# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:16:34 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 2-[[2-fluoro-5-[[[4-[(Z)-(4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino]methyl]phenyl]carbonylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@H](NC(=O)c1cc(CNc2ccc(cc2)\C=C3/SC(=S)NC3=O)ccc1F)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
 T04  T04  '2-[[2-fluoro-5-[[[4-[(Z)-(4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino]methyl]phenyl]carbonylamino]pentanedioic acid'  ligand  53  35  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T04
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
 T04  OE1   O  OC    -1  -0.633    3.9409   5.1506   0.1941
 T04  CD    C  C      0   0.412    4.6626   4.4404  -0.5383
 T04  OE2   O  O      0  -0.609    5.0550   4.7280  -1.6862
 T04  CG    C  CH2    0  -0.578    5.0831   3.0814   0.0485
 T04  CB    C  CH2    0  -0.443    6.0781   2.2835  -0.7789
 T04  C     C  C      0   0.414    7.6468   0.2932  -0.9127
 T04  O     O  O      0  -0.596    7.3848  -0.7601  -1.5166
 T04  OXT   O  OC    -1  -0.619    8.7373   0.8989  -0.8847
 T04  N     N  NH1    0  -0.612    5.3548   0.1120   0.0474
 T04  CAU   C  C      0   0.536    5.3300  -0.9008   0.9194
 T04  OBC   O  O      0  -0.494    6.2177  -1.1327   1.7282
 T04  CAT   C  CR6    0  -0.239    4.0745  -1.7173   0.8903
 T04  CAQ   C  CR16   0  -0.316    2.8211  -1.1086   0.8359
 T04  CAS   C  CR6    0   0.531    4.1130  -3.1000   0.9745
 T04  CAR   C  CR16   0  -0.396    2.9643  -3.8680   1.0030
 T04  CAP   C  CR16   0  -0.264    1.7332  -3.2358   0.9615
 T04  CAO   C  CR6    0   0.082    1.6484  -1.8481   0.8792
 T04  CAN   C  CH2    0  -0.336    0.3081  -1.1664   0.8495
 T04  NAY   N  NH1    0  -0.684   -0.4627  -1.6199  -0.2844
 T04  CAA   C  CR6    0   0.413   -1.7920  -1.4386  -0.4302
 T04  CAC   C  CR16   0  -0.338   -2.4317  -1.8728  -1.6103
 T04  CAE   C  CR16   0  -0.279   -3.7857  -1.7276  -1.7644
 T04  CAB   C  CR16   0  -0.336   -2.5877  -0.8365   0.5654
 T04  CAG   C  CR16   0  -0.299   -3.9462  -0.7004   0.3937
 T04  CAF   C  CR6    0   0.135   -4.5950  -1.1408  -0.7711
 T04  CAH   C  C1     0  -0.248   -5.9996  -1.0362  -1.0330
 T04  CAI   C  CR5    0  -0.346   -7.0160  -0.5203  -0.3069
 T04  SBG   S  S2     0   0.181   -6.9711   0.2329   1.2775
 T04  CAL   C  CR5    0   0.058   -8.6855   0.5276   1.2723
 T04  SBH   S  S1     0  -0.230   -9.4826   1.2581   2.5008
 T04  NAX   N  NR15   0  -0.633   -9.2239   0.0672   0.1239
 T04  CAK   C  CR5    0   0.636   -8.3927  -0.5289  -0.8132
 T04  FAS   F  F      0  -0.298    5.2950  -3.7264   0.9984
 T04  OBE   O  O      0  -0.422   -8.7886  -0.9692  -1.8684
 T04  CA    C  CH1    0  -0.195    6.5044   0.9732  -0.1152
