# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:19:46 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2R,4S)-2-[(1S)-1-{[(2R)-2-carboxy-2-(thiophen-3-yl)acetyl]amino}-1-methoxy-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@](NC(=O)[C@H](C(O)=O)c1cscc1)(C=O)[C@@H]2N[C@@H](C(O)=O)C(C)(C)S2
#
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
 TJ7  TJ7  '(2R,4S)-2-[(1S)-1-{[(2R)-2-carboxy-2-(thiophen-3-yl)acetyl]amino}-1-methoxy-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  45  27  .  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_TJ7
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
 TJ7  O7   O  O      0  -0.350  -0.7545  -0.3279   2.0665
 TJ7  C15  C  C1     0   0.151  -0.8641   0.7378   1.5299
 TJ7  C6   C  CT     0   0.424  -0.6662   0.9683   0.0293
 TJ7  O5   O  O2     0  -0.492  -0.4711   2.3557  -0.0636
 TJ7  C14  C  CH3    0  -0.424  -0.1346   2.8855  -1.3265
 TJ7  C    C  CH1    0  -0.300  -1.9469   0.5558  -0.7431
 TJ7  S    S  S2     0  -0.006  -2.2238  -1.2657  -0.6888
 TJ7  C3   C  CT     0  -0.211  -3.9537  -1.0911  -0.0904
 TJ7  C4   C  CH3    0  -0.631  -4.9110  -1.1726  -1.2759
 TJ7  C5   C  CH3    0  -0.630  -4.2386  -2.1986   0.9126
 TJ7  C1   C  CH1    0  -0.169  -3.9363   0.3123   0.5723
 TJ7  C2   C  C      0   0.417  -5.3645   0.8804   0.7433
 TJ7  O1   O  OC    -1  -0.595  -6.0247   0.4143   1.6895
 TJ7  O    O  O      0  -0.595  -5.7364   1.7287  -0.0893
 TJ7  N    N  NH1    0  -0.579  -3.1145   1.1995  -0.2218
 TJ7  N1   N  NH1    0  -0.691   0.4407   0.2115  -0.4670
 TJ7  C7   C  C      0   0.617   1.6612   0.2523   0.1270
 TJ7  O2   O  O      0  -0.463   1.8589   0.9069   1.1318
 TJ7  C8   C  CH1    0  -0.635   2.7055  -0.5936  -0.5725
 TJ7  C9   C  C      0   0.447   2.4535  -2.0947  -0.1953
 TJ7  O4   O  O      0  -0.578   2.3054  -2.3231   1.0148
 TJ7  O3   O  OC    -1  -0.590   2.4478  -2.9022  -1.1376
 TJ7  C10  C  CR5    0   0.234   4.1016  -0.1841  -0.2217
 TJ7  C13  C  CR15   0  -0.228   5.0103   0.3742  -1.1705
 TJ7  C12  C  CR15   0  -0.467   6.2283   0.6695  -0.6406
 TJ7  S1   S  S2     0   0.198   6.2886   0.2743   1.0251
 TJ7  C11  C  CR15   0  -0.524   4.6720  -0.2930   1.0132
 TJ7  H1   H  H      0   0.208  -1.1699   1.6457   2.0786
 TJ7  H2   H  HCH3   0   0.217  -0.9633   2.8470  -2.0389
 TJ7  H3   H  HCH3   0   0.245   0.1254   3.9305  -1.1682
 TJ7  H4   H  HCH3   0   0.215   0.7277   2.3840  -1.7736
 TJ7  H5   H  HCH1   0   0.301  -1.7978   0.8482  -1.7860
 TJ7  H6   H  HCH3   0   0.231  -4.7685  -0.3479  -1.9743
 TJ7  H7   H  HCH3   0   0.234  -4.7623  -2.1027  -1.8249
 TJ7  H8   H  HCH3   0   0.228  -5.9488  -1.1529  -0.9365
 TJ7  H9   H  HCH3   0   0.238  -5.2398  -2.0735   1.3246
 TJ7  H10  H  HCH3   0   0.229  -4.1890  -3.1832   0.4454
 TJ7  H11  H  HCH3   0   0.232  -3.5245  -2.1764   1.7363
 TJ7  H12  H  HCH1   0   0.235  -3.5003   0.1908   1.5688
 TJ7  H14  H  HNH1   0   0.359  -3.6822   1.5999  -0.9569
 TJ7  H16  H  HNH1   0   0.403   0.3434  -0.2907  -1.3362
 TJ7  H17  H  HCH1   0   0.265   2.5766  -0.4797  -1.6523
 TJ7  H19  H  HCR5   0   0.259   4.7565   0.5459  -2.2079
 TJ7  H20  H  HCR5   0   0.290   7.0860   1.0948  -1.1377
 TJ7  H21  H  HCR5   0   0.280   4.2259  -0.6805   1.9138

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
 TJ7  C12  C13  aromatic  1.361  0.020  1.361
 TJ7  C12  S1   aromatic  1.713  0.020  1.713
