# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:24:36 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (5Z)-3-benzyl-5-[(2-hydroxy-3-nitrophenyl)methylidene]-2-thioxo-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(cccc1[N+]([O-])=O)/C=C/2SC(=S)N(Cc3ccccc3)C/2=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
 GN8  GN8  (5Z)-3-benzyl-5-[(2-hydroxy-3-nitrophenyl)methylidene]-2-thioxo-1,3-thiazolidin-4-one  ligand  37  25  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GN8
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
 GN8  OAA   O  O      0  -0.391   3.0074  -1.7134   1.9953
 GN8  CAU   C  CR5    0   0.693   1.8846  -1.9817   2.3372
 GN8  CAW   C  CR5    0  -0.291   0.6383  -1.4337   1.7605
 GN8  CAF   C  C1     0  -0.279   0.6453  -0.4983   0.8053
 GN8  CAR   C  CR6    0  -0.030  -0.5336   0.0658   0.1540
 GN8  CAQ   C  CR6    0   0.342  -0.5834   1.4506  -0.0971
 GN8  OAC   O  OH1    0  -0.572   0.3672   2.2809   0.3180
 GN8  CAT   C  CR6    0   0.180  -1.7027   1.9560  -0.7697
 GN8  NAY   N  N      1   0.337  -1.8134   3.3697  -1.0692
 GN8  OAD   O  O      0  -0.369  -0.8045   3.9882  -1.3057
 GN8  OAB   O  O     -1  -0.381  -2.9240   3.8498  -1.0872
 GN8  CAN   C  CR16   0  -0.269  -2.7486   1.1317  -1.1627
 GN8  CAJ   C  CR16   0  -0.259  -2.6871  -0.2252  -0.9175
 GN8  CAK   C  CR16   0  -0.276  -1.5842  -0.7473  -0.2615
 GN8  SAP   S  S2     0   0.244  -0.7448  -2.1366   2.5637
 GN8  CAV   C  CR5    0   0.036   0.2679  -3.0767   3.6282
 GN8  SAE   S  S1     0  -0.182  -0.3783  -4.0579   4.7628
 GN8  NAX   N  NR5    0  -0.492   1.5846  -2.8654   3.3647
 GN8  CAO   C  CH2    0  -0.422   2.6689  -3.5198   4.0928
 GN8  CAS   C  CR6    0   0.131   3.2900  -4.6350   3.2946
 GN8  CAL   C  CR16   0  -0.293   4.6110  -4.5407   2.8723
 GN8  CAM   C  CR16   0  -0.286   2.5547  -5.7738   2.9707
 GN8  CAI   C  CR16   0  -0.241   3.1326  -6.7961   2.2327
 GN8  CAG   C  CR16   0  -0.263   4.4550  -6.6966   1.8168
 GN8  CAH   C  CR16   0  -0.243   5.1940  -5.5679   2.1409
 GN8  HAC   H  HOH1   0   0.496   0.9756   1.8501   0.9310
 GN8  HAK   H  HCR6   0   0.291  -1.5199  -1.8172  -0.1092
 GN8  HAJ   H  HCR6   0   0.283  -3.4849  -0.8738  -1.2482
 GN8  HAN   H  HCR6   0   0.304  -3.6028   1.5509  -1.6748
 GN8  HAF   H  H      0   0.319   1.6249  -0.1535   0.4829
 GN8  HAO1  H  HCH2   0   0.300   2.2496  -3.8854   5.0292
 GN8  HAO2  H  HCH2   0   0.301   3.4093  -2.7594   4.3380
