# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:47:15 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-[(3~{R})-3-[4-azanyl-3-(4-hydroxyphenyl)pyrazolo[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)n2nc(c3ccc(O)cc3)c4c(N)ncnc24
#
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
 J0E  J0E  1-[(3~{R})-3-[4-azanyl-3-(4-hydroxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one  ligand  49  27  .  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_J0E
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
 J0E  N1   N  NR5   0  -0.384  -0.4429   0.4982   0.3304
 J0E  N2   N  NT    0  -0.459  -3.7498  -1.1265  -0.0854
 J0E  C3   C  CH1   0  -0.095  -1.8234   0.1818   0.6276
 J0E  N4   N  N     0  -0.466  -0.5453   2.8787   0.0434
 J0E  C5   C  CH2   0  -0.439  -3.4215  -0.7833   2.3075
 J0E  C6   C  CH2   0  -0.327  -3.9086  -1.7376   1.2245
 J0E  C8   C  CH2   0  -0.595  -6.1779  -0.9247  -0.3883
 J0E  C11  C  CR5   0   0.274   1.6458   0.1019   0.0512
 J0E  C12  C  CR6   0   0.010   2.8702  -0.7000  -0.0260
 J0E  C13  C  CR16  0  -0.318   4.0378  -0.2943   0.6172
 J0E  C14  C  CR16  0  -0.367   5.1893  -1.0636   0.5663
 J0E  C15  C  CR6   0   0.353   5.1909  -2.2690  -0.1310
 J0E  C16  C  CR16  0  -0.326   4.0248  -2.6937  -0.7673
 J0E  C17  C  CR16  0  -0.270   2.8830  -1.9162  -0.7109
 J0E  C18  C  CR16  0   0.057   0.2662   3.8766  -0.2385
 J0E  C    C  CR6   0   0.433   2.2019   2.6582  -0.4657
 J0E  O    O  O     0  -0.501  -4.5466   0.0077  -1.8638
 J0E  C1   C  CR56  0  -0.274   1.4636   1.5038  -0.1130
 J0E  C10  C  CH2   0  -0.309  -2.3720  -0.8117  -0.4013
 J0E  C2   C  CR56  0   0.585   0.0957   1.7074   0.0895
 J0E  C4   C  CH2   0  -0.442  -1.9799  -0.3586   2.0475
 J0E  C7   C  C     0   0.566  -4.7602  -0.6318  -0.8426
 J0E  C9   C  CH3   0  -0.650  -7.2292  -0.3623  -1.3291
 J0E  N3   N  N     0  -0.280   0.4911  -0.4655   0.3119
 J0E  N5   N  N     0  -0.478   1.5717   3.8356  -0.4978
 J0E  O1   O  OH1   0  -0.627   6.2771  -3.0571  -0.2203
 J0E  H1   H  HCH1  0   0.272  -2.3717   1.1213   0.5301
 J0E  H2   H  HCH2  0   0.232  -4.0742   0.0941   2.3293
 J0E  H3   H  HCH2  0   0.249  -3.4976  -1.2656   3.2835
 J0E  H4   H  HCH2  0   0.278  -4.9412  -2.0256   1.3962
 J0E  H5   H  HCH2  0   0.249  -3.3180  -2.6589   1.2461
 J0E  H6   H  HCH2  0   0.268  -6.3066  -2.0059  -0.2887
 J0E  H7   H  HCH2  0   0.264  -6.3290  -0.5176   0.6156
 J0E  H8   H  HCR6  0   0.274   4.0511   0.6219   1.1954
 J0E  H9   H  HCR6  0   0.277   6.0817  -0.7258   1.0806
 J0E  H10  H  HCR6  0   0.268   4.0204  -3.6302  -1.3112
 J0E  H11  H  HCR6  0   0.256   1.9887  -2.2544  -1.2183
 J0E  H12  H  HCR6  0   0.254  -0.1827   4.8639  -0.2766
 J0E  H13  H  HNH2  0   0.406   3.9407   3.4876  -1.0860
 J0E  H14  H  HNH2  0   0.414   3.9980   1.7792  -0.9134
 J0E  H15  H  HCH2  0   0.254  -1.7822  -1.7328  -0.3725
 J0E  H16  H  HCH2  0   0.275  -2.3030  -0.4020  -1.4056
 J0E  H17  H  HCH2  0   0.237  -1.3154  -1.2179   2.1741
 J0E  H18  H  HCH2  0   0.254  -1.6665   0.4000   2.7676
 J0E  H19  H  HCH3  0   0.227  -7.1725   0.7234  -1.3943
 J0E  H20  H  HCH3  0   0.227  -7.1300  -0.7646  -2.3365
 J0E  H21  H  HCH3  0   0.231  -8.2231  -0.6211  -0.9654
