# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:57:32 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: (2R)-2-[[3-[[3-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]methyl]phenyl]carbonylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@H](NC(=O)c1cccc(COc2cccc(c2)\C=C3/SC(=O)NC3=O)c1)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
 N04  N04  '(2R)-2-[[3-[[3-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]methyl]phenyl]carbonylamino]pentanedioic acid'  ligand  52  34  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N04
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
 N04  OE2   O  O      0  -0.609  -9.4170  -2.2489  -0.4935
 N04  CD    C  C      0   0.411  -8.3149  -2.8062  -0.6651
 N04  OE1   O  OC    -1  -0.633  -8.1186  -3.8833  -1.2674
 N04  CG    C  CH2    0  -0.576  -7.0610  -2.1144  -0.1025
 N04  CB    C  CH2    0  -0.444  -7.3112  -0.8762   0.7440
 N04  C     C  C      0   0.413  -6.3600   0.8709   2.3209
 N04  OXT   O  OC    -1  -0.618  -6.9432   0.5260   3.3682
 N04  O     O  O      0  -0.600  -6.0418   2.0233   1.9816
 N04  N     N  NH1    0  -0.634  -5.1359   0.1132   0.2846
 N04  CAU   C  C      0   0.544  -3.8222   0.2760   0.4777
 N04  OBC   O  O      0  -0.501  -3.2616   0.0155   1.5365
 N04  CAT   C  CR6    0  -0.023  -3.0323   0.7674  -0.6975
 N04  CAQ   C  CR16   0  -0.317  -1.7848   1.3350  -0.4555
 N04  CAS   C  CR16   0  -0.302  -3.4721   0.6417  -2.0139
 N04  CAR   C  CR16   0  -0.228  -2.6842   1.0944  -3.0616
 N04  CAP   C  CR16   0  -0.291  -1.4489   1.6712  -2.8060
 N04  CAO   C  CR6    0   0.119  -0.9921   1.7957  -1.4981
 N04  CAN   C  CH2    0  -0.274   0.3636   2.3672  -1.2143
 N04  CAA   C  C1     0  -0.385   3.0995   2.7757  -0.6417
 N04  CAB   C  C1     0  -0.216   4.4540   2.8961  -0.3505
 N04  CAG   C  C1     0  -0.337   5.2789   1.7898  -0.2786
 N04  CAC   C  C      0   0.415   2.5630   1.5132  -0.8818
 N04  CAE   C  C1     0  -0.406   3.3923   0.3956  -0.8240
 N04  CAF   C  C      0   0.172   4.7447   0.5153  -0.5082
 N04  CAH   C  C1     0  -0.246   5.5103  -0.7191  -0.4398
 N04  SBG   S  S2     0   0.095   7.7260   0.1209   1.0450
 N04  CAL   C  CR5    0   0.427   8.8762  -1.1836   1.4090
 N04  NAX   N  NR15   0  -0.683   8.4488  -2.3458   0.8299
 N04  CA    C  CH1    0  -0.194  -6.0337  -0.2881   1.3445
 N04  CAK   C  CR5    0   0.637   7.2761  -2.3325   0.1134
 N04  CAI   C  CR5    0  -0.307   6.6938  -0.9678   0.1362
 N04  OAY   O  O2     0  -0.467   1.2729   1.2736  -1.1778
 N04  HG1C  H  HCH2   0   0.216  -6.4931  -2.8461   0.4836
 N04  HG2C  H  HCH2   0   0.222  -6.4084  -1.8682  -0.9477
