# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 07:18:56 2021
#   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  54  34  .  2021-08-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.442   0.3716  26.2301  122.7323
 N04  CD    C  C     0   0.560   1.3681  26.0964  123.3973
 N04  OE1   O  OH1   0  -0.595   1.5550  26.7113  124.5597
 N04  CG    C  CH2   0  -0.591   2.5470  25.2363  123.0313
 N04  CB    C  CH2   0  -0.495   2.3465  24.5086  121.7127
 N04  C     C  C     0   0.536   4.7942  24.3472  121.1832
 N04  OXT   O  OH1   0  -0.584   4.8944  24.8817  119.9772
 N04  O     O  O     0  -0.439   5.5981  24.5161  122.0649
 N04  N     N  NH1   0  -0.671   3.1524  22.8068  120.1934
 N04  CAU   C  C     0   0.551   4.0114  21.9138  119.6709
 N04  OBC   O  O     0  -0.481   5.1252  21.7439  120.1474
 N04  CAT   C  CR6   0  -0.010   3.5374  21.1397  118.4878
 N04  CAQ   C  CR16  0  -0.321   2.1918  20.8423  118.2957
 N04  CAS   C  CR16  0  -0.281   4.4848  20.6705  117.5806
 N04  CAR   C  CR16  0  -0.228   4.0802  19.9312  116.4823
 N04  CAP   C  CR16  0  -0.289   2.7368  19.6300  116.3013
 N04  CAO   C  CR6   0   0.048   1.7841  20.0784  117.2080
 N04  CAN   C  CH2   0  -0.253   0.3270  19.7550  116.9956
 N04  CAA   C  CR16  0  -0.356   0.7306  17.4221  118.5606
 N04  CAB   C  CR16  0  -0.220   0.9317  16.3499  119.4221
 N04  CAG   C  CR16  0  -0.337   0.3167  16.2915  120.6584
 N04  CAC   C  CR6   0   0.425  -0.1012  18.4665  118.9549
 N04  CAE   C  CR16  0  -0.414  -0.7142  18.4199  120.2030
 N04  CAF   C  CR6   0   0.173  -0.5284  17.3338  121.0584
 N04  CAH   C  C1    0  -0.248  -1.2313  17.3750  122.3305
 N04  SBG   S  S2    0   0.094  -1.1059  14.6862  123.0903
 N04  CAL   C  C     0   0.428  -1.9437  14.3374  124.6188
 N04  NAX   N  NH1   0  -0.683  -2.4519  15.4957  125.1365
 N04  CA    C  CH1   0  -0.131   3.5032  23.5643  121.3688
 N04  CAK   C  C     0   0.637  -2.2580  16.6675  124.4451
 N04  CAI   C  C     0  -0.306  -1.4938  16.3928  123.2030
 N04  OAY   O  O2    0  -0.482  -0.3763  19.5551  118.2056
 N04  OBH   O  O     0  -0.391  -2.0260  13.2417  125.0979
 N04  HE1   H  HOH1  0   0.481   0.7886  27.2664  124.7671
 N04  HG1C  H  HCH2  0   0.292   3.4305  25.8794  123.0113
 N04  HG2C  H  HCH2  0   0.289   2.7155  24.5241  123.8446
 N04  HB1C  H  HCH2  0   0.275   1.4402  23.9021  121.7671
 N04  HB2C  H  HCH2  0   0.264   2.2051  25.2237  120.8989
 N04  HA    H  HCH1  0   0.290   3.6693  22.8838  122.2086
 N04  HXT   H  HOH1  0   0.485   5.7110  25.3993  119.9102
 N04  H     H  HNH1  0   0.416   2.3101  23.0532  119.6983
 N04  HAQ   H  HCR6  0   0.260   1.4525  21.1773  119.0133
 N04  HAS   H  HCR6  0   0.264   5.5337  20.8884  117.7313
 N04  HAR   H  HCR6  0   0.266   4.8132  19.5739  115.7714
 N04  HAP   H  HCR6  0   0.265   2.4310  19.0307  115.4516
 N04  HAN1  H  HCH2  0   0.285  -0.1764  20.5952  116.5153
 N04  HAN2  H  HCH2  0   0.249   0.2205  18.8955  116.3251
 N04  HAA   H  HCR6  0   0.287   1.2343  17.4214  117.6042
 N04  HAB   H  HCR6  0   0.272   1.5925  15.5496  119.1168
 N04  HAE   H  HCR6  0   0.274  -1.3528  19.2417  120.5052