 GN8  HAM   H  HCR6   0   0.250   1.5262  -5.8708   3.2978
 GN8  HAI   H  HCR6   0   0.259   2.5513  -7.6754   1.9868
 GN8  HAG   H  HCR6   0   0.259   4.9058  -7.4962   1.2437
 GN8  HAH   H  HCR6   0   0.258   6.2238  -5.4805   1.8197
 GN8  HAL   H  HCR6   0   0.255   5.1904  -3.6593   3.1178

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
 GN8  OAA  CAU   double    1.204  0.020  1.204
 GN8  CAU  NAX   single    1.388  0.020  1.388
 GN8  CAU  CAW   single    1.479  0.020  1.479
 GN8  CAW  CAF   double    1.337  0.020  1.337
 GN8  CAW  SAP   single    1.747  0.020  1.747
 GN8  CAF  CAR   single    1.460  0.020  1.460
 GN8  CAF  HAF   single    0.930  0.020  1.080
 GN8  CAR  CAQ   aromatic  1.408  0.020  1.408
 GN8  CAR  CAK   aromatic  1.392  0.020  1.392
 GN8  CAQ  OAC   single    1.329  0.020  1.329
 GN8  CAQ  CAT   aromatic  1.400  0.020  1.400
 GN8  OAC  HAC   single    0.850  0.020  0.980
 GN8  CAT  CAN   aromatic  1.388  0.020  1.388
 GN8  CAT  NAY   single    1.449  0.020  1.449
 GN8  NAY  OAD   double    1.207  0.020  1.207
 GN8  NAY  OAB   single    1.210  0.020  1.210
 GN8  CAN  CAJ   aromatic  1.380  0.020  1.380
 GN8  CAN  HAN   single    0.930  0.020  1.080
 GN8  CAJ  CAK   aromatic  1.385  0.020  1.385
 GN8  CAJ  HAJ   single    0.930  0.020  1.080
 GN8  CAK  HAK   single    0.930  0.020  1.080
 GN8  SAP  CAV   single    1.744  0.020  1.744
 GN8  CAV  SAE   double    1.633  0.020  1.633
 GN8  CAV  NAX   single    1.359  0.020  1.359
 GN8  NAX  CAO   single    1.461  0.020  1.461
 GN8  CAO  CAS   single    1.506  0.020  1.506
 GN8  CAO  HAO1  single    0.970  0.020  1.090
 GN8  CAO  HAO2  single    0.970  0.020  1.090
 GN8  CAS  CAM   aromatic  1.394  0.020  1.394
 GN8  CAS  CAL   aromatic  1.390  0.020  1.390
 GN8  CAL  CAH   aromatic  1.389  0.020  1.389
 GN8  CAL  HAL   single    0.930  0.020  1.080
 GN8  CAM  CAI   aromatic  1.387  0.020  1.387
 GN8  CAM  HAM   single    0.930  0.020  1.080
 GN8  CAI  CAG   aromatic  1.390  0.020  1.390
 GN8  CAI  HAI   single    0.930  0.020  1.080
 GN8  CAG  CAH   aromatic  1.387  0.020  1.387
 GN8  CAG  HAG   single    0.930  0.020  1.080
 GN8  CAH  HAH   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
 GN8  NAX   CAU  CAW   110.02  3.000
 GN8  CAW   CAU  OAA   126.35  3.000
 GN8  NAX   CAU  OAA   123.62  3.000
 GN8  SAP   CAW  CAF   127.89  3.000
 GN8  SAP   CAW  CAU   109.81  3.000
 GN8  CAF   CAW  CAU   122.24  3.000
 GN8  HAF   CAF  CAR   118.20  3.000
