# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Nov 21 11:51:24 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (2~{S},4~{R})-2-thiophen-2-yl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CS[C@H](N1)c2sccc2
#
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
 V7W  V7W  "(2S,4R)-2-(thiophen-2-yl)thiazolidine-4-carboxylic acid"  ligand  22  13  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V7W
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
 V7W  C1  C  C     0   0.546  34.0513  -10.3029  -13.0870
 V7W  C2  C  CR15  0  -0.237  33.7310  -11.3272  -11.9972
 V7W  C3  C  CH2   0  -0.536  33.5089  -12.6990  -12.6139
 V7W  C4  C  CR15  0  -0.286  31.3223  -11.3577  -11.9394
 V7W  C5  C  CR5   0  -0.083  30.2693  -11.8849  -11.0312
 V7W  C6  C  CR15  0  -0.237  28.9176  -11.7424  -11.1223
 V7W  C7  C  CR15  0  -0.178  28.2195  -12.4560  -10.1084
 V7W  C8  C  CR15  0  -0.470  29.0602  -13.1217   -9.2706
 V7W  O1  O  OH1   0  -0.581  33.3451   -9.1890  -12.9701
 V7W  O2  O  O     0  -0.432  34.8886  -10.4803  -13.9343
 V7W  S1  S  S2    0  -0.010  31.8033  -12.5974  -13.2287
 V7W  S2  S  S2    0   0.216  30.7050  -12.8795   -9.6949
 V7W  N1  N  NR15  0  -0.576  32.5480  -11.0955  -11.2123
 V7W  H1  H  HCR5  0   0.317  34.6036  -11.3549  -11.3345
 V7W  H2  H  HCH2  0   0.291  33.6101  -13.4789  -11.8607
 V7W  H3  H  HCH2  0   0.292  34.1829  -12.9144  -13.4394
 V7W  H4  H  HCR5  0   0.289  30.9225  -10.4918  -12.4774
 V7W  H5  H  HCR5  0   0.261  28.4358  -11.1537  -11.8913
 V7W  H6  H  HCR5  0   0.263  27.1436  -12.4652  -10.0067
 V7W  H7  H  HCR5  0   0.290  28.8009  -13.7221   -8.4120
 V7W  H8  H  HOH1  0   0.482  33.6004   -8.5571  -13.6604
 V7W  H9  H  HNR5  0   0.380  32.5262  -10.1943  -10.7528

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
 V7W  S1  C3  single    1.816  0.020  1.816
 V7W  S1  C4  single    1.852  0.020  1.852
 V7W  O2  C1  double    1.204  0.020  1.204
 V7W  O1  C1  single    1.324  0.020  1.324
 V7W  C1  C2  single    1.530  0.020  1.530
 V7W  C3  C2  single    1.520  0.020  1.520
 V7W  C4  N1  single    1.449  0.020  1.449
 V7W  C4  C5  single    1.487  0.020  1.487
 V7W  C2  N1  single    1.439  0.020  1.439
 V7W  C5  C6  aromatic  1.362  0.020  1.362
 V7W  C5  S2  aromatic  1.722  0.020  1.722
 V7W  C6  C7  aromatic  1.423  0.020  1.423
 V7W  C7  C8  aromatic  1.361  0.020  1.361
 V7W  S2  C8  aromatic  1.716  0.020  1.716
 V7W  C2  H1  single    0.970  0.020  1.090
 V7W  C3  H2  single    0.970  0.020  1.090
 V7W  C3  H3  single    0.970  0.020  1.090
 V7W  C4  H4  single    0.970  0.020  1.090
 V7W  C6  H5  single    0.930  0.020  1.080
 V7W  C7  H6  single    0.930  0.020  1.080
 V7W  C8  H7  single    0.930  0.020  1.080
 V7W  O1  H8  single    0.850  0.020  0.980
 V7W  N1  H9  single    0.890  0.020  1.040

