# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 06:35:40 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-[(2S)-4-(5-bromo-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)c2c(Br)cnc3[nH]ncc23
#
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
 ZYW  ZYW  1-[(2S)-4-(5-bromo-1H-pyrazolo[3,4-b]pyridin-4-yl)morpholin-2-yl]methanamine  ligand  32  18  .  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_ZYW
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
 ZYW  BR    BR  BR    0  -0.027   0.4260   2.0328   1.1399
 ZYW  CAM   C   CR6   0  -0.285   1.2440   0.3856   0.7175
 ZYW  CAC   C   CR16  0  -0.059   2.6069   0.2603   1.0260
 ZYW  NAJ   N   N     0  -0.431   3.3580  -0.7662   0.6863
 ZYW  CAP   C   CR56  0   0.522   2.7113  -1.7021  -0.0005
 ZYW  NAK   N   NR15  0  -0.516   3.2284  -2.8584  -0.4597
 ZYW  NAI   N   N     0  -0.224   2.3154  -3.6061  -1.0828
 ZYW  CAD   C   CR15  0  -0.117   1.1855  -2.9494  -1.0372
 ZYW  CAO   C   CR56  0  -0.193   1.3512  -1.7070  -0.3606
 ZYW  CAN   C   CR6   0   0.477   0.5477  -0.6119   0.0241
 ZYW  NAQ   N   NT    0  -0.519  -0.7891  -0.5046  -0.2754
 ZYW  CAH   C   CH2   0  -0.318  -1.7671  -0.4760   0.8070
 ZYW  CAG   C   CH2   0  -0.345  -1.3227  -1.1686  -1.4504
 ZYW  CAF   C   CH2   0  -0.176  -2.5927  -0.4469  -1.8654
 ZYW  OAL   O   O2    0  -0.484  -3.5387  -0.4121  -0.8236
 ZYW  CAR   C   CH1   0   0.038  -3.0340   0.2206   0.3336
 ZYW  CAE   C   CH2   0  -0.300  -4.1023   0.2039   1.4108
 ZYW  NAA   N   NH2   0  -0.797  -5.2651   0.9824   1.0215
 ZYW  HAC   H   HCR6  0   0.281   3.1008   1.0589   1.5683
 ZYW  HAK   H   HNR5  0   0.420   4.1805  -3.1792  -0.3786
 ZYW  HAD   H   HCR5  0   0.271   0.3014  -3.3778  -1.4798
 ZYW  HAH1  H   HCH2  0   0.241  -2.0037  -1.5046   1.1166
 ZYW  HAH2  H   HCH2  0   0.263  -1.3704   0.0344   1.6817
 ZYW  HAG1  H   HCH2  0   0.268  -0.6046  -1.1111  -2.2686
 ZYW  HAG2  H   HCH2  0   0.233  -1.5485  -2.2263  -1.2607
 ZYW  HAR   H   HCH1  0   0.207  -2.7710   1.2660   0.1003
 ZYW  HAF1  H   HCH2  0   0.207  -2.3362   0.5691  -2.1950
 ZYW  HAF2  H   HCH2  0   0.244  -3.0522  -0.9690  -2.7060
 ZYW  HAE1  H   HCH2  0   0.226  -4.4157  -0.8293   1.5833
 ZYW  HAE2  H   HCH2  0   0.204  -3.6345   0.5450   2.3453
 ZYW  HAA1  H   HNH2  0   0.350  -5.9904   0.8649   1.7170
 ZYW  HAA2  H   HNH2  0   0.340  -5.0300   1.9673   1.0374

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
 ZYW  BR   CAM   single    1.887  0.020  1.887
 ZYW  CAM  CAC   aromatic  1.403  0.020  1.403
 ZYW  CAM  CAN   aromatic  1.400  0.020  1.400
 ZYW  CAC  NAJ   aromatic  1.316  0.020  1.316
 ZYW  NAJ  CAP   aromatic  1.329  0.020  1.329
 ZYW  CAP  NAK   aromatic  1.347  0.020  1.347
 ZYW  CAP  CAO   aromatic  1.407  0.020  1.407
 ZYW  NAK  NAI   aromatic  1.334  0.020  1.334