 GN8  HAF   CAF  CAW   116.00  3.000
 GN8  CAR   CAF  CAW   125.78  3.000
 GN8  CAK   CAR  CAQ   119.64  3.000
 GN8  CAK   CAR  CAF   121.12  3.000
 GN8  CAQ   CAR  CAF   119.20  3.000
 GN8  CAT   CAQ  OAC   119.76  3.000
 GN8  CAT   CAQ  CAR   117.96  3.000
 GN8  OAC   CAQ  CAR   122.25  3.000
 GN8  HAC   OAC  CAQ   111.74  3.000
 GN8  CAN   CAT  NAY   117.58  3.000
 GN8  NAY   CAT  CAQ   120.82  3.000
 GN8  CAN   CAT  CAQ   121.59  3.000
 GN8  OAB   NAY  OAD   124.13  3.000
 GN8  OAB   NAY  CAT   117.40  3.000
 GN8  OAD   NAY  CAT   118.46  3.000
 GN8  HAN   CAN  CAJ   120.05  3.000
 GN8  HAN   CAN  CAT   119.95  3.000
 GN8  CAJ   CAN  CAT   119.99  3.000
 GN8  HAJ   CAJ  CAK   120.45  3.000
 GN8  HAJ   CAJ  CAN   120.20  3.000
 GN8  CAK   CAJ  CAN   119.34  3.000
 GN8  HAK   CAK  CAJ   119.10  3.000
 GN8  HAK   CAK  CAR   119.37  3.000
 GN8  CAJ   CAK  CAR   121.47  3.000
 GN8  CAV   SAP  CAW    92.17  3.000
 GN8  NAX   CAV  SAE   127.69  3.000
 GN8  NAX   CAV  SAP   111.11  3.000
 GN8  SAE   CAV  SAP   121.20  3.000
 GN8  CAO   NAX  CAV   123.55  3.000
 GN8  CAO   NAX  CAU   119.58  3.000
 GN8  CAV   NAX  CAU   116.87  3.000
 GN8  HAO2  CAO  HAO1  107.61  3.000
 GN8  HAO2  CAO  CAS   110.86  3.000
 GN8  HAO1  CAO  CAS   111.47  3.000
 GN8  HAO2  CAO  NAX   107.70  3.000
 GN8  HAO1  CAO  NAX   107.04  3.000
 GN8  CAS   CAO  NAX   111.95  3.000
 GN8  CAM   CAS  CAL   119.09  3.000
 GN8  CAL   CAS  CAO   120.19  3.000
 GN8  CAM   CAS  CAO   120.72  3.000
 GN8  HAL   CAL  CAH   119.77  3.000
 GN8  HAL   CAL  CAS   119.65  3.000
 GN8  CAH   CAL  CAS   120.57  3.000
 GN8  HAM   CAM  CAI   119.35  3.000
 GN8  HAM   CAM  CAS   120.25  3.000
 GN8  CAI   CAM  CAS   120.41  3.000
 GN8  HAI   CAI  CAG   120.08  3.000
 GN8  HAI   CAI  CAM   119.73  3.000
 GN8  CAG   CAI  CAM   120.19  3.000
 GN8  HAG   CAG  CAH   120.19  3.000
 GN8  HAG   CAG  CAI   120.12  3.000
 GN8  CAH   CAG  CAI   119.68  3.000
 GN8  HAH   CAH  CAG   120.21  3.000
 GN8  HAH   CAH  CAL   119.73  3.000
 GN8  CAG   CAH  CAL   120.06  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
 GN8  CONST_01  CAN  CAT  CAQ  CAR    0.00   0.0  0
 GN8  CONST_02  CAN  CAJ  CAK  CAR    0.00   0.0  0
 GN8  CONST_03  CAJ  CAK  CAR  CAQ    0.00   0.0  0
 GN8  CONST_04  CAJ  CAN  CAT  CAQ    0.00   0.0  0
 GN8  CONST_05  CAK  CAR  CAQ  CAT    0.00   0.0  0
 GN8  CONST_06  CAK  CAJ  CAN  CAT    0.00   0.0  0
 GN8  CONST_07  CAG  CAI  CAM  CAS    0.00   0.0  0
 GN8  CONST_08  CAG  CAH  CAL  CAS    0.00   0.0  0
