# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:47:31 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-5-[(3,4-dichlorophenyl)methyl]pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CN2C=Nc3n(ncc3C2=O)[C@@H]4CC[S](=O)(=O)C4)cc1Cl
#
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
 GZK  GZK  1-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-5-[(3,4-dichlorophenyl)methyl]pyrazolo[3,4-d]pyrimidin-4-one  ligand  40  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GZK
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
 GZK  CAL  C   CH2   0  -0.472  -5.0634   0.7937  -0.6667
 GZK  CAM  C   CH2   0  -0.616  -6.1412  -0.1816  -1.1042
 GZK  SAN  S   S     0   1.224  -5.9056  -1.5910  -0.0070
 GZK  OAO  O   OS    0  -0.683  -6.6330  -1.3463   1.2372
 GZK  OAZ  O   OS    0  -0.674  -6.1279  -2.8528  -0.7066
 GZK  CAY  C   CH2   0  -0.613  -4.1370  -1.3043   0.2830
 GZK  CAK  C   CH1   0  -0.099  -3.7900  -0.0466  -0.5260
 GZK  NAG  N   NR5   0  -0.382  -2.7028   0.6902   0.0655
 GZK  NAH  N   N     0  -0.257  -2.8358   1.2677   1.2712
 GZK  CAI  C   CR15  0  -0.050  -1.6962   1.8586   1.5346
 GZK  CAJ  C   CR56  0  -0.333  -0.7846   1.6642   0.4772
 GZK  CAB  C   CR6   0   0.571   0.5604   2.0545   0.1959
 GZK  OAA  O   O     0  -0.444   1.2984   2.7317   0.8834
 GZK  CAF  C   CR56  0   0.611  -1.4799   0.9009  -0.4481
 GZK  NAE  N   N     0  -0.460  -1.0180   0.4591  -1.6361
 GZK  CAD  C   CR16  0   0.185   0.2017   0.8118  -1.8687
 GZK  NAC  N   NR6   0  -0.520   0.9921   1.5523  -1.0479
 GZK  CAP  C   CH2   0  -0.412   2.3655   1.8483  -1.4472
 GZK  CAQ  C   CR6   0   0.141   3.3739   1.1065  -0.6106
 GZK  CAR  C   CR16  0  -0.251   3.3558  -0.2815  -0.5696
 GZK  CAS  C   CR6   0   0.022   4.2908  -0.9741   0.1825
 GZK  CL1  CL  CL    0  -0.094   4.2412  -2.6955   0.2134
 GZK  CAW  C   CR6   0  -0.017   5.2612  -0.2806   0.8983
 GZK  CL2  CL  CL    0  -0.095   6.4339  -1.1249   1.8339
 GZK  CAV  C   CR16  0  -0.202   5.2844   1.1048   0.8579
 GZK  CAU  C   CR16  0  -0.296   4.3416   1.7918   0.1114
 GZK  H1   H   HCH2  0   0.299  -4.9291   1.5856  -1.4019
 GZK  H2   H   HCH2  0   0.278  -5.3252   1.2523   0.2881
 GZK  H3   H   HCH2  0   0.328  -7.1596   0.1848  -0.9863
 GZK  H4   H   HCH2  0   0.311  -5.9891  -0.5238  -2.1287
 GZK  H5   H   HCH2  0   0.320  -4.0055  -1.1468   1.3531
 GZK  H6   H   HCH2  0   0.328  -3.5770  -2.1824  -0.0319
 GZK  H7   H   HCH1  0   0.313  -3.4527  -0.3448  -1.5192
 GZK  H8   H   HCR5  0   0.282  -1.5562   2.3982   2.4583
 GZK  H9   H   HCR6  0   0.309   0.6633   0.5053  -2.7990
 GZK  H10  H   HCH2  0   0.303   2.4666   1.5683  -2.4958
