# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:29:39 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2R)-3-benzyl-2-(2-bromo-4-hydroxy-5-methoxyphenyl)-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc([C@H]2SCC(=O)N2Cc3ccccc3)c(Br)cc1O
#
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
 X55  X55  (2R)-3-benzyl-2-(2-bromo-4-hydroxy-5-methoxyphenyl)-1,3-thiazolidin-4-one  ligand  39  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X55
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
 X55  CAA   C   CH3   0  -0.438   2.4164   2.2112  -2.2689
 X55  OAC   O   OH1   0  -0.622  -0.7229   4.0599  -0.4214
 X55  BRAD  BR  BR    0  -0.050  -3.1817  -0.2623   0.8883
 X55  CAE   C   CR16  0  -0.262   2.8228   2.2328   1.6824
 X55  CAF   C   CR16  0  -0.244   3.4811   1.1463   1.1185
 X55  CAG   C   CR16  0  -0.234   1.5530   2.0651   2.2149
 X55  CAH   C   CR16  0  -0.294   2.8618  -0.0937   1.0658
 X55  CAI   C   CR16  0  -0.284   0.9403   0.8199   2.1702
 X55  CAJ   C   CR16  0  -0.306  -1.7397   2.0060   0.0793
 X55  CAK   C   CR16  0  -0.370   0.3366   0.6569  -1.1451
 X55  CAL   C   CH2   0  -0.668   0.8571  -3.3968  -1.8263
 X55  CAM   C   CH2   0  -0.403   0.8852  -1.5989   1.4789
 X55  OAN   O   O2    0  -0.486   1.3095   2.8218  -1.6339
 X55  SAO   S   S2    0   0.040  -0.4480  -2.2295  -2.2623
 X55  CAP   C   CR5   0   0.576   1.4054  -2.9744  -0.4810
 X55  CAQ   C   CR6   0   0.139   1.5789  -0.2638   1.5809
 X55  CAR   C   CR6   0   0.295  -0.7011   2.7200  -0.4822
 X55  CAS   C   CR6   0  -0.206  -1.7273   0.6134   0.0442
 X55  CAT   C   CR6   0   0.333   0.3538   2.0318  -1.1114
 X55  CAU   C   CR6   0   0.198  -0.6930  -0.0845  -0.5548
 X55  CAV   C   CR15  0  -0.320  -0.5637  -1.5844  -0.5499
 X55  NAW   N   NR5   0  -0.422   0.6483  -2.0267   0.1080
 X55  HAA   H   HCH3  0   0.232   2.1098   1.6352  -3.1458
 X55  HAAA  H   HCH3  0   0.264   3.0722   3.0165  -2.5890
 X55  HAAB  H   HCH3  0   0.237   2.9601   1.5584  -1.5826
 X55  HOAC  H   HOH1  0   0.477   0.0735   4.4269  -0.8253
 X55  HAF   H   HCR6  0   0.255   4.4778   1.2688   0.7137
 X55  HAG   H   HCR6  0   0.251   1.0331   2.9042   2.6586
 X55  HAH   H   HCR6  0   0.250   3.3782  -0.9322   0.6139
 X55  HAI   H   HCR6  0   0.244  -0.0565   0.6969   2.5767
 X55  HAJ   H   HCR6  0   0.285  -2.5479   2.5463   0.5550
 X55  HAK   H   HCR6  0   0.285   1.1454   0.1104  -1.6128
 X55  HAL   H   HCH2  0   0.309   0.4819  -4.4187  -1.7473
 X55  HALA  H   HCH2  0   0.312   1.6480  -3.3796  -2.5746
 X55  HAM   H   HCH2  0   0.284   1.4763  -2.3729   1.9686
 X55  HAMA  H   HCH2  0   0.272  -0.0753  -1.5621   1.9977