 N04  HB1C  H  HCH2   0   0.211  -7.8251  -0.1108   0.1531
 N04  HB2C  H  HCH2   0   0.227  -7.9815  -1.1210   1.5686
 N04  HA    H  HCH1   0   0.229  -5.5372  -1.0760   1.9175
 N04  H     H  HNH1   0   0.392  -5.5565   0.5414  -0.5245
 N04  HAQ   H  HCR6   0   0.255  -1.4315   1.4275   0.5641
 N04  HAS   H  HCR6   0   0.257  -4.4201   0.1723  -2.2444
 N04  HAR   H  HCR6   0   0.266  -3.0324   0.9886  -4.0802
 N04  HAP   H  HCR6   0   0.261  -0.8377   2.0242  -3.6280
 N04  HAN1  H  HCH2   0   0.248   0.6527   3.0799  -1.9934
 N04  HAN2  H  HCH2   0   0.248   0.3657   2.8958  -0.2554
 N04  HAA   H  H      0   0.292   2.4905   3.6683  -0.6859
 N04  HAB   H  H      0   0.271   4.8676   3.8813  -0.1818
 N04  HAE   H  H      0   0.272   2.9689  -0.5824  -1.0207
 N04  HAG   H  H      0   0.256   6.3318   1.9409  -0.0876
 N04  HAH   H  H      0   0.290   5.0371  -1.5808  -0.9000
 N04  HAX   H  HNR5   0   0.443   8.9861  -3.1973   0.9434
 N04  OBE   O  O      0  -0.406   6.8064  -3.2981  -0.4376
 N04  OBH   O  O      0  -0.392   9.8698  -1.0318   2.0624

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
 N04  OE1  CD    deloc     1.250  0.020  1.250
 N04  CD   OE2   deloc     1.247  0.020  1.247
 N04  CD   CG    single    1.539  0.020  1.539
 N04  CG   CB    single    1.521  0.020  1.521
 N04  CB   CA    single    1.529  0.020  1.529
 N04  C    OXT   deloc     1.247  0.020  1.247
 N04  C    O     deloc     1.243  0.020  1.243
 N04  C    CA    single    1.550  0.020  1.550
 N04  N    CAU   single    1.338  0.020  1.338
 N04  N    CA    single    1.446  0.020  1.446
 N04  CAU  OBC   double    1.226  0.020  1.226
 N04  CAU  CAT   single    1.499  0.020  1.499
 N04  CAT  CAQ   aromatic  1.392  0.020  1.392
 N04  CAT  CAS   aromatic  1.394  0.020  1.394
 N04  CAQ  CAO   aromatic  1.388  0.020  1.388
 N04  CAS  CAR   aromatic  1.387  0.020  1.387
 N04  CAR  CAP   aromatic  1.387  0.020  1.387
 N04  CAP  CAO   aromatic  1.391  0.020  1.391
 N04  CAO  CAN   single    1.498  0.020  1.498
 N04  CAN  OAY   single    1.423  0.020  1.423
 N04  CAA  CAC   aromatic  1.393  0.020  1.393
 N04  CAA  CAB   aromatic  1.391  0.020  1.391
 N04  CAC  CAE   aromatic  1.393  0.020  1.393
 N04  CAC  OAY   single    1.345  0.020  1.345
 N04  CAE  CAF   aromatic  1.394  0.020  1.394
 N04  CAB  CAG   aromatic  1.382  0.020  1.382
 N04  CAG  CAF   aromatic  1.401  0.020  1.401
 N04  CAF  CAH   single    1.454  0.020  1.454
 N04  CAH  CAI   double    1.340  0.020  1.340
 N04  SBG  CAL   single    1.777  0.020  1.777
 N04  SBG  CAI   single    1.754  0.020  1.754