 GZK  H11  H   HCH2  0   0.301   2.5322   2.9225  -1.3859
 GZK  H12  H   HCR6  0   0.283   2.6139  -0.8413  -1.1255
 GZK  H13  H   HCR6  0   0.291   6.0366   1.6442   1.4168
 GZK  H14  H   HCR6  0   0.271   4.3641   2.8734   0.0960

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
 GZK  OAO  SAN  double    1.462  0.020  1.462
 GZK  CAI  NAH  aromatic  1.310  0.020  1.310
 GZK  CAI  CAJ  aromatic  1.410  0.020  1.410
 GZK  NAH  NAG  aromatic  1.344  0.020  1.344
 GZK  OAA  CAB  double    1.215  0.020  1.215
 GZK  CAJ  CAB  single    1.428  0.020  1.428
 GZK  CAJ  CAF  aromatic  1.386  0.020  1.386
 GZK  SAN  CAY  single    1.815  0.020  1.815
 GZK  SAN  OAZ  double    1.460  0.020  1.460
 GZK  SAN  CAM  single    1.802  0.020  1.802
 GZK  CAY  CAK  single    1.535  0.020  1.535
 GZK  CAB  NAC  single    1.409  0.020  1.409
 GZK  NAG  CAF  aromatic  1.343  0.020  1.343
 GZK  NAG  CAK  single    1.440  0.020  1.440
 GZK  CAF  NAE  single    1.349  0.020  1.349
 GZK  CAM  CAL  single    1.518  0.020  1.518
 GZK  CAK  CAL  single    1.532  0.020  1.532
 GZK  NAC  CAP  single    1.461  0.020  1.461
 GZK  NAC  CAD  single    1.359  0.020  1.359
 GZK  CAU  CAV  aromatic  1.385  0.020  1.385
 GZK  CAU  CAQ  aromatic  1.388  0.020  1.388
 GZK  CAP  CAQ  single    1.506  0.020  1.506
 GZK  CAV  CAW  aromatic  1.386  0.020  1.386
 GZK  NAE  CAD  double    1.291  0.020  1.291
 GZK  CAQ  CAR  aromatic  1.389  0.020  1.389
 GZK  CAW  CL2  single    1.722  0.020  1.722
 GZK  CAW  CAS  aromatic  1.391  0.020  1.391
 GZK  CAR  CAS  aromatic  1.386  0.020  1.386
 GZK  CAS  CL1  single    1.722  0.020  1.722
 GZK  CAL  H1   single    0.970  0.020  1.090
 GZK  CAL  H2   single    0.970  0.020  1.090
 GZK  CAM  H3   single    0.970  0.020  1.090
 GZK  CAM  H4   single    0.970  0.020  1.090
 GZK  CAY  H5   single    0.970  0.020  1.090
 GZK  CAY  H6   single    0.970  0.020  1.090
 GZK  CAK  H7   single    0.970  0.020  1.090
 GZK  CAI  H8   single    0.930  0.020  1.080
 GZK  CAD  H9   single    0.930  0.020  1.080
 GZK  CAP  H10  single    0.970  0.020  1.090
 GZK  CAP  H11  single    0.970  0.020  1.090
 GZK  CAR  H12  single    0.930  0.020  1.080
 GZK  CAV  H13  single    0.930  0.020  1.080
 GZK  CAU  H14  single    0.930  0.020  1.080

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
 GZK  H2   CAL  H1   108.35  3.000
 GZK  H2   CAL  CAK  110.46  3.000
 GZK  H1   CAL  CAK  111.00  3.000
 GZK  H2   CAL  CAM  110.60  3.000
 GZK  H1   CAL  CAM  111.11  3.000
 GZK  CAK  CAL  CAM  105.32  3.000
 GZK  H4   CAM  H3   109.74  3.000
 GZK  H4   CAM  SAN  107.96  3.000