 X55  HAV   H   HCR5  0   0.301  -1.4213  -2.0464  -0.0587
 X55  OAB   O   O     0  -0.482   2.4039  -3.4707   0.0073
 X55  HAE   H   HCR6  0   0.251   3.3007   3.2036   1.7086

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
 X55  OAN   CAA   single    1.415  0.020  1.415
 X55  CAA   HAA   single    0.970  0.020  1.090
 X55  CAA   HAAA  single    0.970  0.020  1.090
 X55  CAA   HAAB  single    0.970  0.020  1.090
 X55  OAB   CAP   double    1.217  0.020  1.217
 X55  CAR   OAC   single    1.341  0.020  1.341
 X55  OAC   HOAC  single    0.850  0.020  0.980
 X55  BRAD  CAS   single    1.896  0.020  1.896
 X55  CAG   CAE   aromatic  1.387  0.020  1.387
 X55  CAE   CAF   aromatic  1.390  0.020  1.390
 X55  CAE   HAE   single    0.930  0.020  1.080
 X55  CAH   CAF   aromatic  1.387  0.020  1.387
 X55  CAF   HAF   single    0.930  0.020  1.080
 X55  CAI   CAG   aromatic  1.388  0.020  1.388
 X55  CAG   HAG   single    0.930  0.020  1.080
 X55  CAQ   CAH   aromatic  1.393  0.020  1.393
 X55  CAH   HAH   single    0.930  0.020  1.080
 X55  CAI   CAQ   aromatic  1.389  0.020  1.389
 X55  CAI   HAI   single    0.930  0.020  1.080
 X55  CAS   CAJ   aromatic  1.393  0.020  1.393
 X55  CAJ   CAR   aromatic  1.380  0.020  1.380
 X55  CAJ   HAJ   single    0.930  0.020  1.080
 X55  CAU   CAK   aromatic  1.399  0.020  1.399
 X55  CAK   CAT   aromatic  1.375  0.020  1.375
 X55  CAK   HAK   single    0.930  0.020  1.080
 X55  CAP   CAL   single    1.513  0.020  1.513
 X55  CAL   SAO   single    1.804  0.020  1.804
 X55  CAL   HAL   single    0.970  0.020  1.090
 X55  CAL   HALA  single    0.970  0.020  1.090
 X55  CAM   NAW   single    1.455  0.020  1.455
 X55  CAM   CAQ   single    1.508  0.020  1.508
 X55  CAM   HAM   single    0.970  0.020  1.090
 X55  CAM   HAMA  single    0.970  0.020  1.090
 X55  CAT   OAN   single    1.346  0.020  1.346
 X55  CAV   SAO   single    1.834  0.020  1.834
 X55  NAW   CAP   single    1.348  0.020  1.348
 X55  CAR   CAT   aromatic  1.408  0.020  1.408
 X55  CAS   CAU   aromatic  1.384  0.020  1.384
 X55  CAV   CAU   single    1.505  0.020  1.505
 X55  NAW   CAV   single    1.448  0.020  1.448
 X55  CAV   HAV   single    0.970  0.020  1.090

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
 X55  HAAB  CAA  HAAA  109.13  3.000
 X55  HAAB  CAA  HAA   109.20  3.000
 X55  HAAA  CAA  HAA   108.87  3.000
 X55  HAAB  CAA  OAN   111.44  3.000
 X55  HAAA  CAA  OAN   106.53  3.000
 X55  HAA   CAA  OAN   111.60  3.000
 X55  HOAC  OAC  CAR   110.32  3.000
 X55  HAE   CAE  CAG   120.22  3.000
 X55  HAE   CAE  CAF   120.12  3.000
 X55  CAG   CAE  CAF   119.66  3.000
