# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 05:21:48 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (2R)-2-[(5Z)-5-(5-bromo-2-oxo-1H-indol-3-ylidene)-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H](N1C(=S)SC(/C1=O)=C/2C(=O)Nc3ccc(Br)cc/23)C(O)=O
#
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
 Z89  Z89  '(2R)-2-[(5Z)-5-(5-bromo-2-oxo-1H-indol-3-ylidene)-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]butanedioic acid'  ligand  35  26  .  2021-08-26  2021-08-26  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z89
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
 Z89  C     C   C     0   0.584  -3.6196   1.5775  -1.5972
 Z89  N     N   NR5   0  -0.486  -2.2040   0.1462  -0.2610
 Z89  OXT   O   OH1   0  -0.577  -4.6457   2.4003  -1.5122
 Z89  CA    C   CH1   0  -0.272  -2.8963   1.4221  -0.2631
 Z89  CB    C   CH2   0  -0.592  -3.7511   1.6518   0.9784
 Z89  CG    C   C     0   0.572  -2.9777   1.4864   2.2591
 Z89  CAA   C   CR56  0   0.397   3.1525  -2.1913   0.0918
 Z89  CAB   C   CR56  0   0.033   2.2319  -1.1307  -0.0030
 Z89  CAC   C   CR16  0  -0.355   2.7011   0.1777   0.0193
 Z89  CAD   C   CR6   0  -0.105   4.0685   0.3859   0.1345
 Z89  BRAE  BR  BR    0  -0.039   4.7215   2.1573   0.1666
 Z89  CAF   C   CR16  0  -0.228   4.9685  -0.6685   0.2245
 Z89  CAG   C   CR16  0  -0.293   4.5101  -1.9799   0.2040
 Z89  CAH   C   CR5   0   0.133   0.9159  -1.7409  -0.0928
 Z89  CAI   C   CR5   0   0.552   1.1498  -3.2229  -0.0460
 Z89  NAJ   N   NR15  0  -0.765   2.4866  -3.4026   0.0590
 Z89  OAK   O   O     0  -0.423   0.2869  -4.0754  -0.0946
 Z89  CAL   C   CR5   0  -0.454  -0.3580  -1.3099  -0.1858
 Z89  CAM   C   CR5   0   0.689  -0.8151   0.0953  -0.2616
 Z89  CAW   C   CR5   0   0.027  -2.8513  -1.0450  -0.3123
 Z89  SAX   S   S1    0  -0.157  -4.4582  -1.2931  -0.4363
 Z89  SAY   S   S2    0   0.303  -1.7353  -2.3851  -0.2431
 Z89  OAZ   O   O     0  -0.383  -0.1161   1.0699  -0.3386
 Z89  OD1   O   OH1   0  -0.590  -3.7661   1.6395   3.3128
 Z89  OD2   O   O     0  -0.430  -1.7976   1.2550   2.3355
 Z89  O     O   O     0  -0.419  -3.2309   1.0608  -2.6093
 Z89  HO    H   HOH1  0   0.495  -5.0505   2.5286  -2.3844
 Z89  HA    H   HCH1  0   0.354  -2.1122   2.1854  -0.2785
 Z89  HB    H   HCH2  0   0.325  -4.1352   2.6741   0.9549
 Z89  HBA   H   HCH2  0   0.305  -4.6244   0.9986   0.9989
 Z89  HAF   H   HCR6  0   0.293   6.0306  -0.4844   0.3110
 Z89  HAG   H   HCR6  0   0.291   5.2061  -2.8041   0.2754
 Z89  HNAJ  H   HNR5  0   0.429   2.9291  -4.3078   0.1178
 Z89  HOD1  H   HOH1  0   0.485  -3.2527   1.5465   4.1297
 Z89  HAC   H   HCR6  0   0.302   2.0195   1.0086  -0.0511

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
 Z89  CA   C     single    1.526  0.020  1.526
 Z89  C    O     double    1.201  0.020  1.201
 Z89  C    OXT   single    1.318  0.020  1.318
 Z89  CAW  N     single    1.357  0.020  1.357
 Z89  N    CAM   single    1.390  0.020  1.390
 Z89  N    CA    single    1.452  0.020  1.452