 N04  CAL  NAX   single    1.367  0.020  1.367
 N04  CAL  OBH   double    1.199  0.020  1.199
 N04  NAX  CAK   single    1.374  0.020  1.374
 N04  CAK  OBE   double    1.207  0.020  1.207
 N04  CAK  CAI   single    1.484  0.020  1.484
 N04  CG   HG1C  single    0.970  0.020  1.090
 N04  CG   HG2C  single    0.970  0.020  1.090
 N04  CB   HB1C  single    0.970  0.020  1.090
 N04  CB   HB2C  single    0.970  0.020  1.090
 N04  CA   HA    single    0.970  0.020  1.090
 N04  N    H     single    0.860  0.020  1.020
 N04  CAQ  HAQ   single    0.930  0.020  1.080
 N04  CAS  HAS   single    0.930  0.020  1.080
 N04  CAR  HAR   single    0.930  0.020  1.080
 N04  CAP  HAP   single    0.930  0.020  1.080
 N04  CAN  HAN1  single    0.970  0.020  1.090
 N04  CAN  HAN2  single    0.970  0.020  1.090
 N04  CAA  HAA   single    0.930  0.020  1.080
 N04  CAB  HAB   single    0.930  0.020  1.080
 N04  CAE  HAE   single    0.930  0.020  1.080
 N04  CAG  HAG   single    0.930  0.020  1.080
 N04  CAH  HAH   single    0.930  0.020  1.080
 N04  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
 N04  CG    CD   OE1   115.83  3.000
 N04  CG    CD   OE2   117.97  3.000
 N04  OE1   CD   OE2   126.19  3.000
 N04  HG2C  CG   HG1C  104.71  3.000
 N04  HG2C  CG   CB    110.15  3.000
 N04  HG1C  CG   CB    109.33  3.000
 N04  HG2C  CG   CD    107.72  3.000
 N04  HG1C  CG   CD    108.52  3.000
 N04  CB    CG   CD    115.82  3.000
 N04  HB2C  CB   HB1C  106.06  3.000
 N04  HB2C  CB   CA    107.63  3.000
 N04  HB1C  CB   CA    109.58  3.000
 N04  HB2C  CB   CG    109.83  3.000
 N04  HB1C  CB   CG    110.24  3.000
 N04  CA    CB   CG    113.22  3.000
 N04  CA    C    O     117.87  3.000
 N04  CA    C    OXT   114.87  3.000
 N04  O     C    OXT   127.26  3.000
 N04  H     N    CA    116.58  3.000
 N04  H     N    CAU   118.31  3.000
 N04  CA    N    CAU   122.53  3.000
 N04  CAT   CAU  OBC   120.38  3.000
 N04  CAT   CAU  N     116.38  3.000
 N04  OBC   CAU  N     123.22  3.000
 N04  CAS   CAT  CAQ   118.94  3.000
 N04  CAS   CAT  CAU   123.01  3.000
 N04  CAQ   CAT  CAU   118.02  3.000
 N04  HAQ   CAQ  CAO   119.49  3.000
 N04  HAQ   CAQ  CAT   119.41  3.000
 N04  CAO   CAQ  CAT   121.10  3.000
 N04  HAS   CAS  CAR   118.57  3.000
 N04  HAS   CAS  CAT   121.10  3.000
 N04  CAR   CAS  CAT   120.32  3.000
 N04  HAR   CAR  CAP   120.06  3.000
 N04  HAR   CAR  CAS   119.77  3.000
 N04  CAP   CAR  CAS   120.17  3.000
 N04  HAP   CAP  CAO   119.93  3.000
 N04  HAP   CAP  CAR   119.88  3.000
 N04  CAO   CAP  CAR   120.20  3.000
 N04  CAN   CAO  CAP   120.63  3.000
 N04  CAN   CAO  CAQ   120.06  3.000
