# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 17:50:03 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2R)-2-(4-hydroxy-3-methoxyphenyl)-3-(pyridin-2-ylmethyl)-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)[C@H]2SCC(=O)N2Cc3ccccn3
#
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
 5PE  5PE  (2R)-2-(4-hydroxy-3-methoxyphenyl)-3-(pyridin-2-ylmethyl)-1,3-thiazolidin-4-one  ligand  38  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5PE
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
 5PE  CAA   C  CH3   0  -0.433   3.1044   2.4956  -1.6935
 5PE  OAN   O  O2    0  -0.489   3.6778   1.8149  -0.5951
 5PE  CAT   C  CR6   0   0.310   2.9989   0.7807  -0.0525
 5PE  CAJ   C  CR16  0  -0.406   1.7858   0.2909  -0.5090
 5PE  CAR   C  CR6   0   0.278   3.6110   0.1933   1.0659
 5PE  OAC   O  OH1   0  -0.628   4.7890   0.6433   1.5377
 5PE  CAH   C  CR16  0  -0.333   2.9902  -0.8715   1.7008
 5PE  CAI   C  CR16  0  -0.288   1.7779  -1.3608   1.2351
 5PE  CAS   C  CR6   0   0.116   1.1727  -0.7863   0.1280
 5PE  CAU   C  CH1   0  -0.291  -0.1595  -1.2641  -0.3733
 5PE  SAO   S  S2    0   0.034  -0.1282  -3.0621  -0.7186
 5PE  CAK   C  CH2   0  -0.676  -1.8265  -3.2752  -0.1458
 5PE  CAP   C  C     0   0.572  -2.1592  -2.0658   0.7005
 5PE  OAB   O  O     0  -0.475  -3.1730  -1.9825   1.3687
 5PE  NAV   N  NT    0  -0.435  -1.2202  -1.1014   0.6050
 5PE  CAL   C  CH2   0  -0.387  -1.4411   0.2059   1.1987
 5PE  CAQ   C  CR6   0   0.260  -2.2040   1.1155   0.2721
 5PE  CAG   C  CR16  0  -0.329  -3.5565   1.3715   0.4658
 5PE  CAE   C  CR16  0  -0.150  -4.2149   2.1996  -0.4311
 5PE  CAD   C  CR16  0  -0.327  -3.5023   2.7354  -1.4923
 5PE  CAF   C  CR16  0  -0.074  -2.1563   2.4173  -1.6039
 5PE  NAM   N  N     0  -0.408  -1.5184   1.6322  -0.7459
 5PE  HAA1  H  HCH3  0   0.265   3.7966   3.2893  -1.9629
 5PE  HAA2  H  HCH3  0   0.232   2.9697   1.8354  -2.5538
 5PE  HAA3  H  HCH3  0   0.228   2.1406   2.9418  -1.4342
 5PE  HAJ   H  HCR6  0   0.282   1.2876   0.7472  -1.3542
 5PE  HAC   H  HOH1  0   0.473   5.1027   1.3828   1.0027
 5PE  HAH   H  HCR6  0   0.266   3.4672  -1.3188   2.5641
 5PE  HAI   H  HCR6  0   0.252   1.3099  -2.1958   1.7409
 5PE  HAU   H  HCH1  0   0.298  -0.4152  -0.7276  -1.2902
 5PE  HAK1  H  HCH2  0   0.306  -2.5351  -3.3287  -0.9744
 5PE  HAK2  H  HCH2  0   0.311  -1.9196  -4.1863   0.4438
 5PE  HAL1  H  HCH2  0   0.281  -1.9750   0.0715   2.1376
 5PE  HAL2  H  HCH2  0   0.286  -0.4706   0.6438   1.4339
