# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 23:44:50 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: (2R)-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
 UJP  UJP  "(2R)-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 OK
;

data_comp_UJP
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
 UJP  C02  C  C      0   0.442  -38.5060  56.3582  78.4289
 UJP  C04  C  CR15   0  -0.500  -39.6907  55.7600  79.2168
 UJP  C06  C  CH2    0  -0.553  -41.2691  55.1374  77.2258
 UJP  C07  C  CH2    0  -0.416  -41.7417  56.4172  77.9378
 UJP  C08  C  CH2    0  -0.407  -40.9601  56.6024  79.2482
 UJP  O01  O  O      0  -0.591  -38.7862  57.1989  77.5516
 UJP  O03  O  OC    -1  -0.610  -37.3765  55.9251  78.7258
 UJP  S05  S  S2     0  -0.064  -40.2334  54.2133  78.4025
 UJP  H1   H  HCR5   0   0.261  -39.3685  55.4880  80.2247
 UJP  H2   H  HCH2   0   0.261  -42.0963  54.4981  76.9192
 UJP  H3   H  HCH2   0   0.258  -40.6857  55.3754  76.3378
 UJP  H4   H  HCH2   0   0.233  -41.5927  57.2667  77.2735
 UJP  H5   H  HCH2   0   0.229  -42.8105  56.3571  78.1453
 UJP  H6   H  HCH2   0   0.233  -40.7272  57.6530  79.4284
 UJP  H7   H  HCH2   0   0.225  -41.5739  56.2661  80.0862

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
 UJP  C06  C07  single  1.539  0.020  1.539
 UJP  C06  S05  single  1.820  0.020  1.820
 UJP  C07  C08  single  1.537  0.020  1.537
 UJP  O01  C02  deloc   1.247  0.020  1.247
 UJP  S05  C04  single  1.830  0.020  1.830
 UJP  C02  O03  deloc   1.246  0.020  1.246
 UJP  C02  C04  single  1.543  0.020  1.543
 UJP  C08  C04  single  1.524  0.020  1.524
 UJP  C04  H1   single  0.970  0.020  1.090
 UJP  C06  H2   single  0.970  0.020  1.090
 UJP  C06  H3   single  0.970  0.020  1.090
 UJP  C07  H4   single  0.970  0.020  1.090
 UJP  C07  H5   single  0.970  0.020  1.090
 UJP  C08  H6   single  0.970  0.020  1.090
 UJP  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
 UJP  O03  C02  O01  127.29  3.000
 UJP  O03  C02  C04  116.08  3.000
 UJP  O01  C02  C04  116.61  3.000
 UJP  H1   C04  S05  106.70  3.000
 UJP  H1   C04  C08  111.36  3.000
 UJP  S05  C04  C08  103.26  3.000
 UJP  H1   C04  C02  109.95  3.000
 UJP  C08  C04  C02  115.83  3.000
 UJP  S05  C04  C02  109.15  3.000
 UJP  H3   C06  H2   107.79  3.000
 UJP  H3   C06  S05  109.48  3.000
 UJP  H2   C06  S05  108.43  3.000
 UJP  H3   C06  C07  111.11  3.000
 UJP  H2   C06  C07  112.64  3.000
 UJP  S05  C06  C07  107.33  3.000
 UJP  H5   C07  H4   107.06  3.000
 UJP  H5   C07  C08  110.05  3.000
 UJP  H4   C07  C08  110.89  3.000
 UJP  H5   C07  C06  110.07  3.000
 UJP  H4   C07  C06  108.94  3.000
 UJP  C08  C07  C06  109.78  3.000
 UJP  H7   C08  H6   106.85  3.000
 UJP  H7   C08  C07  109.35  3.000
 UJP  H6   C08  C07  111.43  3.000
 UJP  H7   C08  C04  108.30  3.000
 UJP  H6   C08  C04  110.97  3.000
 UJP  C07  C08  C04  109.85  3.000
 UJP  C06  S05  C04   91.56  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
 UJP  Var_01  C07  C06  S05  C04   -30.09  30.0  1
 UJP  Var_02  C06  C07  C08  C04    18.37  30.0  1
 UJP  Var_03  S05  C06  C07  C08    11.43  30.0  1
 UJP  Var_04  H2   C06  S05  C04  -152.03  30.0  1
 UJP  Var_05  H3   C06  S05  C04    90.62  30.0  1
 UJP  Var_06  H4   C07  C08  C04  -102.06  30.0  1
 UJP  Var_07  H5   C07  C08  C04   139.67  30.0  1
 UJP  Var_08  H6   C08  C07  C06   141.76  30.0  1
 UJP  Var_09  H7   C08  C07  C06  -100.35  30.0  1
 UJP  Var_10  H2   C06  C07  C08   130.71  30.0  1
 UJP  Var_11  H3   C06  C07  C08  -108.23  30.0  1
 UJP  Var_12  H4   C07  C06  S05   133.04  30.0  1
 UJP  Var_13  H5   C07  C06  S05  -109.86  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
 UJP  chir_01  C04  S05  C02  C08  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
 UJP  plan-1  C02  0.020
 UJP  plan-1  C04  0.020
 UJP  plan-1  O01  0.020
 UJP  plan-1  O03  0.020

