   110.34  3.000
 J3H  H8   C5   N2   105.64  3.000
 J3H  H8   C5   C9   108.47  3.000
 J3H  N2   C5   C9   110.51  3.000
 J3H  H8   C5   C6   109.39  3.000
 J3H  C9   C5   C6   110.91  3.000
 J3H  N2   C5   C6   111.74  3.000
 J3H  H10  C6   H9   107.08  3.000
 J3H  H10  C6   C7   110.56  3.000
 J3H  H9   C6   C7   109.69  3.000
 J3H  H10  C6   C5   109.71  3.000
 J3H  H9   C6   C5   109.21  3.000
 J3H  C7   C6   C5   110.52  3.000
 J3H  H12  C7   H11  107.10  3.000
 J3H  H12  C7   C8   109.18  3.000
 J3H  H11  C7   C8   109.34  3.000
 J3H  H12  C7   C6   110.11  3.000
 J3H  H11  C7   C6   109.97  3.000
 J3H  C8   C7   C6   111.05  3.000
 J3H  H14  C8   H13  106.70  3.000
 J3H  H14  C8   N5   110.88  3.000
 J3H  H13  C8   N5   108.15  3.000
 J3H  H14  C8   C7   110.80  3.000
 J3H  H13  C8   C7   109.94  3.000
 J3H  N5   C8   C7   110.27  3.000
 J3H  H16  C9   H15  108.02  3.000
 J3H  H16  C9   N5   109.05  3.000
 J3H  H15  C9   N5   109.99  3.000
 J3H  H16  C9   C5   109.73  3.000
 J3H  H15  C9   C5   110.64  3.000
 J3H  N5   C9   C5   109.39  3.000
 J3H  C    N1   C1   112.04  3.000
 J3H  N3   N2   C5   121.06  3.000
 J3H  N3   N2   C1   111.35  3.000
 J3H  C5   N2   C1   127.59  3.000
 J3H  N2   N3   C4   107.21  3.000
 J3H  H18  N4   H17  117.96  3.000
 J3H  H18  N4   C3   120.01  3.000
 J3H  H17  N4   C3   121.95  3.000
 J3H  C9   N5   C8   113.15  3.000
 J3H  C8   N5   C10  125.07  3.000
 J3H  C9   N5   C10  120.33  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
 J3H  CONST_01  N    C    N1   C1      0.00   0.0  0
 J3H  CONST_02  N    C3   C2   C1      0.00   0.0  0
 J3H  CONST_03  N3   C4   C2   C1      0.00   0.0  0
 J3H  CONST_04  C4   N3   N2   C1      0.00   0.0  0
 J3H  CONST_05  C    N1   C1   C2      0.00   0.0  0
 J3H  CONST_06  N3   N2   C1   C2      0.00   0.0  0
 J3H  CONST_07  C    N    C3   C2      0.00   0.0  0
 J3H  CONST_08  N2   N3   C4   C2      0.00   0.0  0
 J3H  CONST_09  N1   C    N    C3      0.00   0.0  0
 J3H  CONST_10  N1   C1   C2   C3      0.00   0.0  0
 J3H  CONST_11  N2   C1   C2   C3    180.00   0.0  0
 J3H  CONST_12  N3   C4   C2   C3    180.00   0.0  0
 J3H  CONST_13  C4   C2   C3   N     180.00   0.0  0
 J3H  CONST_14  N2   C1   N1   C     180.00   0.0  0
 J3H  CONST_15  N1   C1   C2   C4    180.00   0.0  0
 J3H  CONST_16  N2   C1   C2   C4      0.00   0.0  0
 J3H  CONST_17  N3   N2   C1   N1    180.00   0.0  0
 J3H  CONST_18  C5   N2   C1   C2    180.00   0.0  0
 J3H  CONST_19  C5   N2   N3   C4    180.00   0.0  0
 J3H  CONST_20  N1   C1   N2   C5      0.00   0.0  0
 J3H  CONST_21  N4   C3   C2   C1    180.00   0.0  0
 J3H  CONST_22  N4   C3   N    C     180.00   0.0  0
 J3H  CONST_23  N4   C3   C2   C4      0.00   0.0  0
 J3H  CONST_24  H1   C    N1   C1    180.00   0.0  0
 J3H  CONST_25  H7   C4   C2   C1    180.00   0.0  0
 J3H  CONST_26  C9   N5   C10  O       0.00   0.0  0
 J3H  CONST_27  C8   N5   C10  O     180.00   0.0  0
 J3H  CONST_28  C9   N5   C10  C11   180.00   0.0  0
 J3H  CONST_29  C8   N5   C10  C11     0.00   0.0  0
 J3H  CONST_30  H17  N4   C3   C2      0.00   0.0  0
 J3H  CONST_31  H18  N4   C3   C2    180.00   0.0  0
 J3H  Var_01    C8   C7   C6   C5     52.32  30.0  1
 J3H  Var_02    C8   N5   C9   C5    -60.71  30.0  1
 J3H  Var_03    N5   C8   C7   C6    -54.89  30.0  1
 J3H  Var_04    C9   N5   C8   C7     60.27  30.0  1
 J3H  Var_05    N5   C10  C11  C12  -178.61  30.0  1
 J3H  Var_06    H4   C12  C11  C10    60.72  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
 J3H  chir_01  C5  N2  C6  C9  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
 J3H  plan-1  C1   0.020
 J3H  plan-1  C2   0.020
 J3H  plan-1  C3   0.020
 J3H  plan-1  N    0.020
 J3H  plan-1  C    0.020
 J3H  plan-1  C4   0.020
 J3H  plan-1  C5   0.020
 J3H  plan-1  N1   0.020
 J3H  plan-1  N2   0.020
 J3H  plan-1  N3   0.020
 J3H  plan-1  N4   0.020
 J3H  plan-1  H1   0.020
 J3H  plan-1  H7   0.020
 J3H  plan-2  C3   0.020
 J3H  plan-2  N4   0.020
 J3H  plan-2  H17  0.020
 J3H  plan-2  H18  0.020
 J3H  plan-3  O    0.020
 J3H  plan-3  C10  0.020
 J3H  plan-3  C11  0.020
 J3H  plan-3  C8   0.020
 J3H  plan-3  C9   0.020
 J3H  plan-3  N5   0.020