 T04  HG1   H  HCH2   0   0.217    5.4946   3.2495   1.0505
 T04  HB1   H  HCH2   0   0.211    5.6649   2.0727  -1.7709
 T04  HG2   H  HCH2   0   0.224    4.1716   2.4960   0.2144
 T04  HB2   H  HCH2   0   0.227    6.9798   2.8732  -0.9458
 T04  H     H  HNH1   0   0.394    4.6739   0.1089  -0.6959
 T04  HA    H  HCH1   0   0.230    6.8867   1.2076   0.8824
 T04  HAX   H  HNR5   0   0.438  -10.2184   0.1562  -0.0456
 T04  HAQ   H  HCR6   0   0.275    2.7600  -0.0277   0.7822
 T04  HAR   H  HCR6   0   0.285    3.0351  -4.9464   1.0585
 T04  HAP   H  HCR6   0   0.272    0.8321  -3.8354   0.9965
 T04  HAN1  H  HCH2   0   0.264   -0.2348  -1.4076   1.7668
 T04  HAN2  H  HCH2   0   0.258    0.4440  -0.0792   0.8391
 T04  HAY   H  HNH1   0   0.400    0.0546  -1.8967  -1.1039
 T04  HAC   H  HCR6   0   0.269   -1.8457  -2.3327  -2.3966
 T04  HAB   H  HCR6   0   0.281   -2.1405  -0.4619   1.4751
 T04  HAE   H  HCR6   0   0.266   -4.2469  -2.0781  -2.6799
 T04  HAG   H  HCR6   0   0.255   -4.4921  -0.2292   1.1993
 T04  HAH   H  H      0   0.282   -6.3119  -1.4452  -1.9898

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
 T04  OE1  CD    deloc     1.250  0.020  1.250
 T04  CD   OE2   deloc     1.247  0.020  1.247
 T04  CD   CG    single    1.539  0.020  1.539
 T04  CG   CB    single    1.520  0.020  1.520
 T04  CB   CA    single    1.529  0.020  1.529
 T04  C    OXT   deloc     1.248  0.020  1.248
 T04  C    O     deloc     1.242  0.020  1.242
 T04  C    CA    single    1.550  0.020  1.550
 T04  N    CAU   single    1.337  0.020  1.337
 T04  N    CA    single    1.446  0.020  1.446
 T04  CAU  OBC   double    1.223  0.020  1.223
 T04  CAU  CAT   single    1.498  0.020  1.498
 T04  CAT  CAQ   aromatic  1.395  0.020  1.395
 T04  CAT  CAS   aromatic  1.386  0.020  1.386
 T04  CAQ  CAO   aromatic  1.387  0.020  1.387
 T04  CAS  CAR   aromatic  1.382  0.020  1.382
 T04  CAS  FAS   single    1.338  0.020  1.338
 T04  CAR  CAP   aromatic  1.385  0.020  1.385
 T04  CAP  CAO   aromatic  1.393  0.020  1.393
 T04  CAO  CAN   single    1.504  0.020  1.504
 T04  CAN  NAY   single    1.444  0.020  1.444
 T04  NAY  CAA   single    1.349  0.020  1.349
 T04  CAA  CAC   aromatic  1.411  0.020  1.411
 T04  CAA  CAB   aromatic  1.410  0.020  1.410
 T04  CAC  CAE   aromatic  1.370  0.020  1.370
 T04  CAE  CAF   aromatic  1.409  0.020  1.409
 T04  CAB  CAG   aromatic  1.376  0.020  1.376
 T04  CAG  CAF   aromatic  1.404  0.020  1.404
 T04  CAF  CAH   single    1.433  0.020  1.433
 T04  CAH  CAI   double    1.351  0.020  1.351
 T04  CAI  SBG   single    1.755  0.020  1.755
 T04  CAI  CAK   single    1.467  0.020  1.467
 T04  SBG  CAL   single    1.739  0.020  1.739
 T04  CAL  SBH   double    1.637  0.020  1.637