 X55  HAF   CAF  CAH   119.87  3.000
 X55  HAF   CAF  CAE   119.95  3.000
 X55  CAH   CAF  CAE   120.18  3.000
 X55  HAG   CAG  CAI   119.78  3.000
 X55  HAG   CAG  CAE   120.22  3.000
 X55  CAI   CAG  CAE   120.00  3.000
 X55  HAH   CAH  CAQ   119.92  3.000
 X55  HAH   CAH  CAF   119.66  3.000
 X55  CAQ   CAH  CAF   120.42  3.000
 X55  HAI   CAI  CAQ   119.57  3.000
 X55  HAI   CAI  CAG   119.71  3.000
 X55  CAQ   CAI  CAG   120.70  3.000
 X55  HAJ   CAJ  CAS   121.11  3.000
 X55  HAJ   CAJ  CAR   118.86  3.000
 X55  CAS   CAJ  CAR   120.02  3.000
 X55  HAK   CAK  CAU   117.68  3.000
 X55  HAK   CAK  CAT   120.40  3.000
 X55  CAU   CAK  CAT   121.90  3.000
 X55  HALA  CAL  HAL   108.31  3.000
 X55  HALA  CAL  CAP   110.08  3.000
 X55  HAL   CAL  CAP   108.76  3.000
 X55  HALA  CAL  SAO   110.44  3.000
 X55  HAL   CAL  SAO   112.00  3.000
 X55  CAP   CAL  SAO   107.24  3.000
 X55  HAMA  CAM  HAM   106.70  3.000
 X55  HAMA  CAM  NAW   108.31  3.000
 X55  HAM   CAM  NAW   107.62  3.000
 X55  HAMA  CAM  CAQ   110.03  3.000
 X55  HAM   CAM  CAQ   110.41  3.000
 X55  NAW   CAM  CAQ   113.50  3.000
 X55  CAT   OAN  CAA   118.47  3.000
 X55  CAV   SAO  CAL    92.73  3.000
 X55  NAW   CAP  CAL   112.40  3.000
 X55  NAW   CAP  OAB   124.88  3.000
 X55  CAL   CAP  OAB   122.70  3.000
 X55  CAM   CAQ  CAI   120.53  3.000
 X55  CAM   CAQ  CAH   120.45  3.000
 X55  CAI   CAQ  CAH   119.02  3.000
 X55  CAT   CAR  CAJ   119.53  3.000
 X55  CAT   CAR  OAC   121.38  3.000
 X55  CAJ   CAR  OAC   119.09  3.000
 X55  CAU   CAS  CAJ   121.44  3.000
 X55  CAU   CAS  BRAD  122.21  3.000
 X55  CAJ   CAS  BRAD  116.34  3.000
 X55  CAR   CAT  OAN   114.75  3.000
 X55  CAR   CAT  CAK   119.36  3.000
 X55  OAN   CAT  CAK   125.89  3.000
 X55  CAV   CAU  CAS   124.41  3.000
 X55  CAV   CAU  CAK   117.78  3.000
 X55  CAS   CAU  CAK   117.72  3.000
 X55  HAV   CAV  NAW   108.90  3.000
 X55  HAV   CAV  CAU   110.85  3.000
 X55  NAW   CAV  CAU   112.19  3.000
 X55  HAV   CAV  SAO   108.72  3.000
 X55  NAW   CAV  SAO   105.31  3.000
 X55  CAU   CAV  SAO   110.67  3.000
 X55  CAV   NAW  CAP   119.09  3.000
 X55  CAV   NAW  CAM   118.32  3.000
 X55  CAP   NAW  CAM   121.77  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
 X55  CONST_01  CAQ  CAI  CAG  CAE     0.00   0.0  0
 X55  CONST_02  CAQ  CAH  CAF  CAE     0.00   0.0  0
 X55  CONST_03  CAI  CAG  CAE  CAF     0.00   0.0  0
 X55  CONST_04  CAI  CAQ  CAH  CAF     0.00   0.0  0
 X55  CONST_05  CAH  CAF  CAE  CAG     0.00   0.0  0
 X55  CONST_06  CAH  CAQ  CAI  CAG     0.00   0.0  0
 X55  CONST_07  CAK  CAU  CAS  CAJ     0.00   0.0  0
 X55  CONST_08  CAK  CAT  CAR  CAJ     0.00   0.0  0