 J0E  H22  H  HOH1  0   0.477   7.0184  -2.6669   0.2564
 J0E  N    N  NH2   0  -0.815   3.5010   2.6402  -0.7675

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
 J0E  O1   C15  single    1.345  0.020  1.345
 J0E  C15  C16  aromatic  1.395  0.020  1.395
 J0E  C15  C14  aromatic  1.393  0.020  1.393
 J0E  C16  C17  aromatic  1.383  0.020  1.383
 J0E  C14  C13  aromatic  1.386  0.020  1.386
 J0E  C17  C12  aromatic  1.396  0.020  1.396
 J0E  C13  C12  aromatic  1.393  0.020  1.393
 J0E  C12  C11  single    1.466  0.020  1.466
 J0E  C9   C8   single    1.519  0.020  1.519
 J0E  C11  N3   aromatic  1.313  0.020  1.313
 J0E  C11  C1   aromatic  1.423  0.020  1.423
 J0E  N3   N1   aromatic  1.342  0.020  1.342
 J0E  C10  N2   single    1.448  0.020  1.448
 J0E  C10  C3   single    1.532  0.020  1.532
 J0E  C6   N2   single    1.454  0.020  1.454
 J0E  C6   C5   single    1.523  0.020  1.523
 J0E  C8   C7   single    1.517  0.020  1.517
 J0E  N2   C7   single    1.356  0.020  1.356
 J0E  C7   O    double    1.224  0.020  1.224
 J0E  N    C    single    1.334  0.020  1.334
 J0E  C1   C    aromatic  1.415  0.020  1.415
 J0E  C1   C2   aromatic  1.398  0.020  1.398
 J0E  N1   C3   single    1.447  0.020  1.447
 J0E  N1   C2   aromatic  1.346  0.020  1.346
 J0E  C3   C4   single    1.527  0.020  1.527
 J0E  C4   C5   single    1.525  0.020  1.525
 J0E  C    N5   aromatic  1.336  0.020  1.336
 J0E  C2   N4   aromatic  1.336  0.020  1.336
 J0E  N5   C18  aromatic  1.332  0.020  1.332
 J0E  N4   C18  aromatic  1.317  0.020  1.317
 J0E  C3   H1   single    0.970  0.020  1.090
 J0E  C5   H2   single    0.970  0.020  1.090
 J0E  C5   H3   single    0.970  0.020  1.090
 J0E  C6   H4   single    0.970  0.020  1.090
 J0E  C6   H5   single    0.970  0.020  1.090
 J0E  C8   H6   single    0.970  0.020  1.090
 J0E  C8   H7   single    0.970  0.020  1.090
 J0E  C13  H8   single    0.930  0.020  1.080
 J0E  C14  H9   single    0.930  0.020  1.080
 J0E  C16  H10  single    0.930  0.020  1.080
 J0E  C17  H11  single    0.930  0.020  1.080
 J0E  C18  H12  single    0.930  0.020  1.080
 J0E  N    H13  single    0.860  0.020  1.020
 J0E  N    H14  single    0.860  0.020  1.020
 J0E  C10  H15  single    0.970  0.020  1.090
 J0E  C10  H16  single    0.970  0.020  1.090
 J0E  C4   H17  single    0.970  0.020  1.090
 J0E  C4   H18  single    0.970  0.020  1.090
 J0E  C9   H19  single    0.970  0.020  1.090
 J0E  C9   H20  single    0.970  0.020  1.090
 J0E  C9   H21  single    0.970  0.020  1.090
 J0E  O1   H22  single    0.850  0.020  0.980

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
 J0E  N3   N1   C2   111.36  3.000
 J0E  C2   N1   C3   127.96  3.000
 J0E  N3   N1   C3   120.64  3.000
 J0E  C7   N2   C10  120.51  3.000
 J0E  C7   N2   C6   125.10  3.000
 J0E  C10  N2   C6   113.07  3.000
 J0E  H1   C3   C4   109.63  3.000
 J0E  H1   C3   C10  108.55  3.000
 J0E  C4   C3   C10  111.00  3.000
 J0E  H1   C3   N1   105.81  3.000
 J0E  C4   C3   N1   111.47  3.000
 J0E  C10  C3   N1   110.21  3.000
 J0E  C2   N4   C18  112.09  3.000
 J0E  H3   C5   H2   107.16  3.000
 J0E  H3   C5   C4   109.96  3.000
 J0E  H2   C5   C4   110.13  3.000
 J0E  H3   C5   C6   109.67  3.000
