# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:07:51 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: (3R)-thiolane-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CCSC1
#
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
 XH7  XH7  '(3R)-thiolane-3-carboxylic acid'  ligand  15  8  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XH7
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
 XH7  O01   O  O      0  -0.610  -11.6289  13.2813  22.1956
 XH7  C02   C  C      0   0.428  -10.6831  12.7795  21.5560
 XH7  O03   O  OC    -1  -0.593  -10.3017  11.5939  21.5904
 XH7  C04   C  CH1    0  -0.370   -9.9294  13.7468  20.6164
 XH7  C05   C  CH2    0  -0.423   -9.4317  15.0075  21.3216
 XH7  C06   C  CH2    0  -0.540   -8.6352  15.8030  20.2986
 XH7  S07   S  S2     0  -0.083   -7.7329  14.5633  19.2937
 XH7  C08   C  CH2    0  -0.528   -8.7103  13.1474  19.9283
 XH7  H041  H  HCH1   0   0.233  -10.6364  14.0651  19.8387
 XH7  H051  H  HCH2   0   0.242  -10.2536  15.6035  21.7186
 XH7  H052  H  HCH2   0   0.225   -8.7863  14.7303  22.1606
 XH7  H062  H  HCH2   0   0.253   -9.2959  16.3804  19.6512
 XH7  H061  H  HCH2   0   0.262   -7.9236  16.4888  20.7568
 XH7  H082  H  HCH2   0   0.257   -8.9764  12.4983  19.0949
 XH7  H081  H  HCH2   0   0.247   -8.1036  12.5728  20.6268

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
 XH7  C02  O01   deloc   1.247  0.020  1.247
 XH7  O03  C02   deloc   1.246  0.020  1.246
 XH7  C04  C02   single  1.545  0.020  1.545
 XH7  C05  C04   single  1.528  0.020  1.528
 XH7  C06  C05   single  1.521  0.020  1.521
 XH7  S07  C06   single  1.833  0.020  1.833
 XH7  C08  S07   single  1.834  0.020  1.834
 XH7  C04  C08   single  1.523  0.020  1.523
 XH7  C04  H041  single  0.970  0.020  1.090
 XH7  C05  H051  single  0.970  0.020  1.090
 XH7  C05  H052  single  0.970  0.020  1.090
 XH7  C06  H062  single  0.970  0.020  1.090
 XH7  C06  H061  single  0.970  0.020  1.090
 XH7  C08  H082  single  0.970  0.020  1.090
 XH7  C08  H081  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
 XH7  C04   C02  O03   117.60  3.000
 XH7  C04   C02  O01   115.47  3.000
 XH7  O03   C02  O01   126.93  3.000
 XH7  H041  C04  C08   108.03  3.000
 XH7  H041  C04  C05   107.31  3.000
 XH7  C08   C04  C05   105.82  3.000
 XH7  H041  C04  C02   107.35  3.000
 XH7  C08   C04  C02   114.77  3.000
 XH7  C05   C04  C02   113.26  3.000
 XH7  H052  C05  H051  107.69  3.000
 XH7  H052  C05  C06   109.84  3.000
 XH7  H051  C05  C06   110.72  3.000
 XH7  H052  C05  C04   109.70  3.000
 XH7  H051  C05  C04   111.94  3.000
 XH7  C06   C05  C04   106.96  3.000
 XH7  H061  C06  H062  108.19  3.000
 XH7  H061  C06  S07   109.56  3.000
 XH7  H062  C06  S07   109.32  3.000
 XH7  H061  C06  C05   112.86  3.000
 XH7  H062  C06  C05   111.04  3.000
 XH7  S07   C06  C05   105.82  3.000
 XH7  C08   S07  C06    94.02  3.000
 XH7  H081  C08  H082  108.20  3.000
 XH7  H081  C08  S07   109.41  3.000
 XH7  H082  C08  S07   109.00  3.000
 XH7  H081  C08  C04   111.34  3.000
 XH7  H082  C08  C04   112.63  3.000
 XH7  S07   C08  C04   106.21  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
 XH7  Var_01  S07  C06  C05  C04  -37.49  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
 XH7  chir_01  C04  C02  C05  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
 XH7  plan-1  O01  0.020
 XH7  plan-1  C02  0.020
 XH7  plan-1  O03  0.020
 XH7  plan-1  C04  0.020

