# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 22:29:46 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  47  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.348  -0.7879  -1.0723   2.0749
 TJ7  C15  C  C1    0   0.173  -0.8601   0.1007   1.8469
 TJ7  C6   C  CT    0   0.386  -0.6771   0.7050   0.4498
 TJ7  O5   O  O2    0  -0.491  -0.4531   2.0668   0.7035
 TJ7  C14  C  CH3   0  -0.425  -0.1076   2.8913  -0.3913
 TJ7  C    C  CH1   0  -0.265  -1.9751   0.5276  -0.3621
 TJ7  S    S  S2    0   0.049  -2.4030  -1.2065  -0.7131
 TJ7  C3   C  CT    0  -0.210  -4.1176  -1.0651  -0.0511
 TJ7  C4   C  CH3   0  -0.650  -5.0545  -1.8322  -0.9759
 TJ7  C5   C  CH3   0  -0.618  -4.2046  -1.6432   1.3575
 TJ7  C1   C  CH1   0  -0.179  -4.3467   0.4642   0.0007
 TJ7  C2   C  C     0   0.543  -4.8715   1.0256  -1.3142
 TJ7  O1   O  OH1   0  -0.588  -6.1959   1.0098  -1.3581
 TJ7  O    O  O     0  -0.422  -4.1791   1.4510  -2.2041
 TJ7  N    N  NH1   0  -0.586  -3.0876   1.0340   0.4075
 TJ7  N1   N  NH1   0  -0.689   0.4006   0.0772  -0.2560
 TJ7  C7   C  C     0   0.625   1.6277  -0.0521   0.2922
 TJ7  O2   O  O     0  -0.442   1.8832   0.2938   1.4256
 TJ7  C8   C  CH1   0  -0.661   2.6683  -0.6789  -0.6329
 TJ7  C9   C  C     0   0.591   2.7295  -2.1718  -0.3605
 TJ7  O4   O  O     0  -0.414   2.1734  -2.7205   0.5531
 TJ7  O3   O  OH1   0  -0.580   3.4780  -2.7880  -1.2600
 TJ7  C10  C  CR5   0   0.225   4.0208  -0.0454  -0.4658
 TJ7  C13  C  CR15  0  -0.209   4.6146   0.7953  -1.4500
 TJ7  C12  C  CR15  0  -0.464   5.8334   1.2667  -1.0723
 TJ7  S1   S  S2    0   0.230   6.2716   0.6903   0.4794
 TJ7  C11  C  CR15  0  -0.523   4.8122  -0.1863   0.6361
 TJ7  H1   H  H     0   0.211  -1.0945   0.8450   2.6257
 TJ7  H2   H  HCH3  0   0.222  -0.9050   2.9728  -1.1347
 TJ7  H3   H  HCH3  0   0.252   0.0764   3.8826   0.0169
 TJ7  H4   H  HCH3  0   0.219   0.8021   2.5557  -0.8957
 TJ7  H5   H  HCH1  0   0.297  -1.8393   1.0221  -1.3309
 TJ7  H6   H  HCH3  0   0.245  -4.9765  -1.5159  -2.0155
 TJ7  H7   H  HCH3  0   0.253  -4.8161  -2.8955  -0.9399
 TJ7  H8   H  HCH3  0   0.248  -6.0900  -1.7205  -0.6521
 TJ7  H9   H  HCH3  0   0.234  -5.2414  -1.6214   1.7016
 TJ7  H10  H  HCH3  0   0.241  -3.8702  -2.6803   1.3680
 TJ7  H11  H  HCH3  0   0.249  -3.5985  -1.0836   2.0658
 TJ7  H12  H  HCH1  0   0.303  -5.0942   0.6717   0.7720
 TJ7  H13  H  HOH1  0   0.483  -6.5094   1.3441  -2.2125
 TJ7  H14  H  HNH1  0   0.379  -3.1080   2.0459   0.4295
 TJ7  H16  H  HNH1  0   0.417   0.2763  -0.1517  -1.2309
 TJ7  H17  H  HCH1  0   0.335   2.3625  -0.5531  -1.6765
 TJ7  H18  H  HOH1  0   0.488   3.5214  -3.7370  -1.0660