 5PE  HAG   H  HCR6  0   0.269  -4.0803   0.9300   1.3029
 5PE  HAE   H  HCR6  0   0.275  -5.2661   2.4219  -0.3027
 5PE  HAD   H  HCR6  0   0.272  -3.9728   3.3847  -2.2176
 5PE  HAF   H  HCR6  0   0.263  -1.5663   2.8192  -2.4202

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
 5PE  CAA  OAN   single    1.414  0.020  1.414
 5PE  OAN  CAT   single    1.351  0.020  1.351
 5PE  CAT  CAJ   aromatic  1.386  0.020  1.386
 5PE  CAT  CAR   aromatic  1.404  0.020  1.404
 5PE  CAJ  CAS   aromatic  1.393  0.020  1.393
 5PE  CAR  OAC   single    1.346  0.020  1.346
 5PE  CAR  CAH   aromatic  1.386  0.020  1.386
 5PE  CAH  CAI   aromatic  1.388  0.020  1.388
 5PE  CAI  CAS   aromatic  1.386  0.020  1.386
 5PE  CAS  CAU   single    1.501  0.020  1.501
 5PE  CAU  SAO   single    1.831  0.020  1.831
 5PE  CAU  NAV   single    1.452  0.020  1.452
 5PE  SAO  CAK   single    1.805  0.020  1.805
 5PE  CAK  CAP   single    1.513  0.020  1.513
 5PE  CAP  OAB   double    1.217  0.020  1.217
 5PE  CAP  NAV   single    1.350  0.020  1.350
 5PE  NAV  CAL   single    1.453  0.020  1.453
 5PE  CAL  CAQ   single    1.506  0.020  1.506
 5PE  CAQ  CAG   aromatic  1.390  0.020  1.390
 5PE  CAQ  NAM   aromatic  1.332  0.020  1.332
 5PE  CAG  CAE   aromatic  1.387  0.020  1.387
 5PE  CAE  CAD   aromatic  1.386  0.020  1.386
 5PE  CAD  CAF   aromatic  1.388  0.020  1.388
 5PE  CAF  NAM   aromatic  1.326  0.020  1.326
 5PE  CAA  HAA1  single    0.970  0.020  1.090
 5PE  CAA  HAA2  single    0.970  0.020  1.090
 5PE  CAA  HAA3  single    0.970  0.020  1.090
 5PE  CAJ  HAJ   single    0.930  0.020  1.080
 5PE  OAC  HAC   single    0.850  0.020  0.980
 5PE  CAH  HAH   single    0.930  0.020  1.080
 5PE  CAI  HAI   single    0.930  0.020  1.080
 5PE  CAU  HAU   single    0.970  0.020  1.090
 5PE  CAK  HAK1  single    0.970  0.020  1.090
 5PE  CAK  HAK2  single    0.970  0.020  1.090
 5PE  CAL  HAL1  single    0.970  0.020  1.090
 5PE  CAL  HAL2  single    0.970  0.020  1.090
 5PE  CAG  HAG   single    0.930  0.020  1.080
 5PE  CAE  HAE   single    0.930  0.020  1.080
 5PE  CAD  HAD   single    0.930  0.020  1.080
 5PE  CAF  HAF   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
 5PE  HAA3  CAA  HAA2  108.94  3.000
 5PE  HAA3  CAA  HAA1  108.79  3.000
 5PE  HAA2  CAA  HAA1  108.94  3.000
 5PE  HAA3  CAA  OAN   111.70  3.000
 5PE  HAA2  CAA  OAN   111.76  3.000
 5PE  HAA1  CAA  OAN   106.61  3.000
 5PE  CAT   OAN  CAA   118.48  3.000
 5PE  CAR   CAT  CAJ   119.76  3.000
 5PE  CAR   CAT  OAN   114.91  3.000