 X55  CONST_09  CAU  CAS  CAJ  CAR     0.00   0.0  0
 X55  CONST_10  CAU  CAK  CAT  CAR     0.00   0.0  0
 X55  CONST_11  CAT  CAR  CAJ  CAS     0.00   0.0  0
 X55  CONST_12  CAT  CAK  CAU  CAS     0.00   0.0  0
 X55  CONST_13  CAV  CAU  CAS  CAJ   180.00   0.0  0
 X55  CONST_14  CAV  CAU  CAK  CAT   180.00   0.0  0
 X55  CONST_15  CAV  NAW  CAP  CAL     0.00   0.0  0
 X55  CONST_16  CAS  CAJ  CAR  OAC   180.00   0.0  0
 X55  CONST_17  CAK  CAT  CAR  OAC   180.00   0.0  0
 X55  CONST_18  CAR  CAJ  CAS  BRAD  180.00   0.0  0
 X55  CONST_19  CAK  CAU  CAS  BRAD  180.00   0.0  0
 X55  CONST_20  CAV  CAU  CAS  BRAD    0.00   0.0  0
 X55  CONST_21  CAM  CAQ  CAH  CAF   180.00   0.0  0
 X55  CONST_22  CAM  CAQ  CAI  CAG   180.00   0.0  0
 X55  CONST_23  OAN  CAT  CAR  CAJ   180.00   0.0  0
 X55  CONST_24  CAU  CAK  CAT  OAN   180.00   0.0  0
 X55  CONST_25  CAV  NAW  CAP  OAB   180.00   0.0  0
 X55  CONST_26  CAM  NAW  CAP  CAL   180.00   0.0  0
 X55  CONST_27  HAI  CAI  CAG  CAE   180.00   0.0  0
 X55  CONST_28  HAH  CAH  CAF  CAE   180.00   0.0  0
 X55  CONST_29  HAG  CAG  CAE  CAF   180.00   0.0  0
 X55  CONST_30  HAF  CAF  CAE  CAG   180.00   0.0  0
 X55  CONST_31  HAE  CAE  CAF  CAH   180.00   0.0  0
 X55  CONST_32  HAK  CAK  CAT  CAR   180.00   0.0  0
 X55  CONST_33  HAJ  CAJ  CAR  CAT   180.00   0.0  0
 X55  CONST_34  CAM  NAW  CAP  OAB     0.00   0.0  0
 X55  Var_01    NAW  CAP  CAL  SAO    10.51  30.0  1
 X55  Var_02    NAW  CAM  CAQ  CAH   -62.53  30.0  1
 X55  Var_03    CAQ  CAM  NAW  CAP   103.61  30.0  1
 X55  Var_04    HAL  CAL  SAO  CAV   103.89  30.0  1
 X55  Var_05    CAK  CAT  OAN  CAA    -0.73  30.0  2
 X55  Var_06    HAA  CAA  OAN  CAT    62.88  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
 X55  chir_01  CAV  SAO  CAU  NAW  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
 X55  plan-1  CAE   0.020
 X55  plan-1  CAF   0.020
 X55  plan-1  CAG   0.020
 X55  plan-1  CAH   0.020
 X55  plan-1  CAI   0.020
 X55  plan-1  CAM   0.020
 X55  plan-1  CAQ   0.020
 X55  plan-1  HAF   0.020
 X55  plan-1  HAG   0.020
 X55  plan-1  HAH   0.020
 X55  plan-1  HAI   0.020
 X55  plan-1  HAE   0.020
 X55  plan-2  OAC   0.020
 X55  plan-2  BRAD  0.020
 X55  plan-2  CAJ   0.020
 X55  plan-2  CAK   0.020
 X55  plan-2  OAN   0.020
 X55  plan-2  CAR   0.020
 X55  plan-2  CAS   0.020
 X55  plan-2  CAT   0.020
 X55  plan-2  CAU   0.020
 X55  plan-2  CAV   0.020
 X55  plan-2  HAJ   0.020
 X55  plan-2  HAK   0.020
 X55  plan-3  CAL   0.020
 X55  plan-3  CAM   0.020
 X55  plan-3  CAP   0.020
 X55  plan-3  CAV   0.020
 X55  plan-3  NAW   0.020
 X55  plan-3  OAB   0.020

