# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 01:14:53 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-[(2S)-4-(5-phenyl-1H-pyrazolo[3,4-b]pyridin-4-yl)morpholin-2-yl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1CN(CCO1)c2c3cn[nH]c3ncc2c4ccccc4
#
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
 ZY6  ZY6  1-[(2S)-4-(5-phenyl-1H-pyrazolo[3,4-b]pyridin-4-yl)morpholin-2-yl]methanamine  ligand  42  23  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZY6
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
 ZY6  CAE   C  CR16  0  -0.285  -1.4332  -2.1276   1.6011
 ZY6  CAC   C  CR16  0  -0.242  -1.1087  -3.4684   1.7615
 ZY6  CAB   C  CR16  0  -0.265  -0.4997  -4.1667   0.7286
 ZY6  CAD   C  CR16  0  -0.238  -0.2246  -3.5163  -0.4685
 ZY6  CAF   C  CR16  0  -0.272  -0.5532  -2.1792  -0.6299
 ZY6  CAQ   C  CR6   0  -0.004  -1.1571  -1.4642   0.4058
 ZY6  CAR   C  CR6   0  -0.079  -1.5482  -0.0485   0.2181
 ZY6  CAG   C  CR16  0  -0.103  -2.9034   0.2678   0.4045
 ZY6  NAN   N  N     0  -0.443  -3.4762   1.4355   0.1796
 ZY6  CAU   C  CR56  0   0.507  -2.6296   2.3529  -0.2737
 ZY6  NAO   N  NR15  0  -0.521  -2.9259   3.6351  -0.5686
 ZY6  NAM   N  N     0  -0.232  -1.8512   4.3260  -0.9584
 ZY6  CAH   C  CR15  0  -0.125  -0.8373   3.5011  -0.9241
 ZY6  CAT   C  CR56  0  -0.203  -1.2490   2.2033  -0.5025
 ZY6  CAS   C  CR6   0   0.413  -0.6576   0.9487  -0.2275
 ZY6  NAV   N  NT    0  -0.529   0.6808   0.7082  -0.3903
 ZY6  CAL   C  CH2   0  -0.317   1.4638   0.0905   0.6703
 ZY6  CAK   C  CH2   0  -0.346   1.4968   1.5441  -1.2470
 ZY6  CAJ   C  CH2   0  -0.177   2.6520   0.7126  -1.7773
 ZY6  OAP   O  O2    0  -0.484   3.4151   0.1461  -0.7392
 ZY6  CAW   C  CH1   0   0.033   2.6310  -0.6901   0.0852
 ZY6  CAI   C  CH2   0  -0.299   3.5006  -1.2658   1.1870
 ZY6  NAA   N  NH2   0  -0.795   4.5590  -2.1027   0.6505
 ZY6  HAE   H  HCR6  0   0.253  -1.8921  -1.5863   2.4197
 ZY6  HAC   H  HCR6  0   0.256  -1.3276  -3.9639   2.6988
 ZY6  HAB   H  HCR6  0   0.255  -0.2410  -5.2100   0.8544
 ZY6  HAD   H  HCR6  0   0.255   0.2452  -4.0528  -1.2830
 ZY6  HAF   H  HCR6  0   0.253  -0.3361  -1.6840  -1.5679
 ZY6  HAG   H  HCR6  0   0.259  -3.5640  -0.5256   0.7412
 ZY6  HAO   H  HNR5  0   0.415  -3.8263   4.0839  -0.5118
 ZY6  HAH   H  HCR5  0   0.268   0.1430   3.8552  -1.1973
 ZY6  HAL1  H  HCH2  0   0.242   1.8510   0.8736   1.3384
 ZY6  HAL2  H  HCH2  0   0.275   0.8436  -0.5672   1.2721
 ZY6  HAK1  H  HCH2  0   0.266   0.9122   1.8939  -2.0975
 ZY6  HAK2  H  HCH2  0   0.234   1.8824   2.4213  -0.7098
 ZY6  HAW   H  HCH1  0   0.210   2.2191  -1.5180  -0.5157
 ZY6  HAJ1  H  HCH2  0   0.206   2.2504  -0.0706  -2.4353
 ZY6  HAJ2  H  HCH2  0   0.245   3.3179   1.3428  -2.3683
 ZY6  HAI1  H  HCH2  0   0.225   3.9547  -0.4444   1.7480
