# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 00:13:32 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: (2S)-thiolane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCS1
#
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
 UJM  UJM  "(2S)-thiolane-2-carboxylic acid"  ligand  15  8  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UJM
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
 UJM  C02  C  C      0   0.421  -38.1970  56.2801  78.5563
 UJM  C04  C  CR15   0  -0.469  -39.5267  55.7040  79.1037
 UJM  C06  C  CH2    0  -0.542  -41.7591  55.9353  77.6006
 UJM  C07  C  CH2    0  -0.428  -40.7181  54.9480  77.0887
 UJM  C08  C  CH2    0  -0.437  -39.9481  54.4609  78.3084
 UJM  O01  O  O      0  -0.585  -38.2409  57.1590  77.6798
 UJM  O03  O  OC    -1  -0.613  -37.1801  55.7425  79.0404
 UJM  S05  S  S2     0  -0.062  -40.9634  56.8286  78.9864
 UJM  H1   H  HCR5   0   0.254  -39.3928  55.4441  80.1552
 UJM  H2   H  HCH2   0   0.260  -42.0748  56.6443  76.8362
 UJM  H3   H  HCH2   0   0.250  -42.6454  55.4160  77.9671
 UJM  H4   H  HCH2   0   0.241  -41.1962  54.1259  76.5532
 UJM  H5   H  HCH2   0   0.233  -40.0409  55.4448  76.3926
 UJM  H6   H  HCH2   0   0.234  -40.5973  53.8321  78.9231
 UJM  H7   H  HCH2   0   0.243  -39.0777  53.8598  78.0374

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
 UJM  C07  C06  single  1.523  0.020  1.523
 UJM  C07  C08  single  1.522  0.020  1.522
 UJM  C06  S05  single  1.831  0.020  1.831
 UJM  O01  C02  deloc   1.242  0.020  1.242
 UJM  C08  C04  single  1.535  0.020  1.535
 UJM  C02  O03  deloc   1.248  0.020  1.248
 UJM  C02  C04  single  1.549  0.020  1.549
 UJM  C04  S05  single  1.828  0.020  1.828
 UJM  C04  H1   single  0.970  0.020  1.090
 UJM  C06  H2   single  0.970  0.020  1.090
 UJM  C06  H3   single  0.970  0.020  1.090
 UJM  C07  H4   single  0.970  0.020  1.090
 UJM  C07  H5   single  0.970  0.020  1.090
 UJM  C08  H6   single  0.970  0.020  1.090
 UJM  C08  H7   single  0.970  0.020  1.090

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
 UJM  O03  C02  O01  127.40  3.000
 UJM  O03  C02  C04  113.71  3.000
 UJM  O01  C02  C04  118.83  3.000
 UJM  H1   C04  S05  107.74  3.000
 UJM  H1   C04  C08  109.88  3.000
 UJM  S05  C04  C08  104.43  3.000
 UJM  H1   C04  C02  108.89  3.000
 UJM  S05  C04  C02  115.03  3.000
 UJM  C08  C04  C02  110.72  3.000
 UJM  H3   C06  H2   108.07  3.000
 UJM  H3   C06  S05  109.34  3.000
 UJM  H2   C06  S05  109.85  3.000
 UJM  H3   C06  C07  111.08  3.000
 UJM  H2   C06  C07  112.59  3.000
 UJM  S05  C06  C07  105.88  3.000
 UJM  H5   C07  H4   107.57  3.000
 UJM  H5   C07  C08  110.06  3.000
 UJM  H4   C07  C08  111.93  3.000
 UJM  H5   C07  C06  110.09  3.000
 UJM  H4   C07  C06  110.71  3.000
 UJM  C08  C07  C06  106.49  3.000
 UJM  H7   C08  H6   107.24  3.000
 UJM  H7   C08  C07  112.36  3.000
 UJM  H6   C08  C07  109.53  3.000
 UJM  H7   C08  C04  110.83  3.000
 UJM  H6   C08  C04  109.73  3.000
 UJM  C07  C08  C04  107.15  3.000
 UJM  C06  S05  C04   95.16  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
 UJM  Var_01  C06  C07  C08  C04   -49.50  30.0  1
 UJM  Var_02  C07  C06  S05  C04   -11.49  30.0  1
 UJM  Var_03  S05  C06  C07  C08    35.83  30.0  1
 UJM  Var_04  H4   C07  C08  C04  -170.61  30.0  1
 UJM  Var_05  H5   C07  C08  C04    69.81  30.0  1
 UJM  Var_06  H2   C06  S05  C04  -133.31  30.0  1
 UJM  Var_07  H3   C06  S05  C04   108.25  30.0  1
 UJM  Var_08  H6   C08  C07  C06    69.47  30.0  1
 UJM  Var_09  H7   C08  C07  C06  -171.45  30.0  1
 UJM  Var_10  H2   C06  C07  C08   155.87  30.0  1
 UJM  Var_11  H3   C06  C07  C08   -82.76  30.0  1
 UJM  Var_12  H4   C07  C06  S05   157.73  30.0  1
 UJM  Var_13  H5   C07  C06  S05   -83.45  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
 UJM  chir_01  C04  C08  C02  S05  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
 UJM  plan-1  C02  0.020
 UJM  plan-1  C04  0.020
 UJM  plan-1  O01  0.020
 UJM  plan-1  O03  0.020