 5PE  CAJ   CAT  OAN   125.33  3.000
 5PE  HAJ   CAJ  CAS   118.72  3.000
 5PE  HAJ   CAJ  CAT   120.75  3.000
 5PE  CAS   CAJ  CAT   120.52  3.000
 5PE  CAH   CAR  OAC   119.21  3.000
 5PE  CAH   CAR  CAT   119.40  3.000
 5PE  OAC   CAR  CAT   121.39  3.000
 5PE  HAC   OAC  CAR   110.26  3.000
 5PE  HAH   CAH  CAI   120.44  3.000
 5PE  HAH   CAH  CAR   119.01  3.000
 5PE  CAI   CAH  CAR   120.55  3.000
 5PE  HAI   CAI  CAS   120.27  3.000
 5PE  HAI   CAI  CAH   119.53  3.000
 5PE  CAS   CAI  CAH   120.21  3.000
 5PE  CAU   CAS  CAI   121.47  3.000
 5PE  CAU   CAS  CAJ   118.93  3.000
 5PE  CAI   CAS  CAJ   119.56  3.000
 5PE  HAU   CAU  NAV   109.84  3.000
 5PE  HAU   CAU  SAO   109.14  3.000
 5PE  NAV   CAU  SAO   104.45  3.000
 5PE  HAU   CAU  CAS   109.36  3.000
 5PE  NAV   CAU  CAS   112.80  3.000
 5PE  SAO   CAU  CAS   111.12  3.000
 5PE  CAK   SAO  CAU    92.29  3.000
 5PE  HAK2  CAK  HAK1  108.33  3.000
 5PE  HAK2  CAK  CAP   110.30  3.000
 5PE  HAK1  CAK  CAP   108.72  3.000
 5PE  HAK2  CAK  SAO   110.55  3.000
 5PE  HAK1  CAK  SAO   112.06  3.000
 5PE  CAP   CAK  SAO   106.86  3.000
 5PE  NAV   CAP  OAB   124.72  3.000
 5PE  NAV   CAP  CAK   112.25  3.000
 5PE  OAB   CAP  CAK   123.02  3.000
 5PE  CAL   NAV  CAP   120.55  3.000
 5PE  CAL   NAV  CAU   119.17  3.000
 5PE  CAP   NAV  CAU   118.42  3.000
 5PE  HAL2  CAL  HAL1  107.46  3.000
 5PE  HAL2  CAL  CAQ   109.94  3.000
 5PE  HAL1  CAL  CAQ   110.91  3.000
 5PE  HAL2  CAL  NAV   108.31  3.000
 5PE  HAL1  CAL  NAV   108.42  3.000
 5PE  CAQ   CAL  NAV   111.66  3.000
 5PE  NAM   CAQ  CAG   122.41  3.000
 5PE  NAM   CAQ  CAL   116.36  3.000
 5PE  CAG   CAQ  CAL   121.22  3.000
 5PE  HAG   CAG  CAE   120.95  3.000
 5PE  HAG   CAG  CAQ   120.26  3.000
 5PE  CAE   CAG  CAQ   118.80  3.000
 5PE  HAE   CAE  CAD   120.72  3.000
 5PE  HAE   CAE  CAG   120.47  3.000
 5PE  CAD   CAE  CAG   118.81  3.000
 5PE  HAD   CAD  CAF   120.39  3.000
 5PE  HAD   CAD  CAE   121.47  3.000
 5PE  CAF   CAD  CAE   118.15  3.000
 5PE  HAF   CAF  NAM   116.40  3.000
 5PE  HAF   CAF  CAD   120.22  3.000
 5PE  NAM   CAF  CAD   123.37  3.000
 5PE  CAF   NAM  CAQ   118.46  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
 5PE  CONST_01  CAI   CAS  CAJ  CAT    0.00   0.0  0
 5PE  CONST_02  CAI   CAH  CAR  CAT    0.00   0.0  0
 5PE  CONST_03  CAH   CAR  CAT  CAJ    0.00   0.0  0
 5PE  CONST_04  CAH   CAI  CAS  CAJ    0.00   0.0  0
 5PE  CONST_05  CAS   CAJ  CAT  CAR    0.00   0.0  0
 5PE  CONST_06  CAS   CAI  CAH  CAR    0.00   0.0  0