 GN8  CONST_09  CAI  CAM  CAS  CAL    0.00   0.0  0
 GN8  CONST_10  CAI  CAG  CAH  CAL    0.00   0.0  0
 GN8  CONST_11  CAH  CAL  CAS  CAM    0.00   0.0  0
 GN8  CONST_12  CAH  CAG  CAI  CAM    0.00   0.0  0
 GN8  CONST_13  CAV  NAX  CAU  CAW    0.00   0.0  0
 GN8  CONST_14  CAT  CAQ  CAR  CAF  180.00   0.0  0
 GN8  CONST_15  CAJ  CAK  CAR  CAF  180.00   0.0  0
 GN8  CONST_16  NAY  CAT  CAQ  CAR  180.00   0.0  0
 GN8  CONST_17  CAK  CAR  CAQ  OAC  180.00   0.0  0
 GN8  CONST_18  CAN  CAT  CAQ  OAC  180.00   0.0  0
 GN8  CONST_19  CAJ  CAN  CAT  NAY  180.00   0.0  0
 GN8  CONST_20  CAI  CAM  CAS  CAO  180.00   0.0  0
 GN8  CONST_21  CAH  CAL  CAS  CAO  180.00   0.0  0
 GN8  CONST_22  CAV  NAX  CAU  OAA  180.00   0.0  0
 GN8  CONST_23  CAO  NAX  CAU  CAW  180.00   0.0  0
 GN8  CONST_24  HAJ  CAJ  CAK  CAR  180.00   0.0  0
 GN8  CONST_25  HAK  CAK  CAR  CAQ  180.00   0.0  0
 GN8  CONST_26  HAN  CAN  CAT  CAQ  180.00   0.0  0
 GN8  CONST_27  HAI  CAI  CAM  CAS  180.00   0.0  0
 GN8  CONST_28  HAH  CAH  CAL  CAS  180.00   0.0  0
 GN8  CONST_29  HAM  CAM  CAS  CAL  180.00   0.0  0
 GN8  CONST_30  HAG  CAG  CAH  CAL  180.00   0.0  0
 GN8  CONST_31  HAL  CAL  CAS  CAM  180.00   0.0  0
 GN8  CONST_36  CAO  NAX  CAU  OAA    0.00   0.0  0
 GN8  Var_01    CAS  CAO  NAX  CAU  -76.04  30.0  3
 GN8  Var_02    CAR  CAF  CAW  CAU  178.00  30.0  2
 GN8  Var_03    CAQ  CAR  CAF  CAW  138.45  30.0  2
 GN8  Var_04    CAM  CAS  CAO  NAX  -65.36  30.0  2

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
 GN8  plan-1  OAA  0.020
 GN8  plan-1  CAU  0.020
 GN8  plan-1  CAW  0.020
 GN8  plan-1  CAF  0.020
 GN8  plan-1  SAP  0.020
 GN8  plan-1  CAV  0.020
 GN8  plan-1  SAE  0.020
 GN8  plan-1  NAX  0.020
 GN8  plan-1  CAO  0.020
 GN8  plan-2  CAF  0.020
 GN8  plan-2  CAR  0.020
 GN8  plan-2  CAQ  0.020
 GN8  plan-2  OAC  0.020
 GN8  plan-2  CAT  0.020
 GN8  plan-2  NAY  0.020
 GN8  plan-2  CAN  0.020
 GN8  plan-2  CAJ  0.020
 GN8  plan-2  CAK  0.020
 GN8  plan-2  HAK  0.020
 GN8  plan-2  HAJ  0.020
 GN8  plan-2  HAN  0.020
 GN8  plan-3  CAO  0.020
 GN8  plan-3  CAS  0.020
 GN8  plan-3  CAL  0.020
 GN8  plan-3  CAM  0.020
 GN8  plan-3  CAI  0.020
 GN8  plan-3  CAG  0.020
 GN8  plan-3  CAH  0.020
 GN8  plan-3  HAM  0.020
 GN8  plan-3  HAI  0.020
 GN8  plan-3  HAG  0.020
 GN8  plan-3  HAH  0.020
 GN8  plan-3  HAL  0.020
 GN8  plan-4  CAT  0.020
 GN8  plan-4  NAY  0.020
 GN8  plan-4  OAD  0.020
 GN8  plan-4  OAB  0.020