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
 V7W  O2  C1  O1  123.84  3.000
 V7W  O1  C1  C2  112.88  3.000
 V7W  O2  C1  C2  123.24  3.000
 V7W  H1  C2  N1  109.20  3.000
 V7W  H1  C2  C3  109.80  3.000
 V7W  N1  C2  C3  104.27  3.000
 V7W  H1  C2  C1  106.32  3.000
 V7W  N1  C2  C1  116.95  3.000
 V7W  C3  C2  C1  110.23  3.000
 V7W  H3  C3  H2  109.01  3.000
 V7W  H3  C3  S1  109.65  3.000
 V7W  H2  C3  S1  111.19  3.000
 V7W  H3  C3  C2  113.34  3.000
 V7W  H2  C3  C2  110.62  3.000
 V7W  S1  C3  C2  102.94  3.000
 V7W  H4  C4  N1  114.35  3.000
 V7W  H4  C4  S1  106.38  3.000
 V7W  N1  C4  S1  104.52  3.000
 V7W  H4  C4  C5  108.78  3.000
 V7W  N1  C4  C5  110.89  3.000
 V7W  S1  C4  C5  111.82  3.000
 V7W  S2  C5  C6  111.31  3.000
 V7W  S2  C5  C4  119.97  3.000
 V7W  C6  C5  C4  128.66  3.000
 V7W  H5  C6  C7  124.12  3.000
 V7W  H5  C6  C5  123.12  3.000
 V7W  C7  C6  C5  112.75  3.000
 V7W  H6  C7  C8  123.57  3.000
 V7W  H6  C7  C6  124.04  3.000
 V7W  C8  C7  C6  112.39  3.000
 V7W  H7  C8  S2  120.37  3.000
 V7W  H7  C8  C7  127.84  3.000
 V7W  S2  C8  C7  111.77  3.000
 V7W  H8  O1  C1  110.17  3.000
 V7W  C4  S1  C3   92.62  3.000
 V7W  C8  S2  C5   91.77  3.000
 V7W  H9  N1  C4  111.76  3.000
 V7W  H9  N1  C2  114.14  3.000
 V7W  C4  N1  C2  113.12  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
 V7W  CONST_01  C8  C7  C6  C5     0.00   0.0  0
 V7W  CONST_02  C7  C8  S2  C5     0.00   0.0  0
 V7W  CONST_03  C8  S2  C5  C6     0.00   0.0  0
 V7W  CONST_04  S2  C8  C7  C6     0.00   0.0  0
 V7W  CONST_05  S2  C5  C6  C7     0.00   0.0  0
 V7W  CONST_06  C7  C6  C5  C4   180.00   0.0  0
 V7W  CONST_07  C8  S2  C5  C4   180.00   0.0  0
 V7W  CONST_08  H5  C6  C5  C4     0.00   0.0  0
 V7W  CONST_09  H6  C7  C6  C5   180.00   0.0  0
 V7W  CONST_10  H7  C8  S2  C5   180.00   0.0  0
 V7W  CONST_11  H7  C8  C7  C6   180.00   0.0  0
 V7W  CONST_12  H5  C6  C7  C8   180.00   0.0  0
 V7W  CONST_13  H5  C6  C5  S2   180.00   0.0  0
 V7W  CONST_14  H6  C7  C8  S2   180.00   0.0  0
 V7W  CONST_15  H8  O1  C1  C2   180.00   0.0  0
 V7W  CONST_16  H8  O1  C1  O2     0.00   0.0  0
 V7W  Var_01    C4  S1  C3  C2   -28.13  30.0  1
 V7W  Var_02    H2  C3  S1  C4    90.34  30.0  1
 V7W  Var_03    H3  C3  S1  C4  -149.04  30.0  1

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
 V7W  chir_01  C2  C1  C3  N1  positiv
 V7W  chir_02  C4  S1  N1  C5  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
 V7W  plan-1  C4  0.020
 V7W  plan-1  C5  0.020
 V7W  plan-1  C6  0.020
 V7W  plan-1  C7  0.020
 V7W  plan-1  C8  0.020
 V7W  plan-1  S2  0.020
 V7W  plan-1  H5  0.020
 V7W  plan-1  H6  0.020
 V7W  plan-1  H7  0.020
 V7W  plan-2  C1  0.020
 V7W  plan-2  C2  0.020
 V7W  plan-2  O1  0.020
 V7W  plan-2  O2  0.020
 V7W  plan-2  H8  0.020