 ZY6  HAI2  H  HCH2  0   0.203   2.8336  -1.7880   1.8884
 ZY6  HAA1  H  HNH2  0   0.351   5.1365  -2.4336   1.4127
 ZY6  HAA2  H  HNH2  0   0.338   4.1544  -2.9338   0.2365

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
 ZY6  CAE  CAC   aromatic  1.389  0.020  1.389
 ZY6  CAE  CAQ   aromatic  1.395  0.020  1.395
 ZY6  CAC  CAB   aromatic  1.388  0.020  1.388
 ZY6  CAB  CAD   aromatic  1.390  0.020  1.390
 ZY6  CAD  CAF   aromatic  1.386  0.020  1.386
 ZY6  CAF  CAQ   aromatic  1.396  0.020  1.396
 ZY6  CAQ  CAR   single    1.481  0.020  1.481
 ZY6  CAR  CAG   aromatic  1.404  0.020  1.404
 ZY6  CAR  CAS   aromatic  1.409  0.020  1.409
 ZY6  CAG  NAN   aromatic  1.320  0.020  1.320
 ZY6  NAN  CAU   aromatic  1.328  0.020  1.328
 ZY6  CAU  NAO   aromatic  1.349  0.020  1.349
 ZY6  CAU  CAT   aromatic  1.407  0.020  1.407
 ZY6  NAO  NAM   aromatic  1.336  0.020  1.336
 ZY6  NAM  CAH   aromatic  1.308  0.020  1.308
 ZY6  CAH  CAT   aromatic  1.425  0.020  1.425
 ZY6  CAT  CAS   aromatic  1.414  0.020  1.414
 ZY6  CAS  NAV   single    1.369  0.020  1.369
 ZY6  NAV  CAL   single    1.456  0.020  1.456
 ZY6  NAV  CAK   single    1.449  0.020  1.449
 ZY6  CAL  CAW   single    1.521  0.020  1.521
 ZY6  CAK  CAJ   single    1.519  0.020  1.519
 ZY6  CAJ  OAP   single    1.407  0.020  1.407
 ZY6  OAP  CAW   single    1.412  0.020  1.412
 ZY6  CAW  CAI   single    1.517  0.020  1.517
 ZY6  CAI  NAA   single    1.452  0.020  1.452
 ZY6  CAE  HAE   single    0.930  0.020  1.080
 ZY6  CAC  HAC   single    0.930  0.020  1.080
 ZY6  CAB  HAB   single    0.930  0.020  1.080
 ZY6  CAD  HAD   single    0.930  0.020  1.080
 ZY6  CAF  HAF   single    0.930  0.020  1.080
 ZY6  CAG  HAG   single    0.930  0.020  1.080
 ZY6  NAO  HAO   single    0.860  0.020  1.020
 ZY6  CAH  HAH   single    0.930  0.020  1.080
 ZY6  CAL  HAL1  single    0.970  0.020  1.090
 ZY6  CAL  HAL2  single    0.970  0.020  1.090
 ZY6  CAK  HAK1  single    0.970  0.020  1.090
 ZY6  CAK  HAK2  single    0.970  0.020  1.090
 ZY6  CAW  HAW   single    0.970  0.020  1.090
 ZY6  CAJ  HAJ1  single    0.970  0.020  1.090
 ZY6  CAJ  HAJ2  single    0.970  0.020  1.090
 ZY6  CAI  HAI1  single    0.970  0.020  1.090
 ZY6  CAI  HAI2  single    0.970  0.020  1.090
 ZY6  NAA  HAA1  single    0.890  0.020  1.040
 ZY6  NAA  HAA2  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
 ZY6  HAE   CAE  CAQ   119.59  3.000
 ZY6  HAE   CAE  CAC   119.61  3.000
 ZY6  CAQ   CAE  CAC   120.80  3.000
 ZY6  HAC   CAC  CAB   120.20  3.000
 ZY6  HAC   CAC  CAE   119.65  3.000
 ZY6  CAB   CAC  CAE   120.16  3.000
 ZY6  HAB   CAB  CAD   120.26  3.000
 ZY6  HAB   CAB  CAC   120.23  3.000
 ZY6  CAD   CAB  CAC   119.51  3.000
 ZY6  HAD   CAD  CAF   119.56  3.000
 ZY6  HAD   CAD  CAB   120.14  3.000
 ZY6  CAF   CAD  CAB   120.30  3.000
