# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:24:02 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-[(3~{R})-3-(4-azanyl-3-ethynyl-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]prop-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(nc(C#C)c12)[C@@H]3CCCN(C3)C(=O)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
 H8Z  H8Z  1-[(3~{R})-3-(4-azanyl-3-ethynyl-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]prop-2-en-1-one  ligand  38  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H8Z
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
 H8Z  N1   N  N     0  -0.476   3.4532  -2.3224  -0.2102
 H8Z  C2   C  CR16  0   0.061   2.2254  -2.6401  -0.6199
 H8Z  C5   C  CR56  0  -0.267   2.6452  -0.1306   0.1151
 H8Z  C6   C  CR6   0   0.462   3.7029  -1.0665   0.1679
 H8Z  C4   C  CR56  0   0.585   1.4205  -0.6134  -0.3356
 H8Z  CAJ  C  CR5   0   0.185   2.4070   1.2385   0.3929
 H8Z  CAK  C  CSP   0   0.262   3.3318   2.1956   0.8811
 H8Z  CAL  C  CSP1  0  -0.535   4.1533   2.9700   1.2968
 H8Z  CAM  C  CH1   0  -0.094  -0.8413   0.4222  -0.6612
 H8Z  CAN  C  CH2   0  -0.445  -1.1618   1.4415  -1.7502
 H8Z  CAO  C  CH2   0  -0.444  -2.6620   1.4695  -2.0275
 H8Z  CAP  C  CH2   0  -0.323  -3.4563   1.6628  -0.7413
 H8Z  CAR  C  CH2   0  -0.323  -1.7006   0.6716   0.5837
 H8Z  CAU  C  C1    0  -0.327  -3.5021  -1.5093   1.3408
 H8Z  CAV  C  C2    0  -0.468  -4.3524  -2.4436   1.7533
 H8Z  N3   N  N     0  -0.464   1.1622  -1.8665  -0.7155
 H8Z  NAG  N  NH2   0  -0.813   4.9270  -0.7497   0.5784
 H8Z  NAH  N  NR5   0  -0.385   0.5635   0.4309  -0.3113
 H8Z  NAI  N  N     0  -0.261   1.1534   1.5446   0.1303
 H8Z  NAQ  N  NT    0  -0.468  -3.1005   0.6251   0.2173
 H8Z  OAT  O  O     0  -0.499  -5.1282  -0.3513   0.0884
 H8Z  H1   H  HCR6  0   0.259   2.0897  -3.6756  -0.9135
 H8Z  H2   H  H     0   0.289   4.8772   3.6620   1.6636
 H8Z  H3   H  HCH1  0   0.279  -1.0479  -0.5864  -1.0268
 H8Z  H4   H  HCH2  0   0.241  -0.8334   2.4310  -1.4202
 H8Z  H5   H  HCH2  0   0.259  -0.6077   1.1991  -2.6588
 H8Z  H6   H  HCH2  0   0.252  -2.8932   2.2777  -2.7234
 H8Z  H7   H  HCH2  0   0.236  -2.9751   0.5369  -2.5047
 H8Z  H8   H  HCH2  0   0.246  -3.2191   2.6343  -0.2973
 H8Z  H9   H  HCH2  0   0.273  -4.5251   1.6372  -0.9287
 H8Z  H10  H  HCH2  0   0.281  -1.4621  -0.0435   1.3649
 H8Z  H11  H  HCH2  0   0.269  -1.4803   1.6639   0.9883
 H8Z  H12  H  H     0   0.266  -2.4609  -1.6009   1.6137
 H8Z  H14  H  H     0   0.258  -5.4063  -2.4116   1.5117