 GZK  H3   CAM  SAN  108.64  3.000
 GZK  H4   CAM  CAL  111.92  3.000
 GZK  H3   CAM  CAL  114.62  3.000
 GZK  SAN  CAM  CAL  103.55  3.000
 GZK  CAY  SAN  OAZ  111.19  3.000
 GZK  OAZ  SAN  OAO  118.48  3.000
 GZK  CAY  SAN  OAO  108.81  3.000
 GZK  OAZ  SAN  CAM  111.37  3.000
 GZK  CAY  SAN  CAM   95.80  3.000
 GZK  OAO  SAN  CAM  108.80  3.000
 GZK  H6   CAY  H5   109.81  3.000
 GZK  H6   CAY  CAK  113.10  3.000
 GZK  H5   CAY  CAK  111.83  3.000
 GZK  H6   CAY  SAN  109.13  3.000
 GZK  H5   CAY  SAN  107.29  3.000
 GZK  CAK  CAY  SAN  105.39  3.000
 GZK  H7   CAK  NAG  106.28  3.000
 GZK  H7   CAK  CAY  109.02  3.000
 GZK  NAG  CAK  CAY  111.91  3.000
 GZK  H7   CAK  CAL  108.87  3.000
 GZK  NAG  CAK  CAL  112.61  3.000
 GZK  CAY  CAK  CAL  108.05  3.000
 GZK  CAF  NAG  NAH  111.46  3.000
 GZK  CAF  NAG  CAK  127.63  3.000
 GZK  NAH  NAG  CAK  120.91  3.000
 GZK  CAI  NAH  NAG  106.75  3.000
 GZK  H8   CAI  CAJ  128.85  3.000
 GZK  H8   CAI  NAH  120.70  3.000
 GZK  CAJ  CAI  NAH  110.45  3.000
 GZK  CAF  CAJ  CAB  119.43  3.000
 GZK  CAF  CAJ  CAI  104.61  3.000
 GZK  CAB  CAJ  CAI  135.97  3.000
 GZK  NAC  CAB  OAA  120.80  3.000
 GZK  NAC  CAB  CAJ  111.40  3.000
 GZK  OAA  CAB  CAJ  127.80  3.000
 GZK  NAE  CAF  CAJ  126.60  3.000
 GZK  NAE  CAF  NAG  126.67  3.000
 GZK  CAJ  CAF  NAG  106.73  3.000
 GZK  CAD  NAE  CAF  113.13  3.000
 GZK  H9   CAD  NAC  115.16  3.000
 GZK  H9   CAD  NAE  118.71  3.000
 GZK  NAC  CAD  NAE  126.13  3.000
 GZK  CAP  NAC  CAD  119.48  3.000
 GZK  CAD  NAC  CAB  123.31  3.000
 GZK  CAP  NAC  CAB  117.21  3.000
 GZK  H11  CAP  H10  107.06  3.000
 GZK  H11  CAP  CAQ  110.62  3.000
 GZK  H10  CAP  CAQ  110.24  3.000
 GZK  H11  CAP  NAC  109.18  3.000
 GZK  H10  CAP  NAC  107.35  3.000
 GZK  CAQ  CAP  NAC  112.21  3.000
 GZK  CAU  CAQ  CAR  119.15  3.000
 GZK  CAR  CAQ  CAP  120.00  3.000
 GZK  CAU  CAQ  CAP  120.84  3.000
 GZK  H12  CAR  CAS  118.85  3.000
 GZK  H12  CAR  CAQ  120.69  3.000
 GZK  CAS  CAR  CAQ  120.45  3.000
 GZK  CAW  CAS  CL1  120.60  3.000
 GZK  CL1  CAS  CAR  119.34  3.000
 GZK  CAW  CAS  CAR  120.06  3.000
 GZK  CAV  CAW  CL2  119.64  3.000
 GZK  CL2  CAW  CAS  120.69  3.000
 GZK  CAV  CAW  CAS  119.67  3.000
 GZK  H13  CAV  CAU  120.31  3.000
 GZK  H13  CAV  CAW  119.68  3.000
 GZK  CAU  CAV  CAW  120.00  3.000
 GZK  H14  CAU  CAV  119.30  3.000
 GZK  H14  CAU  CAQ  120.04  3.000
 GZK  CAV  CAU  CAQ  120.66  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
 GZK  CONST_01  CAJ  CAI  NAH  NAG     0.00   0.0  0
 GZK  CONST_02  CAI  CAJ  CAF  NAG     0.00   0.0  0
 GZK  CONST_03  CAF  CAJ  CAI  NAH     0.00   0.0  0