 J0E  H2   C5   C6   109.02  3.000
 J0E  C4   C5   C6   110.82  3.000
 J0E  H5   C6   H4   106.66  3.000
 J0E  H5   C6   C5   109.92  3.000
 J0E  H4   C6   C5   110.97  3.000
 J0E  H5   C6   N2   108.22  3.000
 J0E  H4   C6   N2   110.97  3.000
 J0E  C5   C6   N2   110.01  3.000
 J0E  H7   C8   H6   105.55  3.000
 J0E  H7   C8   C9   109.58  3.000
 J0E  H6   C8   C9   109.95  3.000
 J0E  H7   C8   C7   109.40  3.000
 J0E  H6   C8   C7   109.16  3.000
 J0E  C9   C8   C7   112.94  3.000
 J0E  N3   C11  C1   109.64  3.000
 J0E  C1   C11  C12  129.78  3.000
 J0E  N3   C11  C12  120.58  3.000
 J0E  C17  C12  C13  118.20  3.000
 J0E  C13  C12  C11  121.09  3.000
 J0E  C17  C12  C11  120.68  3.000
 J0E  H8   C13  C14  118.61  3.000
 J0E  H8   C13  C12  120.19  3.000
 J0E  C14  C13  C12  121.17  3.000
 J0E  H9   C14  C15  120.42  3.000
 J0E  H9   C14  C13  119.58  3.000
 J0E  C15  C14  C13  119.99  3.000
 J0E  O1   C15  C16  117.81  3.000
 J0E  C16  C15  C14  119.41  3.000
 J0E  O1   C15  C14  122.78  3.000
 J0E  H10  C16  C17  120.23  3.000
 J0E  H10  C16  C15  119.72  3.000
 J0E  C17  C16  C15  120.05  3.000
 J0E  H11  C17  C16  119.18  3.000
 J0E  H11  C17  C12  119.65  3.000
 J0E  C16  C17  C12  121.17  3.000
 J0E  H12  C18  N5   115.26  3.000
 J0E  H12  C18  N4   116.24  3.000
 J0E  N5   C18  N4   128.50  3.000
 J0E  N5   C    C1   118.62  3.000
 J0E  N5   C    N    117.76  3.000
 J0E  C1   C    N    123.62  3.000
 J0E  C2   C1   C    115.33  3.000
 J0E  C2   C1   C11  104.60  3.000
 J0E  C    C1   C11  139.96  3.000
 J0E  H16  C10  H15  107.90  3.000
 J0E  H16  C10  C3   110.70  3.000
 J0E  H15  C10  C3   109.58  3.000
 J0E  H16  C10  N2   110.12  3.000
 J0E  H15  C10  N2   108.91  3.000
 J0E  C3   C10  N2   109.58  3.000
 J0E  C1   C2   N4   126.32  3.000
 J0E  N4   C2   N1   127.01  3.000
 J0E  C1   C2   N1   106.67  3.000
 J0E  H18  C4   H17  107.17  3.000
 J0E  H18  C4   C5   110.63  3.000
 J0E  H17  C4   C5   109.62  3.000
 J0E  H18  C4   C3   109.75  3.000
 J0E  H17  C4   C3   108.87  3.000
 J0E  C5   C4   C3   110.72  3.000
 J0E  O    C7   C8   120.92  3.000
 J0E  O    C7   N2   121.78  3.000
 J0E  C8   C7   N2   117.29  3.000
 J0E  H21  C9   H20  107.70  3.000
 J0E  H21  C9   H19  107.71  3.000
 J0E  H20  C9   H19  107.95  3.000
 J0E  H21  C9   C8   109.68  3.000
 J0E  H20  C9   C8   111.91  3.000
 J0E  H19  C9   C8   111.72  3.000
 J0E  C11  N3   N1   107.73  3.000
 J0E  C    N5   C18  119.01  3.000
 J0E  H22  O1   C15  110.55  3.000
 J0E  H14  N    H13  117.35  3.000
 J0E  H14  N    C    121.74  3.000
 J0E  H13  N    C    119.07  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
 J0E  CONST_01  C12  C11  N3   N1    180.00   0.0  0
 J0E  CONST_02  C1   C11  N3   N1      0.00   0.0  0
 J0E  CONST_03  C11  C1   C2   N1      0.00   0.0  0
 J0E  CONST_04  C    C1   C2   N1    180.00   0.0  0
 J0E  CONST_05  C18  N4   C2   N1    180.00   0.0  0
 J0E  CONST_06  C11  C1   C2   N4    180.00   0.0  0
 J0E  CONST_07  C    C1   C2   N4      0.00   0.0  0
 J0E  CONST_08  N3   N1   C2   N4    180.00   0.0  0
 J0E  CONST_09  C    N5   C18  N4      0.00   0.0  0
 J0E  CONST_10  C16  C17  C12  C11   180.00   0.0  0
 J0E  CONST_11  C14  C13  C12  C11   180.00   0.0  0