 N04  HAG   H  HCR6  0   0.257   0.5391  15.4572  121.3085
 N04  HAH   H  H     0   0.290  -1.6253  18.3476  122.6077
 N04  HAX   H  HNH1  0   0.443  -2.9642  15.4805  126.0104
 N04  OBE   O  O     0  -0.406  -2.6601  17.7453  124.8101

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    single    1.328  0.020  1.328
 N04  CD   OE2   double    1.205  0.020  1.205
 N04  CD   CG    single    1.504  0.020  1.504
 N04  CG   CB    single    1.519  0.020  1.519
 N04  CB   CA    single    1.532  0.020  1.532
 N04  C    OXT   single    1.323  0.020  1.323
 N04  C    O     double    1.205  0.020  1.205
 N04  C    CA    single    1.521  0.020  1.521
 N04  N    CAU   single    1.345  0.020  1.345
 N04  N    CA    single    1.442  0.020  1.442
 N04  CAU  OBC   double    1.223  0.020  1.223
 N04  CAU  CAT   single    1.491  0.020  1.491
 N04  CAT  CAQ   aromatic  1.391  0.020  1.391
 N04  CAT  CAS   aromatic  1.393  0.020  1.393
 N04  CAQ  CAO   aromatic  1.390  0.020  1.390
 N04  CAS  CAR   aromatic  1.384  0.020  1.384
 N04  CAR  CAP   aromatic  1.389  0.020  1.389
 N04  CAP  CAO   aromatic  1.389  0.020  1.389
 N04  CAO  CAN   single    1.508  0.020  1.508
 N04  CAN  OAY   single    1.414  0.020  1.414
 N04  CAA  CAC   aromatic  1.392  0.020  1.392
 N04  CAA  CAB   aromatic  1.390  0.020  1.390
 N04  CAC  CAE   aromatic  1.391  0.020  1.391
 N04  CAC  OAY   single    1.350  0.020  1.350
 N04  CAE  CAF   aromatic  1.395  0.020  1.395
 N04  CAB  CAG   aromatic  1.382  0.020  1.382
 N04  CAG  CAF   aromatic  1.400  0.020  1.400
 N04  CAF  CAH   single    1.454  0.020  1.454
 N04  CAH  CAI   double    1.340  0.020  1.340
 N04  SBG  CAL   single    1.778  0.020  1.778
 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  OE1  HE1   single    0.850  0.020  0.980
 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  OXT  HXT   single    0.850  0.020  0.980
 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   111.55  3.000
 N04  CG    CD   OE2   125.24  3.000
 N04  OE1   CD   OE2   123.21  3.000
 N04  HE1   OE1  CD    109.95  3.000
 N04  HG2C  CG   HG1C  105.79  3.000
 N04  HG2C  CG   CB    110.71  3.000
 N04  HG1C  CG   CB    111.87  3.000
 N04  HG2C  CG   CD    108.18  3.000
 N04  HG1C  CG   CD    107.55  3.000
 N04  CB    CG   CD    112.43  3.000
 N04  HB2C  CB   HB1C  107.06  3.000
 N04  HB2C  CB   CA    109.50  3.000
 N04  HB1C  CB   CA    107.18  3.000
 N04  HB2C  CB   CG    110.49  3.000
 N04  HB1C  CB   CG    109.41  3.000
 N04  CA    CB   CG    112.98  3.000
 N04  CA    C    O     123.30  3.000
 N04  CA    C    OXT   112.54  3.000
 N04  O     C    OXT   124.05  3.000
 N04  HXT   OXT  C     110.03  3.000
 N04  H     N    CA    118.40  3.000
 N04  H     N    CAU   120.36  3.000
 N04  CA    N    CAU   120.68  3.000
 N04  CAT   CAU  OBC   121.76  3.000
 N04  CAT   CAU  N     116.74  3.000
 N04  OBC   CAU  N     121.50  3.000
 N04  CAS   CAT  CAQ   119.72  3.000
 N04  CAS   CAT  CAU   118.38  3.000
 N04  CAQ   CAT  CAU   121.87  3.000
 N04  HAQ   CAQ  CAO   119.21  3.000
 N04  HAQ   CAQ  CAT   120.16  3.000
 N04  CAO   CAQ  CAT   120.60  3.000