 TJ7  O    C2   deloc     1.245  0.020  1.245
 TJ7  C13  C10  aromatic  1.427  0.020  1.427
 TJ7  C5   C3   single    1.521  0.020  1.521
 TJ7  S1   C11  aromatic  1.713  0.020  1.713
 TJ7  C2   O1   deloc     1.244  0.020  1.244
 TJ7  C2   C1   single    1.546  0.020  1.546
 TJ7  C10  C11  aromatic  1.365  0.020  1.365
 TJ7  C10  C8   single    1.497  0.020  1.497
 TJ7  C3   C1   single    1.552  0.020  1.552
 TJ7  C3   C4   single    1.526  0.020  1.526
 TJ7  C3   S    single    1.839  0.020  1.839
 TJ7  C1   N    single    1.447  0.020  1.447
 TJ7  O4   C9   deloc     1.240  0.020  1.240
 TJ7  C8   C9   single    1.568  0.020  1.568
 TJ7  C8   C7   single    1.515  0.020  1.515
 TJ7  C9   O3   deloc     1.241  0.020  1.241
 TJ7  S    C    single    1.843  0.020  1.843
 TJ7  N1   C7   single    1.358  0.020  1.358
 TJ7  N1   C6   single    1.430  0.020  1.430
 TJ7  C7   O2   double    1.215  0.020  1.215
 TJ7  N    C    single    1.432  0.020  1.432
 TJ7  O7   C15  double    1.198  0.020  1.198
 TJ7  C    C6   single    1.551  0.020  1.551
 TJ7  C6   C15  single    1.531  0.020  1.531
 TJ7  C6   O5   single    1.404  0.020  1.404
 TJ7  O5   C14  single    1.410  0.020  1.410
 TJ7  C15  H1   single    0.930  0.020  1.080
 TJ7  C14  H2   single    0.970  0.020  1.090
 TJ7  C14  H3   single    0.970  0.020  1.090
 TJ7  C14  H4   single    0.970  0.020  1.090
 TJ7  C    H5   single    0.970  0.020  1.090
 TJ7  C4   H6   single    0.970  0.020  1.090
 TJ7  C4   H7   single    0.970  0.020  1.090
 TJ7  C4   H8   single    0.970  0.020  1.090
 TJ7  C5   H9   single    0.970  0.020  1.090
 TJ7  C5   H10  single    0.970  0.020  1.090
 TJ7  C5   H11  single    0.970  0.020  1.090
 TJ7  C1   H12  single    0.970  0.020  1.090
 TJ7  N    H14  single    0.890  0.020  1.040
 TJ7  N1   H16  single    0.860  0.020  1.020
 TJ7  C8   H17  single    0.970  0.020  1.090
 TJ7  C13  H19  single    0.930  0.020  1.080
 TJ7  C12  H20  single    0.930  0.020  1.080
 TJ7  C11  H21  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
 TJ7  H1   C15  C6   113.52  3.000
 TJ7  H1   C15  O7   122.29  3.000
 TJ7  C6   C15  O7   124.13  3.000
 TJ7  N1   C6   C    109.00  3.000
 TJ7  C    C6   O5   110.15  3.000
 TJ7  N1   C6   O5   113.11  3.000
 TJ7  O5   C6   C15  103.39  3.000
 TJ7  C    C6   C15  109.95  3.000
 TJ7  N1   C6   C15  111.14  3.000
 TJ7  C14  O5   C6   117.62  3.000
 TJ7  H4   C14  H3   108.14  3.000
 TJ7  H4   C14  H2   108.38  3.000
 TJ7  H3   C14  H2   108.04  3.000
 TJ7  H4   C14  O5   112.47  3.000
 TJ7  H3   C14  O5   106.70  3.000
 TJ7  H2   C14  O5   112.91  3.000
 TJ7  H5   C    N    109.78  3.000
 TJ7  H5   C    S    108.23  3.000
 TJ7  N    C    S    108.12  3.000
 TJ7  H5   C    C6   106.93  3.000
 TJ7  N    C    C6   111.86  3.000
 TJ7  S    C    C6   111.85  3.000
 TJ7  C3   S    C     93.27  3.000
 TJ7  C1   C3   C5   112.26  3.000
 TJ7  C1   C3   C4   112.77  3.000
 TJ7  C5   C3   C4   110.85  3.000
 TJ7  C4   C3   S    109.41  3.000
 TJ7  C1   C3   S    102.37  3.000
 TJ7  C5   C3   S    108.76  3.000
 TJ7  H8   C4   H7   107.55  3.000
 TJ7  H8   C4   H6   108.04  3.000
 TJ7  H7   C4   H6   107.76  3.000
 TJ7  H8   C4   C3   110.72  3.000
 TJ7  H7   C4   C3   110.56  3.000
 TJ7  H6   C4   C3   112.04  3.000
 TJ7  H11  C5   H10  108.18  3.000
 TJ7  H11  C5   H9   108.29  3.000
 TJ7  H10  C5   H9   107.90  3.000