 5PE  CONST_07  CAD   CAE  CAG  CAQ    0.00   0.0  0
 5PE  CONST_08  CAD   CAF  NAM  CAQ    0.00   0.0  0
 5PE  CONST_09  CAF   NAM  CAQ  CAG    0.00   0.0  0
 5PE  CONST_10  CAF   CAD  CAE  CAG    0.00   0.0  0
 5PE  CONST_11  NAM   CAQ  CAG  CAE    0.00   0.0  0
 5PE  CONST_12  NAM   CAF  CAD  CAE    0.00   0.0  0
 5PE  CONST_13  CAU   CAS  CAJ  CAT  180.00   0.0  0
 5PE  CONST_14  CAU   CAS  CAI  CAH  180.00   0.0  0
 5PE  CONST_15  CAK   CAP  NAV  CAU    0.00   0.0  0
 5PE  CONST_16  CAS   CAJ  CAT  OAN  180.00   0.0  0
 5PE  CONST_17  CAH   CAR  CAT  OAN  180.00   0.0  0
 5PE  CONST_18  OAC   CAR  CAT  CAJ  180.00   0.0  0
 5PE  CONST_19  CAI   CAH  CAR  OAC  180.00   0.0  0
 5PE  CONST_20  CAE   CAG  CAQ  CAL  180.00   0.0  0
 5PE  CONST_21  CAF   NAM  CAQ  CAL  180.00   0.0  0
 5PE  CONST_22  OAB   CAP  NAV  CAU  180.00   0.0  0
 5PE  CONST_23  CAL   NAV  CAP  CAK  180.00   0.0  0
 5PE  CONST_24  HAH   CAH  CAR  CAT  180.00   0.0  0
 5PE  CONST_25  HAI   CAI  CAS  CAJ  180.00   0.0  0
 5PE  CONST_26  HAJ   CAJ  CAT  CAR  180.00   0.0  0
 5PE  CONST_27  HAE   CAE  CAG  CAQ  180.00   0.0  0
 5PE  CONST_28  HAF   CAF  NAM  CAQ  180.00   0.0  0
 5PE  CONST_29  HAD   CAD  CAE  CAG  180.00   0.0  0
 5PE  CONST_30  HAG   CAG  CAE  CAD  180.00   0.0  0
 5PE  CONST_31  CAL   NAV  CAP  OAB    0.00   0.0  0
 5PE  Var_01    CAP   CAK  SAO  CAU  -18.72  30.0  1
 5PE  Var_02    NAV   CAP  CAK  SAO   10.33  30.0  1
 5PE  Var_03    CAQ   CAL  NAV  CAU   78.87  30.0  3
 5PE  Var_04    CAG   CAQ  CAL  NAV  103.04  30.0  2
 5PE  Var_05    CAJ   CAT  OAN  CAA    2.09  30.0  2
 5PE  Var_06    HAA1  CAA  OAN  CAT  179.22  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
 5PE  chir_01  CAU  CAS  SAO  NAV  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
 5PE  plan-1  OAN  0.020
 5PE  plan-1  CAT  0.020
 5PE  plan-1  CAJ  0.020
 5PE  plan-1  CAR  0.020
 5PE  plan-1  OAC  0.020
 5PE  plan-1  CAH  0.020
 5PE  plan-1  CAI  0.020
 5PE  plan-1  CAS  0.020
 5PE  plan-1  CAU  0.020
 5PE  plan-1  HAJ  0.020
 5PE  plan-1  HAH  0.020
 5PE  plan-1  HAI  0.020
 5PE  plan-2  CAL  0.020
 5PE  plan-2  CAQ  0.020
 5PE  plan-2  CAG  0.020
 5PE  plan-2  CAE  0.020
 5PE  plan-2  CAD  0.020
 5PE  plan-2  CAF  0.020
 5PE  plan-2  NAM  0.020
 5PE  plan-2  HAG  0.020
 5PE  plan-2  HAE  0.020
 5PE  plan-2  HAD  0.020
 5PE  plan-2  HAF  0.020
 5PE  plan-3  CAU  0.020
 5PE  plan-3  CAK  0.020
 5PE  plan-3  CAP  0.020
 5PE  plan-3  OAB  0.020
 5PE  plan-3  NAV  0.020
 5PE  plan-3  CAL  0.020