 ZYW  NAI  CAD   aromatic  1.308  0.020  1.308
 ZYW  CAD  CAO   aromatic  1.424  0.020  1.424
 ZYW  CAO  CAN   aromatic  1.412  0.020  1.412
 ZYW  CAN  NAQ   single    1.374  0.020  1.374
 ZYW  NAQ  CAH   single    1.459  0.020  1.459
 ZYW  NAQ  CAG   single    1.451  0.020  1.451
 ZYW  CAH  CAR   single    1.521  0.020  1.521
 ZYW  CAG  CAF   single    1.519  0.020  1.519
 ZYW  CAF  OAL   single    1.408  0.020  1.408
 ZYW  OAL  CAR   single    1.412  0.020  1.412
 ZYW  CAR  CAE   single    1.517  0.020  1.517
 ZYW  CAE  NAA   single    1.452  0.020  1.452
 ZYW  CAC  HAC   single    0.930  0.020  1.080
 ZYW  NAK  HAK   single    0.860  0.020  1.020
 ZYW  CAD  HAD   single    0.930  0.020  1.080
 ZYW  CAH  HAH1  single    0.970  0.020  1.090
 ZYW  CAH  HAH2  single    0.970  0.020  1.090
 ZYW  CAG  HAG1  single    0.970  0.020  1.090
 ZYW  CAG  HAG2  single    0.970  0.020  1.090
 ZYW  CAR  HAR   single    0.970  0.020  1.090
 ZYW  CAF  HAF1  single    0.970  0.020  1.090
 ZYW  CAF  HAF2  single    0.970  0.020  1.090
 ZYW  CAE  HAE1  single    0.970  0.020  1.090
 ZYW  CAE  HAE2  single    0.970  0.020  1.090
 ZYW  NAA  HAA1  single    0.890  0.020  1.040
 ZYW  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
 ZYW  CAN   CAM  CAC   121.89  3.000
 ZYW  CAN   CAM  BR    121.14  3.000
 ZYW  CAC   CAM  BR    116.73  3.000
 ZYW  HAC   CAC  NAJ   116.32  3.000
 ZYW  HAC   CAC  CAM   119.12  3.000
 ZYW  NAJ   CAC  CAM   124.55  3.000
 ZYW  CAP   NAJ  CAC   113.88  3.000
 ZYW  CAO   CAP  NAK   106.31  3.000
 ZYW  CAO   CAP  NAJ   127.24  3.000
 ZYW  NAK   CAP  NAJ   126.43  3.000
 ZYW  HAK   NAK  NAI   120.37  3.000
 ZYW  HAK   NAK  CAP   127.46  3.000
 ZYW  NAI   NAK  CAP   112.17  3.000
 ZYW  CAD   NAI  NAK   107.06  3.000
 ZYW  HAD   CAD  CAO   129.60  3.000
 ZYW  HAD   CAD  NAI   119.66  3.000
 ZYW  CAO   CAD  NAI   110.74  3.000
 ZYW  CAN   CAO  CAD   137.72  3.000
 ZYW  CAN   CAO  CAP   118.54  3.000
 ZYW  CAD   CAO  CAP   103.71  3.000
 ZYW  NAQ   CAN  CAO   123.70  3.000
 ZYW  NAQ   CAN  CAM   122.41  3.000
 ZYW  CAO   CAN  CAM   113.86  3.000
 ZYW  CAG   NAQ  CAH   111.29  3.000
 ZYW  CAG   NAQ  CAN   119.90  3.000
 ZYW  CAH   NAQ  CAN   119.46  3.000
 ZYW  HAH2  CAH  HAH1  106.92  3.000
 ZYW  HAH2  CAH  CAR   109.82  3.000
 ZYW  HAH1  CAH  CAR   109.67  3.000
 ZYW  HAH2  CAH  NAQ   111.18  3.000
 ZYW  HAH1  CAH  NAQ   109.55  3.000
 ZYW  CAR   CAH  NAQ   109.65  3.000
 ZYW  HAG2  CAG  HAG1  108.42  3.000
 ZYW  HAG2  CAG  CAF   109.45  3.000
 ZYW  HAG1  CAG  CAF   108.70  3.000
 ZYW  HAG2  CAG  NAQ   112.12  3.000
 ZYW  HAG1  CAG  NAQ   109.96  3.000
 ZYW  CAF   CAG  NAQ   108.14  3.000
 ZYW  HAF2  CAF  HAF1  108.04  3.000
 ZYW  HAF2  CAF  OAL   107.40  3.000
 ZYW  HAF1  CAF  OAL   110.86  3.000
 ZYW  HAF2  CAF  CAG   109.60  3.000
 ZYW  HAF1  CAF  CAG   109.04  3.000