 TJ7  H11  C5   C3   111.14  3.000
 TJ7  H10  C5   C3   111.48  3.000
 TJ7  H9   C5   C3   109.74  3.000
 TJ7  H12  C1   N    109.97  3.000
 TJ7  H12  C1   C2   107.94  3.000
 TJ7  N    C1   C2   111.10  3.000
 TJ7  H12  C1   C3   107.03  3.000
 TJ7  N    C1   C3   109.05  3.000
 TJ7  C2   C1   C3   111.65  3.000
 TJ7  O    C2   O1   127.23  3.000
 TJ7  O1   C2   C1   115.88  3.000
 TJ7  O    C2   C1   116.87  3.000
 TJ7  H14  N    C1   108.83  3.000
 TJ7  H14  N    C    111.78  3.000
 TJ7  C1   N    C    112.80  3.000
 TJ7  H16  N1   C7   118.60  3.000
 TJ7  H16  N1   C6   119.21  3.000
 TJ7  C7   N1   C6   121.87  3.000
 TJ7  C8   C7   O2   124.78  3.000
 TJ7  O2   C7   N1   121.60  3.000
 TJ7  C8   C7   N1   113.62  3.000
 TJ7  H17  C8   C10  108.24  3.000
 TJ7  H17  C8   C9   108.57  3.000
 TJ7  C10  C8   C9   110.82  3.000
 TJ7  H17  C8   C7   108.45  3.000
 TJ7  C9   C8   C7   108.22  3.000
 TJ7  C10  C8   C7   112.46  3.000
 TJ7  O3   C9   O4   128.35  3.000
 TJ7  O3   C9   C8   116.16  3.000
 TJ7  O4   C9   C8   115.48  3.000
 TJ7  C11  C10  C13  111.51  3.000
 TJ7  C11  C10  C8   125.47  3.000
 TJ7  C13  C10  C8   123.03  3.000
 TJ7  H19  C13  C12  123.30  3.000
 TJ7  H19  C13  C10  123.38  3.000
 TJ7  C12  C13  C10  113.32  3.000
 TJ7  H20  C12  S1   120.74  3.000
 TJ7  H20  C12  C13  128.15  3.000
 TJ7  S1   C12  C13  111.11  3.000
 TJ7  C11  S1   C12   92.08  3.000
 TJ7  H21  C11  S1   120.27  3.000
 TJ7  H21  C11  C10  127.75  3.000
 TJ7  S1   C11  C10  111.98  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
 TJ7  CONST_01  S1   C12  C13  C10    0.00   0.0  0
 TJ7  CONST_02  C12  S1   C11  C10    0.00   0.0  0
 TJ7  CONST_03  C11  S1   C12  C13    0.00   0.0  0
 TJ7  CONST_04  S1   C11  C10  C13    0.00   0.0  0
 TJ7  CONST_05  C11  C10  C13  C12    0.00   0.0  0
 TJ7  CONST_06  C12  C13  C10  C8   180.00   0.0  0
 TJ7  CONST_07  S1   C11  C10  C8   180.00   0.0  0
 TJ7  CONST_08  H20  C12  C13  C10  180.00   0.0  0
 TJ7  CONST_09  H21  C11  C10  C13  180.00   0.0  0
 TJ7  CONST_10  H19  C13  C12  S1   180.00   0.0  0
 TJ7  CONST_11  C8   C7   N1   C6   180.00   0.0  0
 TJ7  CONST_12  O2   C7   N1   C6     0.00   0.0  0
 TJ7  CONST_13  H16  N1   C7   O2   180.00   0.0  0
 TJ7  Var_01    C1   C3   S    C    -23.42  30.0  1
 TJ7  Var_02    H9   C5   C3   S    176.48  30.0  3
 TJ7  Var_03    H6   C4   C3   S    -63.92  30.0  3
 TJ7  Var_04    H2   C14  O5   C6    70.12  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
 TJ7  chir_01  C6  C    C15  O5  positiv
 TJ7  chir_02  C   S    N    C6  negativ
 TJ7  chir_03  C1  N    C3   C2  positiv
 TJ7  chir_04  C8  C10  C9   C7  negativ

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
 TJ7  plan-1  C8   0.020
 TJ7  plan-1  C10  0.020
 TJ7  plan-1  C13  0.020
 TJ7  plan-1  C12  0.020
 TJ7  plan-1  S1   0.020
 TJ7  plan-1  C11  0.020
 TJ7  plan-1  H19  0.020
 TJ7  plan-1  H20  0.020
 TJ7  plan-1  H21  0.020
 TJ7  plan-2  C6   0.020
 TJ7  plan-2  N1   0.020
 TJ7  plan-2  C7   0.020
 TJ7  plan-2  O2   0.020
 TJ7  plan-2  C8   0.020
 TJ7  plan-2  H16  0.020
 TJ7  plan-3  C1   0.020
 TJ7  plan-3  C2   0.020
 TJ7  plan-3  O1   0.020
 TJ7  plan-3  O    0.020
 TJ7  plan-4  C8   0.020
 TJ7  plan-4  C9   0.020
 TJ7  plan-4  O4   0.020
 TJ7  plan-4  O3   0.020
 TJ7  plan-5  O7   0.020
 TJ7  plan-5  C15  0.020
 TJ7  plan-5  C6   0.020
 TJ7  plan-5  H1   0.020