 N04  HAS   CAS  CAR   120.09  3.000
 N04  HAS   CAS  CAT   120.06  3.000
 N04  CAR   CAS  CAT   119.85  3.000
 N04  HAR   CAR  CAP   119.89  3.000
 N04  HAR   CAR  CAS   119.98  3.000
 N04  CAP   CAR  CAS   120.13  3.000
 N04  HAP   CAP  CAO   119.77  3.000
 N04  HAP   CAP  CAR   119.67  3.000
 N04  CAO   CAP  CAR   120.55  3.000
 N04  CAN   CAO  CAP   120.10  3.000
 N04  CAN   CAO  CAQ   120.76  3.000
 N04  CAP   CAO  CAQ   119.13  3.000
 N04  HAN2  CAN  HAN1  106.86  3.000
 N04  HAN2  CAN  OAY   111.38  3.000
 N04  HAN1  CAN  OAY   104.84  3.000
 N04  HAN2  CAN  CAO   110.40  3.000
 N04  HAN1  CAN  CAO   110.05  3.000
 N04  OAY   CAN  CAO   112.99  3.000
 N04  HAA   CAA  CAC   121.97  3.000
 N04  HAA   CAA  CAB   118.71  3.000
 N04  CAC   CAA  CAB   119.31  3.000
 N04  HAB   CAB  CAG   119.54  3.000
 N04  HAB   CAB  CAA   118.95  3.000
 N04  CAG   CAB  CAA   121.51  3.000
 N04  HAG   CAG  CAF   121.80  3.000
 N04  HAG   CAG  CAB   118.63  3.000
 N04  CAF   CAG  CAB   119.51  3.000
 N04  OAY   CAC  CAE   115.80  3.000
 N04  OAY   CAC  CAA   124.72  3.000
 N04  CAE   CAC  CAA   119.48  3.000
 N04  HAE   CAE  CAF   119.87  3.000
 N04  HAE   CAE  CAC   118.97  3.000
 N04  CAF   CAE  CAC   121.17  3.000
 N04  CAH   CAF  CAE   116.75  3.000
 N04  CAH   CAF  CAG   124.25  3.000
 N04  CAE   CAF  CAG   119.00  3.000
 N04  HAH   CAH  CAI   114.80  3.000
 N04  HAH   CAH  CAF   115.11  3.000
 N04  CAI   CAH  CAF   130.07  3.000
 N04  CAI   SBG  CAL    91.80  3.000
 N04  OBH   CAL  NAX   126.71  3.000
 N04  OBH   CAL  SBG   123.74  3.000
 N04  NAX   CAL  SBG   109.55  3.000
 N04  HAX   NAX  CAK   121.21  3.000
 N04  HAX   NAX  CAL   120.13  3.000
 N04  CAK   NAX  CAL   118.66  3.000
 N04  HA    CA   N     109.64  3.000
 N04  HA    CA   C     106.56  3.000
 N04  N     CA   C     112.18  3.000
 N04  HA    CA   CB    109.01  3.000
 N04  N     CA   CB    108.85  3.000
 N04  C     CA   CB    110.54  3.000
 N04  OBE   CAK  CAI   126.16  3.000
 N04  CAI   CAK  NAX   109.63  3.000
 N04  OBE   CAK  NAX   124.21  3.000
 N04  CAK   CAI  SBG   110.36  3.000
 N04  CAK   CAI  CAH   120.68  3.000
 N04  SBG   CAI  CAH   128.92  3.000
 N04  CAC   OAY  CAN   119.19  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_33  H    N    CAU  CAT     0.00   0.0  0
 N04  CONST_34  CA   N    CAU  OBC     0.00   0.0  0
 N04  CONST_35  HE1  OE1  CD   OE2     0.00   0.0  0
 N04  CONST_36  HXT  OXT  C    O       0.00   0.0  0
 N04  Var_01    SBG  CAI  CAH  CAF    -1.61   0.0  2
 N04  Var_02    CAI  CAH  CAF  CAG   -17.35  30.0  2
 N04  Var_03    CAQ  CAT  CAU  N     -29.56  30.0  2
 N04  Var_04    OAY  CAN  CAO  CAQ   -35.27  30.0  2
 N04  Var_05    CAA  CAC  OAY  CAN    -7.56  30.0  3
 N04  Var_06    CB   CG   CD   OE2    -1.05  30.0  3
 N04  Var_07    CA   CB   CG   CD   -176.56  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  CAF  0.020
 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  OBH  0.020
 N04  plan-1  HAH  0.020
 N04  plan-1  HAX  0.020
 N04  plan-1  OBE  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-5  HE1  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
 N04  plan-6  HXT  0.020