 TJ7  H19  H  HCR5  0   0.271   4.1477   1.0350  -2.3955
 TJ7  H20  H  HCR5  0   0.299   6.4929   1.9198  -1.6220
 TJ7  H21  H  HCR5  0   0.296   4.6160  -0.7580   1.5303

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  1.360  0.020  1.360
 TJ7  C12  S1   aromatic  1.712  0.020  1.712
 TJ7  O    C2   double    1.205  0.020  1.205
 TJ7  C13  C10  aromatic  1.424  0.020  1.424
 TJ7  C5   C3   single    1.525  0.020  1.525
 TJ7  S1   C11  aromatic  1.710  0.020  1.710
 TJ7  C2   O1   single    1.325  0.020  1.325
 TJ7  C2   C1   single    1.523  0.020  1.523
 TJ7  C10  C11  aromatic  1.364  0.020  1.364
 TJ7  C10  C8   single    1.503  0.020  1.503
 TJ7  C3   C1   single    1.547  0.020  1.547
 TJ7  C3   C4   single    1.524  0.020  1.524
 TJ7  C3   S    single    1.843  0.020  1.843
 TJ7  C1   N    single    1.441  0.020  1.441
 TJ7  O4   C9   double    1.202  0.020  1.202
 TJ7  C8   C9   single    1.519  0.020  1.519
 TJ7  C8   C7   single    1.527  0.020  1.527
 TJ7  C9   O3   single    1.322  0.020  1.322
 TJ7  S    C    single    1.820  0.020  1.820
 TJ7  N1   C7   single    1.350  0.020  1.350
 TJ7  N1   C6   single    1.433  0.020  1.433
 TJ7  C7   O2   double    1.212  0.020  1.212
 TJ7  N    C    single    1.444  0.020  1.444
 TJ7  O7   C15  double    1.197  0.020  1.197
 TJ7  C    C6   single    1.541  0.020  1.541
 TJ7  C6   C15  single    1.533  0.020  1.533
 TJ7  C6   O5   single    1.403  0.020  1.403
 TJ7  O5   C14  single    1.413  0.020  1.413
 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  O1   H13  single    0.850  0.020  0.980
 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  O3   H18  single    0.850  0.020  0.980
 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   113.76  3.000
 TJ7  H1   C15  O7   122.67  3.000
 TJ7  C6   C15  O7   123.54  3.000
 TJ7  N1   C6   C    108.87  3.000
 TJ7  C    C6   O5   109.96  3.000
 TJ7  N1   C6   O5   113.21  3.000
 TJ7  O5   C6   C15  103.70  3.000
 TJ7  C    C6   C15  109.52  3.000
 TJ7  N1   C6   C15  111.46  3.000
 TJ7  C14  O5   C6   117.72  3.000
 TJ7  H4   C14  H3   108.19  3.000
 TJ7  H4   C14  H2   108.43  3.000
 TJ7  H3   C14  H2   108.10  3.000
 TJ7  H4   C14  O5   112.45  3.000
 TJ7  H3   C14  O5   106.40  3.000
 TJ7  H2   C14  O5   113.07  3.000
 TJ7  H5   C    N    114.09  3.000
 TJ7  H5   C    S    106.77  3.000
 TJ7  N    C    S    104.81  3.000
 TJ7  H5   C    C6   108.02  3.000
 TJ7  N    C    C6   109.12  3.000
 TJ7  S    C    C6   114.16  3.000
 TJ7  C3   S    C     94.38  3.000
 TJ7  C1   C3   C5   109.59  3.000
 TJ7  C1   C3   C4   115.27  3.000
 TJ7  C5   C3   C4   109.55  3.000
 TJ7  C4   C3   S    108.38  3.000