 T04  CAL  NAX   single    1.349  0.020  1.349
 T04  NAX  CAK   single    1.387  0.020  1.387
 T04  CAK  OBE   double    1.210  0.020  1.210
 T04  CG   HG1   single    0.970  0.020  1.090
 T04  CB   HB1   single    0.970  0.020  1.090
 T04  CG   HG2   single    0.970  0.020  1.090
 T04  CB   HB2   single    0.970  0.020  1.090
 T04  CAQ  HAQ   single    0.930  0.020  1.080
 T04  CAR  HAR   single    0.930  0.020  1.080
 T04  CAP  HAP   single    0.930  0.020  1.080
 T04  CAN  HAN1  single    0.970  0.020  1.090
 T04  CAN  HAN2  single    0.970  0.020  1.090
 T04  NAY  HAY   single    0.860  0.020  1.020
 T04  CAC  HAC   single    0.930  0.020  1.080
 T04  CAB  HAB   single    0.930  0.020  1.080
 T04  CAE  HAE   single    0.930  0.020  1.080
 T04  CAG  HAG   single    0.930  0.020  1.080
 T04  CAH  HAH   single    0.930  0.020  1.080
 T04  N    H     single    0.860  0.020  1.020
 T04  CA   HA    single    0.970  0.020  1.090
 T04  NAX  HAX   single    0.860  0.020  1.020

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
 T04  CG    CD   OE2   117.96  3.000
 T04  CG    CD   OE1   115.86  3.000
 T04  OE2   CD   OE1   126.18  3.000
 T04  HG2   CG   HG1   104.82  3.000
 T04  HG2   CG   CB    110.26  3.000
 T04  HG1   CG   CB    109.40  3.000
 T04  HG2   CG   CD    107.59  3.000
 T04  HG1   CG   CD    108.41  3.000
 T04  CB    CG   CD    115.77  3.000
 T04  HB2   CB   HB1   106.11  3.000
 T04  HB2   CB   CA    107.41  3.000
 T04  HB1   CB   CA    109.47  3.000
 T04  HB2   CB   CG    109.92  3.000
 T04  HB1   CB   CG    110.31  3.000
 T04  CA    CB   CG    113.32  3.000
 T04  CA    C    OXT   114.81  3.000
 T04  CA    C    O     117.81  3.000
 T04  OXT   C    O     127.37  3.000
 T04  H     N    CA    117.13  3.000
 T04  H     N    CAU   117.79  3.000
 T04  CA    N    CAU   122.65  3.000
 T04  CAT   CAU  OBC   121.18  3.000
 T04  CAT   CAU  N     114.58  3.000
 T04  OBC   CAU  N     124.17  3.000
 T04  CAS   CAT  CAQ   117.57  3.000
 T04  CAS   CAT  CAU   121.29  3.000
 T04  CAQ   CAT  CAU   121.07  3.000
 T04  HAQ   CAQ  CAO   119.05  3.000
 T04  HAQ   CAQ  CAT   119.20  3.000
 T04  CAO   CAQ  CAT   121.73  3.000
 T04  FAS   CAS  CAR   118.28  3.000
 T04  FAS   CAS  CAT   119.52  3.000
 T04  CAR   CAS  CAT   122.18  3.000
 T04  HAR   CAR  CAP   120.99  3.000
 T04  HAR   CAR  CAS   120.02  3.000
 T04  CAP   CAR  CAS   118.99  3.000
 T04  HAP   CAP  CAO   120.19  3.000
 T04  HAP   CAP  CAR   119.09  3.000
 T04  CAO   CAP  CAR   120.73  3.000
 T04  CAN   CAO  CAP   120.47  3.000
 T04  CAN   CAO  CAQ   120.74  3.000
 T04  CAP   CAO  CAQ   118.79  3.000
 T04  HAN2  CAN  HAN1  106.78  3.000
 T04  HAN2  CAN  NAY   111.73  3.000
 T04  HAN1  CAN  NAY   108.94  3.000