 Z89  OXT  HO    single    0.850  0.020  0.980
 Z89  CA   CB    single    1.525  0.020  1.525
 Z89  CA   HA    single    0.970  0.020  1.090
 Z89  CB   CG    single    1.505  0.020  1.505
 Z89  CB   HB    single    0.970  0.020  1.090
 Z89  CB   HBA   single    0.970  0.020  1.090
 Z89  OD2  CG    double    1.205  0.020  1.205
 Z89  CG   OD1   single    1.325  0.020  1.325
 Z89  NAJ  CAA   single    1.383  0.020  1.383
 Z89  CAA  CAB   aromatic  1.408  0.020  1.408
 Z89  CAA  CAG   aromatic  1.379  0.020  1.379
 Z89  CAH  CAB   single    1.453  0.020  1.453
 Z89  CAB  CAC   aromatic  1.390  0.020  1.390
 Z89  CAC  CAD   aromatic  1.388  0.020  1.388
 Z89  CAC  HAC   single    0.930  0.020  1.080
 Z89  CAF  CAD   aromatic  1.389  0.020  1.389
 Z89  CAD  BRAE  single    1.888  0.020  1.888
 Z89  CAG  CAF   aromatic  1.389  0.020  1.389
 Z89  CAF  HAF   single    0.930  0.020  1.080
 Z89  CAG  HAG   single    0.930  0.020  1.080
 Z89  CAI  CAH   single    1.501  0.020  1.501
 Z89  CAL  CAH   double    1.348  0.020  1.348
 Z89  OAK  CAI   double    1.214  0.020  1.214
 Z89  CAI  NAJ   single    1.353  0.020  1.353
 Z89  NAJ  HNAJ  single    0.860  0.020  1.020
 Z89  SAY  CAL   single    1.748  0.020  1.748
 Z89  CAL  CAM   single    1.480  0.020  1.480
 Z89  CAM  OAZ   double    1.202  0.020  1.202
 Z89  SAY  CAW   single    1.745  0.020  1.745
 Z89  SAX  CAW   double    1.631  0.020  1.631
 Z89  OD1  HOD1  single    0.850  0.020  0.980

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
 Z89  O     C    CA    122.66  3.000
 Z89  O     C    OXT   125.10  3.000
 Z89  CA    C    OXT   112.11  3.000
 Z89  CAW   N    CAM   116.41  3.000
 Z89  CAM   N    CA    120.58  3.000
 Z89  CAW   N    CA    122.96  3.000
 Z89  HO    OXT  C     110.45  3.000
 Z89  HA    CA   CB    107.94  3.000
 Z89  HA    CA   N     105.75  3.000
 Z89  CB    CA   N     113.49  3.000
 Z89  HA    CA   C     104.85  3.000
 Z89  CB    CA   C     115.52  3.000
 Z89  N     CA   C     108.48  3.000
 Z89  HBA   CB   HB    106.22  3.000
 Z89  HBA   CB   CG    109.25  3.000
 Z89  HB    CB   CG    107.56  3.000
 Z89  HBA   CB   CA    111.96  3.000
 Z89  HB    CB   CA    108.70  3.000
 Z89  CG    CB   CA    112.84  3.000
 Z89  OD2   CG   OD1   123.68  3.000
 Z89  OD1   CG   CB    110.99  3.000
 Z89  OD2   CG   CB    125.33  3.000
 Z89  NAJ   CAA  CAG   127.63  3.000
 Z89  CAG   CAA  CAB   122.28  3.000
 Z89  NAJ   CAA  CAB   110.09  3.000
 Z89  CAH   CAB  CAC   134.57  3.000
 Z89  CAC   CAB  CAA   119.17  3.000
 Z89  CAH   CAB  CAA   106.26  3.000
 Z89  HAC   CAC  CAD   120.88  3.000
 Z89  HAC   CAC  CAB   120.76  3.000
 Z89  CAD   CAC  CAB   118.36  3.000
 Z89  CAF   CAD  BRAE  119.14  3.000
 Z89  BRAE  CAD  CAC   118.87  3.000
 Z89  CAF   CAD  CAC   121.99  3.000
 Z89  HAF   CAF  CAG   119.08  3.000
 Z89  HAF   CAF  CAD   120.81  3.000
 Z89  CAG   CAF  CAD   120.11  3.000
 Z89  HAG   CAG  CAF   120.40  3.000
 Z89  HAG   CAG  CAA   121.50  3.000
 Z89  CAF   CAG  CAA   118.09  3.000
 Z89  CAL   CAH  CAI   117.72  3.000