 J0E  CONST_12  C2   N1   N3   C11     0.00   0.0  0
 J0E  CONST_13  N5   C    C1   C11   180.00   0.0  0
 J0E  CONST_14  C15  C16  C17  C12     0.00   0.0  0
 J0E  CONST_15  C15  C14  C13  C12     0.00   0.0  0
 J0E  CONST_16  C    C1   C11  C12     0.00   0.0  0
 J0E  CONST_17  C2   C1   C11  C12   180.00   0.0  0
 J0E  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 J0E  CONST_19  C16  C17  C12  C13     0.00   0.0  0
 J0E  CONST_22  C17  C16  C15  C14     0.00   0.0  0
 J0E  CONST_23  C17  C12  C13  C14     0.00   0.0  0
 J0E  CONST_26  C1   C    N5   C18     0.00   0.0  0
 J0E  CONST_27  C1   C2   N4   C18     0.00   0.0  0
 J0E  CONST_28  N3   C11  C1   C     180.00   0.0  0
 J0E  CONST_29  N3   N1   C2   C1      0.00   0.0  0
 J0E  CONST_30  N3   C11  C1   C2      0.00   0.0  0
 J0E  CONST_31  N5   C    C1   C2      0.00   0.0  0
 J0E  CONST_32  N5   C18  N4   C2      0.00   0.0  0
 J0E  CONST_33  C11  N3   N1   C3    180.00   0.0  0
 J0E  CONST_34  C1   C2   N1   C3    180.00   0.0  0
 J0E  CONST_35  N4   C2   N1   C3      0.00   0.0  0
 J0E  CONST_36  N    C    C1   C11     0.00   0.0  0
 J0E  CONST_37  O1   C15  C14  C13   180.00   0.0  0
 J0E  CONST_38  O1   C15  C16  C17   180.00   0.0  0
 J0E  CONST_39  N    C    N5   C18   180.00   0.0  0
 J0E  CONST_40  C2   C1   C    N     180.00   0.0  0
 J0E  CONST_41  H11  C17  C12  C11     0.00   0.0  0
 J0E  CONST_42  H8   C13  C12  C11     0.00   0.0  0
 J0E  CONST_43  H10  C16  C17  C12   180.00   0.0  0
 J0E  CONST_44  H9   C14  C13  C12   180.00   0.0  0
 J0E  CONST_45  H12  C18  N5   C     180.00   0.0  0
 J0E  CONST_46  C8   C7   N2   C6      0.00   0.0  0
 J0E  CONST_47  O    C7   N2   C6    180.00   0.0  0
 J0E  CONST_48  C10  N2   C7   C8    180.00   0.0  0
 J0E  CONST_49  C10  N2   C7   O       0.00   0.0  0
 J0E  CONST_50  H13  N    C    C1    180.00   0.0  0
 J0E  CONST_51  H14  N    C    C1      0.00   0.0  0
 J0E  Var_01    C4   C5   C6   N2    -55.66  30.0  1
 J0E  Var_02    C6   N2   C10  C3    -60.66  30.0  1
 J0E  Var_03    C6   C5   C4   C3     52.49  30.0  1
 J0E  Var_04    C10  N2   C6   C5     60.98  30.0  1
 J0E  Var_05    C9   C8   C7   N2   -178.22  30.0  2
 J0E  Var_06    H19  C9   C8   C7    -61.87  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
 J0E  chir_01  C3  C10  N1  C4  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
 J0E  plan-1  C11  0.020
 J0E  plan-1  C12  0.020
 J0E  plan-1  C13  0.020
 J0E  plan-1  C14  0.020
 J0E  plan-1  C15  0.020
 J0E  plan-1  C16  0.020
 J0E  plan-1  C17  0.020
 J0E  plan-1  O1   0.020
 J0E  plan-1  H8   0.020
 J0E  plan-1  H9   0.020
 J0E  plan-1  H10  0.020
 J0E  plan-1  H11  0.020
 J0E  plan-2  N1   0.020
 J0E  plan-2  C3   0.020
 J0E  plan-2  N4   0.020
 J0E  plan-2  C11  0.020
 J0E  plan-2  C12  0.020
 J0E  plan-2  C18  0.020
 J0E  plan-2  C    0.020
 J0E  plan-2  C1   0.020
 J0E  plan-2  C2   0.020
 J0E  plan-2  N3   0.020
 J0E  plan-2  N5   0.020
 J0E  plan-2  H12  0.020
 J0E  plan-2  N    0.020
 J0E  plan-3  C    0.020
 J0E  plan-3  H13  0.020
 J0E  plan-3  H14  0.020
 J0E  plan-3  N    0.020
 J0E  plan-4  N2   0.020
 J0E  plan-4  C6   0.020
 J0E  plan-4  C8   0.020
 J0E  plan-4  O    0.020
 J0E  plan-4  C10  0.020
 J0E  plan-4  C7   0.020