 ZY6  HAF   CAF  CAQ   119.69  3.000
 ZY6  HAF   CAF  CAD   119.63  3.000
 ZY6  CAQ   CAF  CAD   120.68  3.000
 ZY6  CAR   CAQ  CAF   120.66  3.000
 ZY6  CAR   CAQ  CAE   120.74  3.000
 ZY6  CAF   CAQ  CAE   118.55  3.000
 ZY6  CAS   CAR  CAG   119.51  3.000
 ZY6  CAS   CAR  CAQ   123.34  3.000
 ZY6  CAG   CAR  CAQ   116.97  3.000
 ZY6  HAG   CAG  NAN   115.80  3.000
 ZY6  HAG   CAG  CAR   117.63  3.000
 ZY6  NAN   CAG  CAR   126.55  3.000
 ZY6  CAU   NAN  CAG   113.11  3.000
 ZY6  CAT   CAU  NAO   106.32  3.000
 ZY6  CAT   CAU  NAN   127.40  3.000
 ZY6  NAO   CAU  NAN   126.25  3.000
 ZY6  HAO   NAO  NAM   120.33  3.000
 ZY6  HAO   NAO  CAU   127.41  3.000
 ZY6  NAM   NAO  CAU   112.26  3.000
 ZY6  CAH   NAM  NAO   106.85  3.000
 ZY6  HAH   CAH  CAT   129.57  3.000
 ZY6  HAH   CAH  NAM   119.44  3.000
 ZY6  CAT   CAH  NAM   110.99  3.000
 ZY6  CAS   CAT  CAH   138.13  3.000
 ZY6  CAS   CAT  CAU   118.23  3.000
 ZY6  CAH   CAT  CAU   103.57  3.000
 ZY6  NAV   CAS  CAT   122.78  3.000
 ZY6  NAV   CAS  CAR   122.07  3.000
 ZY6  CAT   CAS  CAR   115.15  3.000
 ZY6  CAK   NAV  CAL   111.88  3.000
 ZY6  CAK   NAV  CAS   121.29  3.000
 ZY6  CAL   NAV  CAS   120.90  3.000
 ZY6  HAL2  CAL  HAL1  107.20  3.000
 ZY6  HAL2  CAL  CAW   109.91  3.000
 ZY6  HAL1  CAL  CAW   109.21  3.000
 ZY6  HAL2  CAL  NAV   110.70  3.000
 ZY6  HAL1  CAL  NAV   109.25  3.000
 ZY6  CAW   CAL  NAV   110.50  3.000
 ZY6  HAK2  CAK  HAK1  108.29  3.000
 ZY6  HAK2  CAK  CAJ   109.93  3.000
 ZY6  HAK1  CAK  CAJ   108.13  3.000
 ZY6  HAK2  CAK  NAV   111.67  3.000
 ZY6  HAK1  CAK  NAV   110.16  3.000
 ZY6  CAJ   CAK  NAV   108.60  3.000
 ZY6  HAJ2  CAJ  HAJ1  108.09  3.000
 ZY6  HAJ2  CAJ  OAP   107.53  3.000
 ZY6  HAJ1  CAJ  OAP   110.67  3.000
 ZY6  HAJ2  CAJ  CAK   109.70  3.000
 ZY6  HAJ1  CAJ  CAK   108.74  3.000
 ZY6  OAP   CAJ  CAK   112.03  3.000
 ZY6  CAW   OAP  CAJ   111.59  3.000
 ZY6  HAW   CAW  CAI   108.96  3.000
 ZY6  HAW   CAW  OAP   109.50  3.000
 ZY6  CAI   CAW  OAP   109.30  3.000
 ZY6  HAW   CAW  CAL   107.95  3.000
 ZY6  CAI   CAW  CAL   110.80  3.000
 ZY6  OAP   CAW  CAL   110.29  3.000
 ZY6  HAI2  CAI  HAI1  106.34  3.000
 ZY6  HAI2  CAI  NAA   113.83  3.000
 ZY6  HAI1  CAI  NAA   108.65  3.000
 ZY6  HAI2  CAI  CAW   107.20  3.000
 ZY6  HAI1  CAI  CAW   109.00  3.000
 ZY6  NAA   CAI  CAW   111.60  3.000
 ZY6  HAA2  NAA  HAA1  105.52  3.000
 ZY6  HAA2  NAA  CAI   109.44  3.000
 ZY6  HAA1  NAA  CAI   109.04  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
 ZY6  CONST_01  CAD   CAB  CAC  CAE     0.00   0.0  0
 ZY6  CONST_02  CAD   CAF  CAQ  CAE     0.00   0.0  0
 ZY6  CONST_05  CAF   CAQ  CAE  CAC     0.00   0.0  0
 ZY6  CONST_06  CAR   CAQ  CAE  CAC   180.00   0.0  0
 ZY6  CONST_07  CAF   CAD  CAB  CAC     0.00   0.0  0
 ZY6  CONST_08  CAQ   CAE  CAC  CAB     0.00   0.0  0