 Z89  CAL   CAH  CAB   136.53  3.000
 Z89  CAI   CAH  CAB   105.75  3.000
 Z89  OAK   CAI  NAJ   127.74  3.000
 Z89  NAJ   CAI  CAH   106.71  3.000
 Z89  OAK   CAI  CAH   125.54  3.000
 Z89  HNAJ  NAJ  CAI   123.84  3.000
 Z89  HNAJ  NAJ  CAA   124.97  3.000
 Z89  CAI   NAJ  CAA   111.18  3.000
 Z89  SAY   CAL  CAM   109.81  3.000
 Z89  CAM   CAL  CAH   126.81  3.000
 Z89  SAY   CAL  CAH   123.38  3.000
 Z89  OAZ   CAM  CAL   126.42  3.000
 Z89  OAZ   CAM  N     123.48  3.000
 Z89  CAL   CAM  N     110.09  3.000
 Z89  SAY   CAW  SAX   121.09  3.000
 Z89  SAX   CAW  N     127.35  3.000
 Z89  SAY   CAW  N     111.56  3.000
 Z89  CAW   SAY  CAL    91.89  3.000
 Z89  HOD1  OD1  CG    110.12  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
 Z89  CONST_01  CAD   CAC  CAB  CAA      0.00   0.0  0
 Z89  CONST_02  CAD   CAF  CAG  CAA      0.00   0.0  0
 Z89  CONST_03  CAF   CAG  CAA  CAB      0.00   0.0  0
 Z89  CONST_04  CAF   CAD  CAC  CAB      0.00   0.0  0
 Z89  CONST_05  CAG   CAA  CAB  CAC      0.00   0.0  0
 Z89  CONST_06  CAG   CAF  CAD  CAC      0.00   0.0  0
 Z89  CONST_07  CAH   CAI  NAJ  CAA      0.00   0.0  0
 Z89  CONST_08  CAW   N    CAM  CAL      0.00   0.0  0
 Z89  CONST_09  BRAE  CAD  CAC  CAB    180.00   0.0  0
 Z89  CONST_10  CAG   CAF  CAD  BRAE   180.00   0.0  0
 Z89  CONST_11  CAL   CAM  N    CA     180.00   0.0  0
 Z89  CONST_12  OAK   CAI  NAJ  CAA    180.00   0.0  0
 Z89  CONST_13  OAZ   CAM  N    CAW    180.00   0.0  0
 Z89  CONST_14  HAC   CAC  CAB  CAA    180.00   0.0  0
 Z89  CONST_15  HAF   CAF  CAG  CAA    180.00   0.0  0
 Z89  CONST_16  HAG   CAG  CAA  CAB    180.00   0.0  0
 Z89  CONST_17  HNAJ  NAJ  CAI  CAH    180.00   0.0  0
 Z89  CONST_18  OAZ   CAM  N    CA       0.00   0.0  0
 Z89  CONST_19  HO    OXT  C    CA     180.00   0.0  0
 Z89  CONST_20  HOD1  OD1  CG   CB     180.00   0.0  0
 Z89  Var_01    SAY   CAL  CAH  CAB   -178.66  30.0  2
 Z89  Var_02    OD2   CG   CB   CA       3.06  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
 Z89  chir_01  CA  C  N  CB  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
 Z89  plan-1  N     0.020
 Z89  plan-1  CA    0.020
 Z89  plan-1  CAH   0.020
 Z89  plan-1  CAL   0.020
 Z89  plan-1  CAM   0.020
 Z89  plan-1  CAW   0.020
 Z89  plan-1  SAX   0.020
 Z89  plan-1  SAY   0.020
 Z89  plan-1  OAZ   0.020
 Z89  plan-2  CAA   0.020
 Z89  plan-2  CAB   0.020
 Z89  plan-2  CAC   0.020
 Z89  plan-2  CAD   0.020
 Z89  plan-2  BRAE  0.020
 Z89  plan-2  CAF   0.020
 Z89  plan-2  CAG   0.020
 Z89  plan-2  CAH   0.020
 Z89  plan-2  CAI   0.020
 Z89  plan-2  NAJ   0.020
 Z89  plan-2  OAK   0.020
 Z89  plan-2  CAL   0.020
 Z89  plan-2  HAF   0.020
 Z89  plan-2  HAG   0.020
 Z89  plan-2  HNAJ  0.020
 Z89  plan-2  HAC   0.020
 Z89  plan-3  C     0.020
 Z89  plan-3  OXT   0.020
 Z89  plan-3  CA    0.020
 Z89  plan-3  O     0.020
 Z89  plan-3  HO    0.020
 Z89  plan-4  CB    0.020
 Z89  plan-4  CG    0.020
 Z89  plan-4  OD1   0.020
 Z89  plan-4  OD2   0.020
 Z89  plan-4  HOD1  0.020

