# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:52:19 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (2~{R},4~{R})-1,3-thiazolidine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CS[C@@H](N1)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
 5XB  5XB  '(2~{R},4~{R})-1,3-thiazolidine-2,4-dicarboxylic acid'  ligand  18  11  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5XB
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
 5XB  C2   C  CH1   0  -0.310   1.1063  -0.1226  -0.5955
 5XB  C4   C  CH1   0  -0.209  -1.1909  -0.1478  -0.4410
 5XB  C5   C  CH2   0  -0.564  -0.9540  -1.3576   0.4980
 5XB  S1   S  S2    0  -0.008   0.8209  -1.7154   0.3531
 5XB  C4A  C  C     0   0.540  -2.4416   0.6066  -0.0543
 5XB  O42  O  O     0  -0.425  -2.4539   1.7250   0.3890
 5XB  C2A  C  C     0   0.553   2.4335   0.4513  -0.1643
 5XB  O21  O  OH1   0  -0.577   2.3736   1.7353   0.1311
 5XB  O22  O  O     0  -0.433   3.4327  -0.2175  -0.1180
 5XB  N3   N  NH1   0  -0.550  -0.0328   0.7112  -0.4059
 5XB  H1   H  HCH1  0   0.329   1.1949  -0.4004  -1.6490
 5XB  H2   H  HCH1  0   0.312  -1.3155  -0.5294  -1.4594
 5XB  H3   H  HCH2  0   0.282  -1.1972  -1.1146   1.5327
 5XB  H4   H  HCH2  0   0.293  -1.5392  -2.2220   0.1907
 5XB  H5   H  HOH1  0   0.490  -4.3145   0.3463   0.0362
 5XB  H6   H  HOH1  0   0.492   3.2464   2.0593   0.4038
 5XB  H7   H  HNH1  0   0.369   0.0106   1.1908   0.4870
 5XB  O41  O  OH1   0  -0.585  -3.5203  -0.1355  -0.2417

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
 5XB  O22  C2A  double  1.203  0.020  1.203
 5XB  O21  C2A  single  1.319  0.020  1.319
 5XB  C2A  C2   single  1.509  0.020  1.509
 5XB  N3   C2   single  1.424  0.020  1.424
 5XB  N3   C4   single  1.442  0.020  1.442
 5XB  C2   S1   single  1.876  0.020  1.876
 5XB  O42  C4A  double  1.203  0.020  1.203
 5XB  C4   C4A  single  1.511  0.020  1.511
 5XB  C4   C5   single  1.550  0.020  1.550
 5XB  C4A  O41  single  1.323  0.020  1.323
 5XB  S1   C5   single  1.816  0.020  1.816
 5XB  C2   H1   single  0.970  0.020  1.090
 5XB  C4   H2   single  0.970  0.020  1.090
 5XB  C5   H3   single  0.970  0.020  1.090
 5XB  C5   H4   single  0.970  0.020  1.090
 5XB  O41  H5   single  0.850  0.020  0.980
 5XB  O21  H6   single  0.850  0.020  0.980
 5XB  N3   H7   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
 5XB  H1   C2   N3   109.99  3.000
 5XB  H1   C2   C2A  107.51  3.000
 5XB  N3   C2   C2A  116.28  3.000
 5XB  H1   C2   S1   106.50  3.000
 5XB  N3   C2   S1   107.94  3.000
 5XB  C2A  C2   S1   108.20  3.000
 5XB  H2   C4   N3   108.76  3.000
 5XB  H2   C4   C4A  108.54  3.000
 5XB  N3   C4   C4A  111.17  3.000
 5XB  H2   C4   C5   108.00  3.000
 5XB  C4A  C4   C5   111.18  3.000
 5XB  N3   C4   C5   109.11  3.000
 5XB  H4   C5   H3   108.97  3.000
 5XB  H4   C5   S1   110.27  3.000
 5XB  H3   C5   S1   109.73  3.000
 5XB  H4   C5   C4   111.52  3.000
 5XB  H3   C5   C4   111.53  3.000
 5XB  S1   C5   C4   104.77  3.000
 5XB  C5   S1   C2    91.24  3.000
 5XB  O42  C4A  O41  124.43  3.000
 5XB  O41  C4A  C4   111.02  3.000
 5XB  O42  C4A  C4   124.53  3.000
 5XB  O22  C2A  O21  124.76  3.000
 5XB  O21  C2A  C2   113.23  3.000
 5XB  O22  C2A  C2   122.00  3.000
 5XB  H6   O21  C2A  110.32  3.000
 5XB  H7   N3   C4   109.71  3.000
 5XB  H7   N3   C2   111.08  3.000
 5XB  C4   N3   C2   106.88  3.000
 5XB  H5   O41  C4A  110.40  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
 5XB  CONST_01  H6  O21  C2A  C2  180.00   0.0  0
 5XB  CONST_02  H5  O41  C4A  C4  180.00   0.0  0
 5XB  Var_01    C4  C5   S1   C2   10.14  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
 5XB  chir_01  C2  C2A  N3   S1  positiv
 5XB  chir_02  C4  N3   C4A  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
 5XB  plan-1  C4   0.020
 5XB  plan-1  C4A  0.020
 5XB  plan-1  O42  0.020
 5XB  plan-1  H5   0.020
 5XB  plan-1  O41  0.020
 5XB  plan-2  C2   0.020
 5XB  plan-2  C2A  0.020
 5XB  plan-2  O21  0.020
 5XB  plan-2  O22  0.020
 5XB  plan-2  H6   0.020