 N04  CAP   CAO  CAQ   119.26  3.000
 N04  HAN2  CAN  HAN1  107.97  3.000
 N04  HAN2  CAN  OAY   110.33  3.000
 N04  HAN1  CAN  OAY   110.48  3.000
 N04  HAN2  CAN  CAO   110.60  3.000
 N04  HAN1  CAN  CAO   110.64  3.000
 N04  OAY   CAN  CAO   106.85  3.000
 N04  HAA   CAA  CAC   121.62  3.000
 N04  HAA   CAA  CAB   119.05  3.000
 N04  CAC   CAA  CAB   119.33  3.000
 N04  HAB   CAB  CAG   119.52  3.000
 N04  HAB   CAB  CAA   118.94  3.000
 N04  CAG   CAB  CAA   121.54  3.000
 N04  HAG   CAG  CAF   121.85  3.000
 N04  HAG   CAG  CAB   118.61  3.000
 N04  CAF   CAG  CAB   119.48  3.000
 N04  OAY   CAC  CAE   115.93  3.000
 N04  OAY   CAC  CAA   124.67  3.000
 N04  CAE   CAC  CAA   119.40  3.000
 N04  HAE   CAE  CAF   119.85  3.000
 N04  HAE   CAE  CAC   118.94  3.000
 N04  CAF   CAE  CAC   121.21  3.000
 N04  CAH   CAF  CAE   116.65  3.000
 N04  CAH   CAF  CAG   124.32  3.000
 N04  CAE   CAF  CAG   119.03  3.000
 N04  HAH   CAH  CAI   114.83  3.000
 N04  HAH   CAH  CAF   115.12  3.000
 N04  CAI   CAH  CAF   130.02  3.000
 N04  CAI   SBG  CAL    91.79  3.000
 N04  OBH   CAL  NAX   126.70  3.000
 N04  OBH   CAL  SBG   123.72  3.000
 N04  NAX   CAL  SBG   109.58  3.000
 N04  HAX   NAX  CAK   121.26  3.000
 N04  HAX   NAX  CAL   120.08  3.000
 N04  CAK   NAX  CAL   118.65  3.000
 N04  HA    CA   N     107.59  3.000
 N04  HA    CA   C     107.71  3.000
 N04  N     CA   C     112.64  3.000
 N04  HA    CA   CB    107.94  3.000
 N04  N     CA   CB    109.73  3.000
 N04  C     CA   CB    111.04  3.000
 N04  OBE   CAK  CAI   126.16  3.000
 N04  CAI   CAK  NAX   109.61  3.000
 N04  OBE   CAK  NAX   124.22  3.000
 N04  CAK   CAI  SBG   110.36  3.000
 N04  CAK   CAI  CAH   120.72  3.000
 N04  SBG   CAI  CAH   128.86  3.000
 N04  CAC   OAY  CAN   118.80  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
 N04  CONST_01  CAP  CAO  CAQ  CAT    0.00   0.0  0
 N04  CONST_02  CAP  CAR  CAS  CAT    0.00   0.0  0
 N04  CONST_03  CAR  CAS  CAT  CAQ    0.00   0.0  0
 N04  CONST_04  CAR  CAP  CAO  CAQ    0.00   0.0  0
 N04  CONST_05  CAO  CAQ  CAT  CAS    0.00   0.0  0
 N04  CONST_06  CAO  CAP  CAR  CAS    0.00   0.0  0
 N04  CONST_07  CAF  CAE  CAC  CAA    0.00   0.0  0
 N04  CONST_08  CAF  CAG  CAB  CAA    0.00   0.0  0
 N04  CONST_09  CAE  CAC  CAA  CAB    0.00   0.0  0
 N04  CONST_10  CAE  CAF  CAG  CAB    0.00   0.0  0
 N04  CONST_11  CAC  CAA  CAB  CAG    0.00   0.0  0
 N04  CONST_12  CAC  CAE  CAF  CAG    0.00   0.0  0
 N04  CONST_13  CAI  CAK  NAX  CAL    0.00   0.0  0
 N04  CONST_14  CAO  CAQ  CAT  CAU  180.00   0.0  0
 N04  CONST_15  CAR  CAS  CAT  CAU  180.00   0.0  0