 ZY6  CONST_09  CAQ   CAF  CAD  CAB     0.00   0.0  0
 ZY6  CONST_10  CAR   CAQ  CAF  CAD   180.00   0.0  0
 ZY6  CONST_13  NAN   CAG  CAR  CAQ   180.00   0.0  0
 ZY6  CONST_14  CAT   CAS  CAR  CAQ   180.00   0.0  0
 ZY6  CONST_15  CAU   NAN  CAG  CAR     0.00   0.0  0
 ZY6  CONST_16  CAU   CAT  CAS  CAR     0.00   0.0  0
 ZY6  CONST_17  CAH   CAT  CAS  CAR   180.00   0.0  0
 ZY6  CONST_18  CAT   CAS  CAR  CAG     0.00   0.0  0
 ZY6  CONST_19  NAO   CAU  NAN  CAG   180.00   0.0  0
 ZY6  CONST_20  CAT   CAU  NAN  CAG     0.00   0.0  0
 ZY6  CONST_21  CAS   CAR  CAG  NAN     0.00   0.0  0
 ZY6  CONST_22  NAM   NAO  CAU  NAN   180.00   0.0  0
 ZY6  CONST_23  CAH   CAT  CAU  NAN   180.00   0.0  0
 ZY6  CONST_24  CAS   CAT  CAU  NAN     0.00   0.0  0
 ZY6  CONST_25  CAH   NAM  NAO  CAU     0.00   0.0  0
 ZY6  CONST_26  NAM   CAH  CAT  CAU     0.00   0.0  0
 ZY6  CONST_27  CAH   CAT  CAU  NAO     0.00   0.0  0
 ZY6  CONST_28  CAS   CAT  CAU  NAO   180.00   0.0  0
 ZY6  CONST_29  CAT   CAH  NAM  NAO     0.00   0.0  0
 ZY6  CONST_30  CAT   CAU  NAO  NAM     0.00   0.0  0
 ZY6  CONST_31  CAS   CAT  CAH  NAM   180.00   0.0  0
 ZY6  CONST_32  NAV   CAS  CAR  CAQ     0.00   0.0  0
 ZY6  CONST_33  NAV   CAS  CAR  CAG   180.00   0.0  0
 ZY6  CONST_34  NAV   CAS  CAT  CAU   180.00   0.0  0
 ZY6  CONST_35  NAV   CAS  CAT  CAH     0.00   0.0  0
 ZY6  CONST_36  HAB   CAB  CAC  CAE   180.00   0.0  0
 ZY6  CONST_37  HAF   CAF  CAQ  CAE   180.00   0.0  0
 ZY6  CONST_38  HAD   CAD  CAB  CAC   180.00   0.0  0
 ZY6  CONST_39  HAE   CAE  CAC  CAB   180.00   0.0  0
 ZY6  CONST_40  HAC   CAC  CAB  CAD   180.00   0.0  0
 ZY6  CONST_41  HAG   CAG  CAR  CAQ     0.00   0.0  0
 ZY6  CONST_42  HAO   NAO  CAU  NAN     0.00   0.0  0
 ZY6  CONST_43  HAH   CAH  CAT  CAU   180.00   0.0  0
 ZY6  Var_01    CAL   NAV  CAS  CAR   -50.42  30.0  2
 ZY6  Var_02    CAW   CAL  NAV  CAS   151.42  30.0  1
 ZY6  Var_03    CAJ   CAK  NAV  CAS  -152.01  30.0  1
 ZY6  Var_04    OAP   CAJ  CAK  NAV   -56.67  30.0  1
 ZY6  Var_05    HAA1  NAA  CAI  CAW   177.65  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
 ZY6  chir_01  CAW  CAL  OAP  CAI  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
 ZY6  plan-1  CAE  0.020
 ZY6  plan-1  CAC  0.020
 ZY6  plan-1  CAB  0.020
 ZY6  plan-1  CAD  0.020
 ZY6  plan-1  CAF  0.020
 ZY6  plan-1  CAQ  0.020
 ZY6  plan-1  CAR  0.020
 ZY6  plan-1  HAE  0.020
 ZY6  plan-1  HAC  0.020
 ZY6  plan-1  HAB  0.020
 ZY6  plan-1  HAD  0.020
 ZY6  plan-1  HAF  0.020
 ZY6  plan-2  CAQ  0.020
 ZY6  plan-2  CAR  0.020
 ZY6  plan-2  CAG  0.020
 ZY6  plan-2  NAN  0.020
 ZY6  plan-2  CAU  0.020
 ZY6  plan-2  NAO  0.020
 ZY6  plan-2  NAM  0.020
 ZY6  plan-2  CAH  0.020
 ZY6  plan-2  CAT  0.020
 ZY6  plan-2  CAS  0.020
 ZY6  plan-2  NAV  0.020
 ZY6  plan-2  HAG  0.020
 ZY6  plan-2  HAO  0.020
 ZY6  plan-2  HAH  0.020