 T04  HAN2  CAN  CAO   109.84  3.000
 T04  HAN1  CAN  CAO   109.03  3.000
 T04  NAY   CAN  CAO   110.41  3.000
 T04  HAY   NAY  CAA   117.04  3.000
 T04  HAY   NAY  CAN   116.79  3.000
 T04  CAA   NAY  CAN   124.64  3.000
 T04  CAB   CAA  CAC   117.79  3.000
 T04  CAB   CAA  NAY   122.49  3.000
 T04  CAC   CAA  NAY   119.71  3.000
 T04  HAC   CAC  CAE   119.86  3.000
 T04  HAC   CAC  CAA   119.51  3.000
 T04  CAE   CAC  CAA   120.62  3.000
 T04  HAE   CAE  CAF   119.07  3.000
 T04  HAE   CAE  CAC   118.77  3.000
 T04  CAF   CAE  CAC   122.16  3.000
 T04  HAB   CAB  CAG   118.64  3.000
 T04  HAB   CAB  CAA   120.60  3.000
 T04  CAG   CAB  CAA   120.76  3.000
 T04  HAG   CAG  CAF   121.43  3.000
 T04  HAG   CAG  CAB   116.65  3.000
 T04  CAF   CAG  CAB   121.92  3.000
 T04  CAH   CAF  CAG   125.57  3.000
 T04  CAH   CAF  CAE   117.69  3.000
 T04  CAG   CAF  CAE   116.74  3.000
 T04  HAH   CAH  CAI   113.62  3.000
 T04  HAH   CAH  CAF   114.54  3.000
 T04  CAI   CAH  CAF   131.84  3.000
 T04  CAK   CAI  SBG   109.77  3.000
 T04  CAK   CAI  CAH   121.21  3.000
 T04  SBG   CAI  CAH   129.02  3.000
 T04  CAL   SBG  CAI    92.56  3.000
 T04  NAX   CAL  SBH   126.64  3.000
 T04  NAX   CAL  SBG   109.76  3.000
 T04  SBH   CAL  SBG   123.60  3.000
 T04  HAX   NAX  CAK   120.87  3.000
 T04  HAX   NAX  CAL   120.29  3.000
 T04  CAK   NAX  CAL   118.84  3.000
 T04  OBE   CAK  NAX   123.33  3.000
 T04  OBE   CAK  CAI   127.61  3.000
 T04  NAX   CAK  CAI   109.07  3.000
 T04  HA    CA   N     107.64  3.000
 T04  HA    CA   C     107.80  3.000
 T04  N     CA   C     112.50  3.000
 T04  HA    CA   CB    108.03  3.000
 T04  N     CA   CB    109.72  3.000
 T04  C     CA   CB    110.97  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
 T04  CONST_01  CAP  CAO  CAQ  CAT     0.00   0.0  0
 T04  CONST_02  CAP  CAR  CAS  CAT     0.00   0.0  0
 T04  CONST_03  CAR  CAS  CAT  CAQ     0.00   0.0  0
 T04  CONST_04  CAR  CAP  CAO  CAQ     0.00   0.0  0
 T04  CONST_05  CAO  CAQ  CAT  CAS     0.00   0.0  0
 T04  CONST_06  CAO  CAP  CAR  CAS     0.00   0.0  0
 T04  CONST_07  CAF  CAE  CAC  CAA     0.00   0.0  0
 T04  CONST_08  CAF  CAG  CAB  CAA     0.00   0.0  0
 T04  CONST_09  CAG  CAB  CAA  CAC     0.00   0.0  0
 T04  CONST_10  CAG  CAF  CAE  CAC     0.00   0.0  0
 T04  CONST_11  CAB  CAA  CAC  CAE     0.00   0.0  0
 T04  CONST_12  CAB  CAG  CAF  CAE     0.00   0.0  0
 T04  CONST_13  CAL  NAX  CAK  CAI     0.00   0.0  0
 T04  CONST_14  CAO  CAQ  CAT  CAU   180.00   0.0  0
 T04  CONST_15  CAR  CAS  CAT  CAU   180.00   0.0  0
 T04  CONST_16  CAN  CAO  CAQ  CAT   180.00   0.0  0
 T04  CONST_17  FAS  CAS  CAT  CAQ   180.00   0.0  0
 T04  CONST_18  CAN  CAO  CAP  CAR   180.00   0.0  0
 T04  CONST_19  FAS  CAS  CAR  CAP   180.00   0.0  0