 ZYW  OAL   CAF  CAG   111.81  3.000
 ZYW  CAR   OAL  CAF   112.17  3.000
 ZYW  HAR   CAR  CAE   109.18  3.000
 ZYW  HAR   CAR  OAL   109.66  3.000
 ZYW  CAE   CAR  OAL   108.98  3.000
 ZYW  HAR   CAR  CAH   107.53  3.000
 ZYW  CAE   CAR  CAH   111.13  3.000
 ZYW  OAL   CAR  CAH   110.33  3.000
 ZYW  HAE2  CAE  HAE1  106.32  3.000
 ZYW  HAE2  CAE  NAA   113.72  3.000
 ZYW  HAE1  CAE  NAA   108.62  3.000
 ZYW  HAE2  CAE  CAR   107.48  3.000
 ZYW  HAE1  CAE  CAR   108.92  3.000
 ZYW  NAA   CAE  CAR   111.56  3.000
 ZYW  HAA2  NAA  HAA1  105.58  3.000
 ZYW  HAA2  NAA  CAE   109.34  3.000
 ZYW  HAA1  NAA  CAE   109.11  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
 ZYW  CONST_01  CAP   NAJ  CAC  CAM     0.00   0.0  0
 ZYW  CONST_02  CAP   CAO  CAN  CAM     0.00   0.0  0
 ZYW  CONST_03  CAD   CAO  CAN  CAM   180.00   0.0  0
 ZYW  CONST_04  CAO   CAN  CAM  CAC     0.00   0.0  0
 ZYW  CONST_05  NAK   CAP  NAJ  CAC   180.00   0.0  0
 ZYW  CONST_06  CAO   CAP  NAJ  CAC     0.00   0.0  0
 ZYW  CONST_07  CAN   CAM  CAC  NAJ     0.00   0.0  0
 ZYW  CONST_08  NAI   NAK  CAP  NAJ   180.00   0.0  0
 ZYW  CONST_09  CAD   CAO  CAP  NAJ   180.00   0.0  0
 ZYW  CONST_10  CAN   CAO  CAP  NAJ     0.00   0.0  0
 ZYW  CONST_11  CAD   NAI  NAK  CAP     0.00   0.0  0
 ZYW  CONST_12  NAI   CAD  CAO  CAP     0.00   0.0  0
 ZYW  CONST_13  CAD   CAO  CAP  NAK     0.00   0.0  0
 ZYW  CONST_14  CAN   CAO  CAP  NAK   180.00   0.0  0
 ZYW  CONST_15  CAO   CAD  NAI  NAK     0.00   0.0  0
 ZYW  CONST_16  CAO   CAP  NAK  NAI     0.00   0.0  0
 ZYW  CONST_17  CAN   CAO  CAD  NAI   180.00   0.0  0
 ZYW  CONST_18  NAQ   CAN  CAM  CAC   180.00   0.0  0
 ZYW  CONST_19  NAQ   CAN  CAO  CAP   180.00   0.0  0
 ZYW  CONST_20  NAQ   CAN  CAO  CAD     0.00   0.0  0
 ZYW  CONST_21  NAJ   CAC  CAM  BR    180.00   0.0  0
 ZYW  CONST_22  CAO   CAN  CAM  BR    180.00   0.0  0
 ZYW  CONST_23  NAQ   CAN  CAM  BR      0.00   0.0  0
 ZYW  CONST_24  HAK   NAK  CAP  NAJ     0.00   0.0  0
 ZYW  CONST_25  HAC   CAC  NAJ  CAP   180.00   0.0  0
 ZYW  CONST_26  HAD   CAD  CAO  CAP   180.00   0.0  0
 ZYW  Var_01    CAH   NAQ  CAN  CAM   -64.90  30.0  2
 ZYW  Var_02    CAR   CAH  NAQ  CAN   155.87  30.0  1
 ZYW  Var_03    CAF   CAG  NAQ  CAN  -156.43  30.0  1
 ZYW  Var_04    OAL   CAF  CAG  NAQ   -57.11  30.0  1
 ZYW  Var_05    HAA1  NAA  CAE  CAR   173.92  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
 ZYW  chir_01  CAR  CAH  OAL  CAE  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
 ZYW  plan-1  BR   0.020
 ZYW  plan-1  CAM  0.020
 ZYW  plan-1  CAC  0.020
 ZYW  plan-1  NAJ  0.020
 ZYW  plan-1  CAP  0.020
 ZYW  plan-1  NAK  0.020
 ZYW  plan-1  NAI  0.020
 ZYW  plan-1  CAD  0.020
 ZYW  plan-1  CAO  0.020
 ZYW  plan-1  CAN  0.020
 ZYW  plan-1  NAQ  0.020
 ZYW  plan-1  HAC  0.020
 ZYW  plan-1  HAK  0.020
 ZYW  plan-1  HAD  0.020

