# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:14:16 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC[C@@H]1CCSS1
#
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
 LPA  LPA  '5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid'  ligand  25  12  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LPA
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
 LPA  C1   C  C      0   0.410   4.7189   0.0971  -0.1075
 LPA  O1   O  OC    -1  -0.635   5.6722   0.6993   0.4319
 LPA  C2   C  CH2    0  -0.582   3.3244   0.3907   0.4724
 LPA  O2   O  O      0  -0.610   4.7985  -0.7015  -1.0615
 LPA  C3   C  CH2    0  -0.402   2.1721  -0.4104  -0.1111
 LPA  C4   C  CH2    0  -0.414   0.8381  -0.0734   0.5450
 LPA  C5   C  CH2    0  -0.399  -0.3202  -0.8921  -0.0055
 LPA  C6   C  CH1    0  -0.361  -1.6473  -0.6364   0.6910
 LPA  S6   S  S2     0  -0.069  -2.2345   1.1042   0.4456
 LPA  C7   C  CH2    0  -0.410  -2.7457  -1.6057   0.2235
 LPA  C8   C  CH2    0  -0.572  -4.1069  -0.9375   0.1313
 LPA  S8   S  S2     0  -0.056  -3.8394   0.6085  -0.7823
 LPA  H2   H  HCH2   0   0.215   3.3647   0.2386   1.5572
 LPA  H2A  H  HCH2   0   0.218   3.1279   1.4627   0.3475
 LPA  H3   H  HCH2   0   0.204   2.1014  -0.2324  -1.1879
 LPA  H3A  H  HCH2   0   0.202   2.3678  -1.4805   0.0052
 LPA  H4   H  HCH2   0   0.209   0.9118  -0.2378   1.6261
 LPA  H4A  H  HCH2   0   0.210   0.6303   0.9943   0.4135
 LPA  H5   H  HCH2   0   0.226  -0.4423  -0.7111  -1.0782
 LPA  H5A  H  HCH2   0   0.234  -0.0900  -1.9585   0.1049
 LPA  H6   H  HCH1   0   0.285  -1.5165  -0.7179   1.7726
 LPA  H7   H  HCH2   0   0.252  -2.4801  -1.9916  -0.7629
 LPA  H7A  H  HCH2   0   0.270  -2.7882  -2.4574   0.9056
 LPA  H8   H  HCH2   0   0.295  -4.8199  -1.5418  -0.4306
 LPA  H8A  H  HCH2   0   0.280  -4.5279  -0.7133   1.1119

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
 LPA  C2  C1   single  1.539  0.020  1.539
 LPA  C1  O2   deloc   1.247  0.020  1.247
 LPA  C1  O1   deloc   1.250  0.020  1.250
 LPA  C3  C2   single  1.520  0.020  1.520
 LPA  C2  H2   single  0.970  0.020  1.090
 LPA  C2  H2A  single  0.970  0.020  1.090
 LPA  C4  C3   single  1.524  0.020  1.524
 LPA  C3  H3   single  0.970  0.020  1.090
 LPA  C3  H3A  single  0.970  0.020  1.090
 LPA  C5  C4   single  1.522  0.020  1.522
 LPA  C4  H4   single  0.970  0.020  1.090
 LPA  C4  H4A  single  0.970  0.020  1.090
 LPA  C6  C5   single  1.520  0.020  1.520
 LPA  C5  H5   single  0.970  0.020  1.090
 LPA  C5  H5A  single  0.970  0.020  1.090
 LPA  C7  C6   single  1.538  0.020  1.538
 LPA  C6  S6   single  1.853  0.020  1.853
 LPA  C6  H6   single  0.970  0.020  1.090
 LPA  S8  S6   single  2.081  0.020  2.081
 LPA  C8  C7   single  1.519  0.020  1.519
 LPA  C7  H7   single  0.970  0.020  1.090
 LPA  C7  H7A  single  0.970  0.020  1.090
 LPA  C8  S8   single  1.816  0.020  1.816
 LPA  C8  H8   single  0.970  0.020  1.090
 LPA  C8  H8A  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
 LPA  O2   C1  C2  117.94  3.000
 LPA  O2   C1  O1  126.17  3.000
 LPA  C2   C1  O1  115.89  3.000
 LPA  H2A  C2  H2  104.77  3.000
 LPA  H2A  C2  C3  109.61  3.000
 LPA  H2   C2  C3  109.55  3.000
 LPA  H2A  C2  C1  107.81  3.000
 LPA  H2   C2  C1  108.25  3.000
 LPA  C3   C2  C1  116.23  3.000
 LPA  H3A  C3  H3  105.98  3.000
 LPA  H3A  C3  C4  109.09  3.000
 LPA  H3   C3  C4  109.35  3.000
 LPA  H3A  C3  C2  109.82  3.000
 LPA  H3   C3  C2  109.95  3.000
 LPA  C4   C3  C2  112.44  3.000
 LPA  H4A  C4  H4  106.11  3.000
 LPA  H4A  C4  C5  109.67  3.000
 LPA  H4   C4  C5  109.11  3.000
 LPA  H4A  C4  C3  109.25  3.000
 LPA  H4   C4  C3  109.42  3.000
 LPA  C5   C4  C3  113.05  3.000
 LPA  H5A  C5  H5  106.43  3.000
 LPA  H5A  C5  C6  107.50  3.000
 LPA  H5   C5  C6  108.90  3.000
 LPA  H5A  C5  C4  109.09  3.000
 LPA  H5   C5  C4  110.51  3.000
 LPA  C6   C5  C4  114.09  3.000
 LPA  H6   C6  C7  109.85  3.000
 LPA  H6   C6  S6  103.83  3.000
 LPA  C7   C6  S6  108.99  3.000
 LPA  H6   C6  C5  109.67  3.000
 LPA  S6   C6  C5  111.95  3.000
 LPA  C7   C6  C5  112.22  3.000
 LPA  S8   S6  C6   95.67  3.000
 LPA  H7A  C7  H7  107.34  3.000
 LPA  H7A  C7  C8  110.25  3.000
 LPA  H7   C7  C8  108.57  3.000
 LPA  H7A  C7  C6  109.24  3.000
 LPA  H7   C7  C6  108.89  3.000
 LPA  C8   C7  C6  112.41  3.000
 LPA  H8A  C8  H8  108.96  3.000
 LPA  H8A  C8  S8  109.53  3.000
 LPA  H8   C8  S8  107.99  3.000
 LPA  H8A  C8  C7  112.44  3.000
 LPA  H8   C8  C7  111.92  3.000
 LPA  S8   C8  C7  105.84  3.000
 LPA  C8   S8  S6   91.12  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
 LPA  Var_01  S8  C8  C7  C6    48.17  30.0  1
 LPA  Var_02  C7  C8  S8  S6   -49.28  30.0  1
 LPA  Var_03  C6  C5  C4  C3   176.44  30.0  1
 LPA  Var_04  C4  C3  C2  C1   178.75  30.0  1
 LPA  Var_05  C3  C2  C1  O1  -175.81  30.0  2
 LPA  Var_06  C5  C4  C3  C2  -178.60  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
 LPA  chir_01  C6  C5  C7  S6  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
 LPA  plan-1  C1  0.020
 LPA  plan-1  O1  0.020
 LPA  plan-1  C2  0.020
 LPA  plan-1  O2  0.020