 T04  CONST_20  CAE  CAC  CAA  NAY   180.00   0.0  0
 T04  CONST_21  CAG  CAB  CAA  NAY   180.00   0.0  0
 T04  CONST_22  CAH  CAF  CAE  CAC   180.00   0.0  0
 T04  CONST_23  CAH  CAF  CAG  CAB   180.00   0.0  0
 T04  CONST_24  OBE  CAK  NAX  CAL   180.00   0.0  0
 T04  CONST_25  HAR  CAR  CAS  CAT   180.00   0.0  0
 T04  CONST_26  HAP  CAP  CAO  CAQ   180.00   0.0  0
 T04  CONST_27  HAQ  CAQ  CAT  CAS   180.00   0.0  0
 T04  CONST_28  HAE  CAE  CAC  CAA   180.00   0.0  0
 T04  CONST_29  HAG  CAG  CAB  CAA   180.00   0.0  0
 T04  CONST_30  HAB  CAB  CAA  CAC   180.00   0.0  0
 T04  CONST_31  HAC  CAC  CAA  CAB   180.00   0.0  0
 T04  CONST_32  HAX  NAX  CAK  CAI   180.00   0.0  0
 T04  CONST_33  CAC  CAA  NAY  CAN   180.00   0.0  0
 T04  CONST_34  CAB  CAA  NAY  CAN     0.00   0.0  0
 T04  CONST_35  HAY  NAY  CAA  CAC     0.00   0.0  0
 T04  CONST_36  CA   N    CAU  CAT   180.00   0.0  0
 T04  CONST_38  CA   N    CAU  OBC     0.00   0.0  0
 T04  Var_01    CAI  CAH  CAF  CAE  -179.03  30.0  2
 T04  Var_02    SBG  CAI  CAH  CAF    -0.05  30.0  2
 T04  Var_03    CAQ  CAT  CAU  N     -44.64  30.0  2
 T04  Var_04    NAY  CAN  CAO  CAQ   121.08  30.0  2
 T04  Var_05    CAA  NAY  CAN  CAO   164.37  30.0  3
 T04  Var_06    CB   CG   CD   OE1  -173.77  30.0  3
 T04  Var_07    CA   CB   CG   CD    177.43  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
 T04  chir_01  CA  CB  C  N  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
 T04  plan-1  CAH  0.020
 T04  plan-1  CAI  0.020
 T04  plan-1  SBG  0.020
 T04  plan-1  CAL  0.020
 T04  plan-1  SBH  0.020
 T04  plan-1  NAX  0.020
 T04  plan-1  CAK  0.020
 T04  plan-1  OBE  0.020
 T04  plan-1  HAX  0.020
 T04  plan-2  CAU  0.020
 T04  plan-2  CAT  0.020
 T04  plan-2  CAQ  0.020
 T04  plan-2  CAS  0.020
 T04  plan-2  CAR  0.020
 T04  plan-2  CAP  0.020
 T04  plan-2  CAO  0.020
 T04  plan-2  CAN  0.020
 T04  plan-2  FAS  0.020
 T04  plan-2  HAQ  0.020
 T04  plan-2  HAR  0.020
 T04  plan-2  HAP  0.020
 T04  plan-3  NAY  0.020
 T04  plan-3  CAA  0.020
 T04  plan-3  CAC  0.020
 T04  plan-3  CAE  0.020
 T04  plan-3  CAB  0.020
 T04  plan-3  CAG  0.020
 T04  plan-3  CAF  0.020
 T04  plan-3  CAH  0.020
 T04  plan-3  HAC  0.020
 T04  plan-3  HAB  0.020
 T04  plan-3  HAE  0.020
 T04  plan-3  HAG  0.020
 T04  plan-4  N    0.020
 T04  plan-4  CAU  0.020
 T04  plan-4  OBC  0.020
 T04  plan-4  CAT  0.020
 T04  plan-4  CA   0.020
 T04  plan-4  H    0.020
 T04  plan-5  CAN  0.020
 T04  plan-5  NAY  0.020
 T04  plan-5  CAA  0.020
 T04  plan-5  HAY  0.020
 T04  plan-6  OE1  0.020
 T04  plan-6  CD   0.020
 T04  plan-6  OE2  0.020
 T04  plan-6  CG   0.020
 T04  plan-7  C    0.020
 T04  plan-7  O    0.020
 T04  plan-7  OXT  0.020
 T04  plan-7  CA   0.020