 GZK  CONST_04  CAJ  CAF  NAG  NAH     0.00   0.0  0
 GZK  CONST_05  CAF  NAG  NAH  CAI     0.00   0.0  0
 GZK  CONST_06  CAW  CAV  CAU  CAQ     0.00   0.0  0
 GZK  CONST_07  CAW  CAS  CAR  CAQ     0.00   0.0  0
 GZK  CONST_08  CAV  CAU  CAQ  CAR     0.00   0.0  0
 GZK  CONST_09  CAV  CAW  CAS  CAR     0.00   0.0  0
 GZK  CONST_10  CAU  CAV  CAW  CAS     0.00   0.0  0
 GZK  CONST_11  CAU  CAQ  CAR  CAS     0.00   0.0  0
 GZK  CONST_12  CAI  NAH  NAG  CAK   180.00   0.0  0
 GZK  CONST_13  CAJ  CAF  NAG  CAK   180.00   0.0  0
 GZK  CONST_14  NAE  CAF  NAG  CAK     0.00   0.0  0
 GZK  CONST_15  CAD  NAC  CAB  CAJ     0.00   0.0  0
 GZK  CONST_16  NAE  CAD  NAC  CAB     0.00   0.0  0
 GZK  CONST_17  NAC  CAD  NAE  CAF     0.00   0.0  0
 GZK  CONST_18  CAV  CAU  CAQ  CAP   180.00   0.0  0
 GZK  CONST_19  CAS  CAR  CAQ  CAP   180.00   0.0  0
 GZK  CONST_20  CL1  CAS  CAR  CAQ   180.00   0.0  0
 GZK  CONST_21  CL2  CAW  CAS  CAR   180.00   0.0  0
 GZK  CONST_22  CAV  CAW  CAS  CL1   180.00   0.0  0
 GZK  CONST_23  CAU  CAV  CAW  CL2   180.00   0.0  0
 GZK  CONST_24  CAP  NAC  CAB  CAJ   180.00   0.0  0
 GZK  CONST_25  CAD  NAC  CAB  OAA   180.00   0.0  0
 GZK  CONST_26  CAP  NAC  CAD  NAE   180.00   0.0  0
 GZK  CONST_27  H8   CAI  NAH  NAG   180.00   0.0  0
 GZK  CONST_28  H13  CAV  CAU  CAQ   180.00   0.0  0
 GZK  CONST_29  H14  CAU  CAQ  CAR   180.00   0.0  0
 GZK  CONST_30  H12  CAR  CAS  CAW   180.00   0.0  0
 GZK  CONST_31  H9   CAD  NAC  CAB   180.00   0.0  0
 GZK  CONST_32  CAP  NAC  CAB  OAA     0.00   0.0  0
 GZK  Var_01    CAY  SAN  CAM  CAL   -26.83  30.0  1
 GZK  Var_02    CAK  CAY  SAN  CAM     0.39  30.0  1
 GZK  Var_03    CAK  CAL  CAM  SAN    45.64  30.0  1
 GZK  Var_04    CAQ  CAP  NAC  CAB    69.93  30.0  3
 GZK  Var_05    CAU  CAQ  CAP  NAC  -121.85  30.0  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
 GZK  chir_01  CAK  CAY  NAG  CAL  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
 GZK  plan-1  CAP  0.020
 GZK  plan-1  CAQ  0.020
 GZK  plan-1  CAR  0.020
 GZK  plan-1  CAS  0.020
 GZK  plan-1  CL1  0.020
 GZK  plan-1  CAW  0.020
 GZK  plan-1  CL2  0.020
 GZK  plan-1  CAV  0.020
 GZK  plan-1  CAU  0.020
 GZK  plan-1  H12  0.020
 GZK  plan-1  H13  0.020
 GZK  plan-1  H14  0.020
 GZK  plan-2  CAK  0.020
 GZK  plan-2  NAG  0.020
 GZK  plan-2  NAH  0.020
 GZK  plan-2  CAI  0.020
 GZK  plan-2  CAJ  0.020
 GZK  plan-2  CAB  0.020
 GZK  plan-2  OAA  0.020
 GZK  plan-2  CAF  0.020
 GZK  plan-2  NAE  0.020
 GZK  plan-2  CAD  0.020
 GZK  plan-2  NAC  0.020
 GZK  plan-2  CAP  0.020
 GZK  plan-2  H8   0.020
 GZK  plan-2  H9   0.020