 N04  CONST_16  CAN  CAO  CAQ  CAT  180.00   0.0  0
 N04  CONST_17  CAN  CAO  CAP  CAR  180.00   0.0  0
 N04  CONST_18  OAY  CAC  CAA  CAB  180.00   0.0  0
 N04  CONST_19  CAH  CAF  CAG  CAB  180.00   0.0  0
 N04  CONST_20  CAH  CAF  CAE  CAC  180.00   0.0  0
 N04  CONST_21  OAY  CAC  CAE  CAF  180.00   0.0  0
 N04  CONST_22  OBE  CAK  NAX  CAL  180.00   0.0  0
 N04  CONST_23  HAR  CAR  CAS  CAT  180.00   0.0  0
 N04  CONST_24  HAS  CAS  CAT  CAQ  180.00   0.0  0
 N04  CONST_25  HAP  CAP  CAO  CAQ  180.00   0.0  0
 N04  CONST_26  HAQ  CAQ  CAT  CAS  180.00   0.0  0
 N04  CONST_27  HAE  CAE  CAC  CAA  180.00   0.0  0
 N04  CONST_28  HAG  CAG  CAB  CAA  180.00   0.0  0
 N04  CONST_29  HAA  CAA  CAB  CAG  180.00   0.0  0
 N04  CONST_30  HAB  CAB  CAA  CAC  180.00   0.0  0
 N04  CONST_31  HAX  NAX  CAK  CAI  180.00   0.0  0
 N04  CONST_32  CA   N    CAU  CAT  180.00   0.0  0
 N04  CONST_34  CA   N    CAU  OBC    0.00   0.0  0
 N04  Var_01    CAI  CAH  CAF  CAG   18.17  30.0  2
 N04  Var_02    SBG  CAI  CAH  CAF    1.30  30.0  2
 N04  Var_03    CAQ  CAT  CAU  N    160.67  30.0  2
 N04  Var_04    OAY  CAN  CAO  CAQ   86.21  30.0  2
 N04  Var_05    CAA  CAC  OAY  CAN   -2.02  30.0  1
 N04  Var_06    CB   CG   CD   OE2    6.22  30.0  3
 N04  Var_07    CA   CB   CG   CD   176.37  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
 N04  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
 N04  plan-1  CAH  0.020
 N04  plan-1  SBG  0.020
 N04  plan-1  CAL  0.020
 N04  plan-1  NAX  0.020
 N04  plan-1  CAK  0.020
 N04  plan-1  CAI  0.020
 N04  plan-1  HAX  0.020
 N04  plan-1  OBE  0.020
 N04  plan-1  OBH  0.020
 N04  plan-2  CAU  0.020
 N04  plan-2  CAT  0.020
 N04  plan-2  CAQ  0.020
 N04  plan-2  CAS  0.020
 N04  plan-2  CAR  0.020
 N04  plan-2  CAP  0.020
 N04  plan-2  CAO  0.020
 N04  plan-2  CAN  0.020
 N04  plan-2  HAQ  0.020
 N04  plan-2  HAS  0.020
 N04  plan-2  HAR  0.020
 N04  plan-2  HAP  0.020
 N04  plan-3  CAA  0.020
 N04  plan-3  CAB  0.020
 N04  plan-3  CAG  0.020
 N04  plan-3  CAC  0.020
 N04  plan-3  CAE  0.020
 N04  plan-3  CAF  0.020
 N04  plan-3  CAH  0.020
 N04  plan-3  OAY  0.020
 N04  plan-3  HAA  0.020
 N04  plan-3  HAB  0.020
 N04  plan-3  HAE  0.020
 N04  plan-3  HAG  0.020
 N04  plan-4  N    0.020
 N04  plan-4  CAU  0.020
 N04  plan-4  OBC  0.020
 N04  plan-4  CAT  0.020
 N04  plan-4  CA   0.020
 N04  plan-4  H    0.020
 N04  plan-5  OE2  0.020
 N04  plan-5  CD   0.020
 N04  plan-5  OE1  0.020
 N04  plan-5  CG   0.020
 N04  plan-6  C    0.020
 N04  plan-6  OXT  0.020
 N04  plan-6  O    0.020
 N04  plan-6  CA   0.020