 H8Z  H15  H  H     0   0.262  -4.0107  -3.2763   2.3525
 H8Z  H17  H  HNH2  0   0.413   5.1708   0.1856   0.8550
 H8Z  H18  H  HNH2  0   0.410   5.6519  -1.4476   0.5843
 H8Z  CAS  C  C     0   0.544  -3.9741  -0.3731   0.5001

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
 H8Z  CAL  CAK  triple    1.203  0.020  1.203
 H8Z  CAK  CAJ  single    1.418  0.020  1.418
 H8Z  CAP  NAQ  single    1.457  0.020  1.457
 H8Z  CAP  CAO  single    1.524  0.020  1.524
 H8Z  NAI  CAJ  aromatic  1.317  0.020  1.317
 H8Z  NAI  NAH  aromatic  1.335  0.020  1.335
 H8Z  OAT  CAS  double    1.226  0.020  1.226
 H8Z  CAJ  C5   aromatic  1.417  0.020  1.417
 H8Z  NAQ  CAS  single    1.356  0.020  1.356
 H8Z  NAQ  CAR  single    1.448  0.020  1.448
 H8Z  CAS  CAU  single    1.490  0.020  1.490
 H8Z  CAR  CAM  single    1.533  0.020  1.533
 H8Z  CAN  CAO  single    1.526  0.020  1.526
 H8Z  CAN  CAM  single    1.526  0.020  1.526
 H8Z  CAV  CAU  double    1.329  0.020  1.329
 H8Z  CAM  NAH  single    1.448  0.020  1.448
 H8Z  NAH  C4   aromatic  1.351  0.020  1.351
 H8Z  NAG  C6   single    1.329  0.020  1.329
 H8Z  C5   C4   aromatic  1.391  0.020  1.391
 H8Z  C5   C6   aromatic  1.413  0.020  1.413
 H8Z  C4   N3   aromatic  1.335  0.020  1.335
 H8Z  C6   N1   aromatic  1.335  0.020  1.335
 H8Z  N3   C2   aromatic  1.318  0.020  1.318
 H8Z  N1   C2   aromatic  1.333  0.020  1.333
 H8Z  C2   H1   single    0.929  0.020  1.085
 H8Z  CAL  H2   single    0.913  0.020  1.066
 H8Z  CAM  H3   single    0.939  0.020  1.096
 H8Z  CAN  H4   single    0.939  0.020  1.096
 H8Z  CAN  H5   single    0.939  0.020  1.096
 H8Z  CAO  H6   single    0.939  0.020  1.096
 H8Z  CAO  H7   single    0.939  0.020  1.096
 H8Z  CAP  H8   single    0.939  0.020  1.096
 H8Z  CAP  H9   single    0.939  0.020  1.096
 H8Z  CAR  H10  single    0.939  0.020  1.096
 H8Z  CAR  H11  single    0.939  0.020  1.096
 H8Z  CAU  H12  single    0.930  0.020  1.086
 H8Z  CAV  H14  single    0.930  0.020  1.086
 H8Z  CAV  H15  single    0.930  0.020  1.086
 H8Z  NAG  H17  single    0.868  0.020  1.013
 H8Z  NAG  H18  single    0.868  0.020  1.013

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
 H8Z  C6   N1   C2   118.92  3.000
 H8Z  H1   C2   N3   116.08  3.000
 H8Z  H1   C2   N1   115.21  3.000
 H8Z  N3   C2   N1   128.71  3.000
 H8Z  CAJ  C5   C4   104.52  3.000
 H8Z  C4   C5   C6   116.17  3.000
 H8Z  CAJ  C5   C6   139.31  3.000
 H8Z  NAG  C6   C5   122.88  3.000
 H8Z  C5   C6   N1   118.18  3.000
 H8Z  NAG  C6   N1   118.94  3.000