 TJ7  C1   C3   S    103.04  3.000
 TJ7  C5   C3   S    110.83  3.000
 TJ7  H8   C4   H7   107.32  3.000
 TJ7  H8   C4   H6   108.76  3.000
 TJ7  H7   C4   H6   107.39  3.000
 TJ7  H8   C4   C3   110.62  3.000
 TJ7  H7   C4   C3   109.66  3.000
 TJ7  H6   C4   C3   112.89  3.000
 TJ7  H11  C5   H10  108.21  3.000
 TJ7  H11  C5   H9   108.27  3.000
 TJ7  H10  C5   H9   107.89  3.000
 TJ7  H11  C5   C3   112.01  3.000
 TJ7  H10  C5   C3   110.62  3.000
 TJ7  H9   C5   C3   109.72  3.000
 TJ7  H12  C1   N    108.85  3.000
 TJ7  H12  C1   C2   107.66  3.000
 TJ7  N    C1   C2   113.52  3.000
 TJ7  H12  C1   C3   108.20  3.000
 TJ7  N    C1   C3   105.72  3.000
 TJ7  C2   C1   C3   112.73  3.000
 TJ7  O    C2   O1   123.64  3.000
 TJ7  O1   C2   C1   111.63  3.000
 TJ7  O    C2   C1   124.73  3.000
 TJ7  H13  O1   C2   110.38  3.000
 TJ7  H14  N    C1   112.58  3.000
 TJ7  H14  N    C    112.18  3.000
 TJ7  C1   N    C    112.58  3.000
 TJ7  H16  N1   C7   118.85  3.000
 TJ7  H16  N1   C6   118.85  3.000
 TJ7  C7   N1   C6   121.70  3.000
 TJ7  C8   C7   O2   122.68  3.000
 TJ7  O2   C7   N1   122.95  3.000
 TJ7  C8   C7   N1   114.37  3.000
 TJ7  H17  C8   C10  108.00  3.000
 TJ7  H17  C8   C9   107.17  3.000
 TJ7  C10  C8   C9   110.99  3.000
 TJ7  H17  C8   C7   109.88  3.000
 TJ7  C9   C8   C7   108.80  3.000
 TJ7  C10  C8   C7   111.89  3.000
 TJ7  O3   C9   O4   124.48  3.000
 TJ7  O3   C9   C8   111.03  3.000
 TJ7  O4   C9   C8   124.50  3.000
 TJ7  H18  O3   C9   110.20  3.000
 TJ7  C11  C10  C13  112.17  3.000
 TJ7  C11  C10  C8   124.65  3.000
 TJ7  C13  C10  C8   123.18  3.000
 TJ7  H19  C13  C12  123.56  3.000
 TJ7  H19  C13  C10  123.72  3.000
 TJ7  C12  C13  C10  112.72  3.000
 TJ7  H20  C12  S1   120.61  3.000
 TJ7  H20  C12  C13  128.03  3.000
 TJ7  S1   C12  C13  111.36  3.000
 TJ7  C11  S1   C12   92.13  3.000
 TJ7  H21  C11  S1   120.18  3.000
 TJ7  H21  C11  C10  128.21  3.000
 TJ7  S1   C11  C10  111.61  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  H13  O1   C2   C1    180.00   0.0  0
 TJ7  CONST_12  C8   C7   N1   C6    180.00   0.0  0
 TJ7  CONST_13  O2   C7   N1   C6      0.00   0.0  0
 TJ7  CONST_14  H16  N1   C7   O2    180.00   0.0  0
 TJ7  CONST_15  H18  O3   C9   C8    180.00   0.0  0
 TJ7  Var_01    C1   C3   S    C      16.68  30.0  1
 TJ7  Var_02    H9   C5   C3   S    -175.61  30.0  3
 TJ7  Var_03    H6   C4   C3   S     -54.33  30.0  3
 TJ7  Var_04    H2   C14  O5   C6     64.60  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-3  H13  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-4  H18  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