 H8Z  NAH  C4   N3   127.45  3.000
 H8Z  N3   C4   C5   126.03  3.000
 H8Z  NAH  C4   C5   106.52  3.000
 H8Z  NAI  CAJ  CAK  122.19  3.000
 H8Z  NAI  CAJ  C5   110.21  3.000
 H8Z  CAK  CAJ  C5   127.60  3.000
 H8Z  CAL  CAK  CAJ  180.00  3.000
 H8Z  H2   CAL  CAK  180.00  3.000
 H8Z  H3   CAM  NAH  105.65  3.000
 H8Z  H3   CAM  CAR  108.41  3.000
 H8Z  NAH  CAM  CAR  110.28  3.000
 H8Z  H3   CAM  CAN  109.77  3.000
 H8Z  NAH  CAM  CAN  111.86  3.000
 H8Z  CAR  CAM  CAN  110.69  3.000
 H8Z  H5   CAN  H4   107.44  3.000
 H8Z  H5   CAN  CAO  110.60  3.000
 H8Z  H4   CAN  CAO  109.48  3.000
 H8Z  H5   CAN  CAM  109.83  3.000
 H8Z  H4   CAN  CAM  109.03  3.000
 H8Z  CAO  CAN  CAM  110.39  3.000
 H8Z  H7   CAO  H6   107.02  3.000
 H8Z  H7   CAO  CAP  109.11  3.000
 H8Z  H6   CAO  CAP  109.51  3.000
 H8Z  H7   CAO  CAN  110.20  3.000
 H8Z  H6   CAO  CAN  109.74  3.000
 H8Z  CAP  CAO  CAN  111.18  3.000
 H8Z  H9   CAP  H8   107.72  3.000
 H8Z  H9   CAP  NAQ  109.72  3.000
 H8Z  H8   CAP  NAQ  108.21  3.000
 H8Z  H9   CAP  CAO  111.37  3.000
 H8Z  H8   CAP  CAO  110.00  3.000
 H8Z  NAQ  CAP  CAO  109.74  3.000
 H8Z  H11  CAR  H10  106.68  3.000
 H8Z  H11  CAR  NAQ  108.51  3.000
 H8Z  H10  CAR  NAQ  111.93  3.000
 H8Z  H11  CAR  CAM  109.57  3.000
 H8Z  H10  CAR  CAM  110.73  3.000
 H8Z  NAQ  CAR  CAM  109.34  3.000
 H8Z  H12  CAU  CAV  118.60  3.000
 H8Z  H12  CAU  CAS  120.83  3.000
 H8Z  CAV  CAU  CAS  120.57  3.000
 H8Z  H15  CAV  H14  117.03  3.000
 H8Z  H15  CAV  CAU  120.75  3.000
 H8Z  H14  CAV  CAU  122.22  3.000
 H8Z  C4   N3   C2   111.98  3.000
 H8Z  H18  NAG  H17  117.97  3.000
 H8Z  H18  NAG  C6   119.99  3.000
 H8Z  H17  NAG  C6   122.00  3.000
 H8Z  NAI  NAH  CAM  120.90  3.000
 H8Z  CAM  NAH  C4   127.34  3.000
 H8Z  NAI  NAH  C4   111.74  3.000
 H8Z  NAH  NAI  CAJ  107.01  3.000
 H8Z  CAS  NAQ  CAR  126.41  3.000
 H8Z  CAR  NAQ  CAP  112.33  3.000
 H8Z  CAS  NAQ  CAP  120.27  3.000
 H8Z  OAT  CAS  NAQ  121.56  3.000
 H8Z  NAQ  CAS  CAU  118.34  3.000
 H8Z  OAT  CAS  CAU  120.09  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
 H8Z  CONST_01  CAJ  C5   C6   N1   180.00   0.0  0
 H8Z  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 H8Z  CONST_03  C4   N3   C2   N1     0.00   0.0  0
 H8Z  CONST_04  NAH  C4   N3   C2   180.00   0.0  0
 H8Z  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 H8Z  CONST_06  C5   C6   N1   C2     0.00   0.0  0
 H8Z  CONST_07  NAH  NAI  CAJ  C5     0.00   0.0  0
 H8Z  CONST_08  NAI  NAH  C4   C5     0.00   0.0  0
 H8Z  CONST_09  NAI  CAJ  C5   C6   180.00   0.0  0
 H8Z  CONST_10  NAH  C4   C5   C6   180.00   0.0  0
 H8Z  CONST_11  N3   C4   C5   C6     0.00   0.0  0
 H8Z  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 H8Z  CONST_13  CAJ  NAI  NAH  C4     0.00   0.0  0
 H8Z  CONST_14  NAI  CAJ  C5   C4     0.00   0.0  0
 H8Z  CONST_15  NAH  C4   C5   CAJ    0.00   0.0  0
 H8Z  CONST_16  N3   C4   C5   CAJ  180.00   0.0  0
 H8Z  CONST_17  NAI  NAH  C4   N3   180.00   0.0  0
 H8Z  CONST_18  CAM  NAH  C4   C5   180.00   0.0  0
 H8Z  CONST_19  CAM  NAH  NAI  CAJ  180.00   0.0  0
 H8Z  CONST_20  N3   C4   NAH  CAM    0.00   0.0  0
 H8Z  CONST_21  NAG  C6   N1   C2   180.00   0.0  0
 H8Z  CONST_22  CAK  CAJ  C5   C6     0.00   0.0  0
 H8Z  CONST_23  CAK  CAJ  C5   C4   180.00   0.0  0
 H8Z  CONST_24  NAG  C6   C5   C4   180.00   0.0  0
 H8Z  CONST_25  NAG  C6   C5   CAJ    0.00   0.0  0
 H8Z  CONST_26  NAH  NAI  CAJ  CAK  180.00   0.0  0
 H8Z  CONST_27  H1   C2   N1   C6   180.00   0.0  0
 H8Z  CONST_28  OAT  CAS  NAQ  CAP    0.00   0.0  0
 H8Z  CONST_29  CAU  CAS  NAQ  CAP  180.00   0.0  0
 H8Z  CONST_30  OAT  CAS  NAQ  CAR  180.00   0.0  0
 H8Z  CONST_31  CAU  CAS  NAQ  CAR    0.00   0.0  0
 H8Z  CONST_32  H17  NAG  C6   N1   180.00   0.0  0
 H8Z  CONST_33  H18  NAG  C6   N1     0.00   0.0  0
 H8Z  Var_01    CAP  NAQ  CAR  CAM  -62.18  30.0  1
 H8Z  Var_02    CAP  CAO  CAN  CAM   52.32  30.0  1
 H8Z  Var_03    NAQ  CAP  CAO  CAN  -55.68  30.0  1
 H8Z  Var_04    CAR  NAQ  CAP  CAO   61.57  30.0  1
 H8Z  Var_05    NAQ  CAS  CAU  CAV  173.42  30.0  2
 H8Z  Var_06    H14  CAV  CAU  CAS   -0.85   0.0  2

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
 H8Z  chir_01  CAM  CAR  CAN  NAH  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
 H8Z  plan-1  N1   0.020
 H8Z  plan-1  C2   0.020
 H8Z  plan-1  C5   0.020
 H8Z  plan-1  C6   0.020
 H8Z  plan-1  C4   0.020
 H8Z  plan-1  CAJ  0.020
 H8Z  plan-1  CAK  0.020
 H8Z  plan-1  CAL  0.020
 H8Z  plan-1  CAM  0.020
 H8Z  plan-1  N3   0.020
 H8Z  plan-1  NAG  0.020
 H8Z  plan-1  NAH  0.020
 H8Z  plan-1  NAI  0.020
 H8Z  plan-1  H1   0.020
 H8Z  plan-2  C6   0.020
 H8Z  plan-2  NAG  0.020
 H8Z  plan-2  H17  0.020
 H8Z  plan-2  H18  0.020
 H8Z  plan-3  CAP  0.020
 H8Z  plan-3  CAR  0.020
 H8Z  plan-3  CAU  0.020
 H8Z  plan-3  NAQ  0.020
 H8Z  plan-3  OAT  0.020
 H8Z  plan-3  CAS  0.020
 H8Z  plan-4  CAU  0.020
 H8Z  plan-4  CAV  0.020
 H8Z  plan-4  H12  0.020
 H8Z  plan-4  H14  0.020
 H8Z  plan-4  H15  0.020
 H8Z  plan-4  CAS  0.020

