# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 23:59:19 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  26  12  .  2022-03-22  2022-11-17
;
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   0.550   4.6402   0.0919  -0.2039
 LPA  O1   O  OH1   0  -0.598   5.6060   0.8569   0.2988
 LPA  C2   C  CH2   0  -0.580   3.3121   0.3768   0.4393
 LPA  O2   O  O     0  -0.446   4.8363  -0.7257  -1.0684
 LPA  C3   C  CH2   0  -0.418   2.1590  -0.4236  -0.1431
 LPA  C4   C  CH2   0  -0.418   0.8460  -0.1036   0.5602
 LPA  C5   C  CH2   0  -0.403  -0.3239  -0.9022   0.0073
 LPA  C6   C  CH1   0  -0.366  -1.6436  -0.6377   0.7152
 LPA  S6   S  S2    0  -0.065  -2.2174   1.1069   0.4824
 LPA  C7   C  CH2   0  -0.410  -2.7522  -1.5977   0.2448
 LPA  C8   C  CH2   0  -0.573  -4.0954  -0.9045   0.0860
 LPA  S8   S  S2    0  -0.054  -3.7604   0.6292  -0.8262
 LPA  HO1  H  HOH1  0   0.478   6.4497   0.6466  -0.1281
 LPA  H2   H  HCH2  0   0.277   3.4102   0.1801   1.5123
 LPA  H2A  H  HCH2  0   0.275   3.1180   1.4510   0.3587
 LPA  H3   H  HCH2  0   0.228   2.0609  -0.2119  -1.2112
 LPA  H3A  H  HCH2  0   0.227   2.3675  -1.4928  -0.0552
 LPA  H4   H  HCH2  0   0.220   0.9473  -0.3059   1.6321
 LPA  H4A  H  HCH2  0   0.220   0.6383   0.9675   0.4672
 LPA  H5   H  HCH2  0   0.230  -0.4506  -0.7061  -1.0622
 LPA  H5A  H  HCH2  0   0.238  -0.1071  -1.9725   0.1032
 LPA  H6   H  HCH1  0   0.288  -1.5067  -0.7271   1.7954
 LPA  H7   H  HCH2  0   0.253  -2.4649  -2.0201  -0.7202
 LPA  H7A  H  HCH2  0   0.271  -2.8363  -2.4265   0.9503
 LPA  H8   H  HCH2  0   0.296  -4.7939  -1.5016  -0.5010
 LPA  H8A  H  HCH2  0   0.280  -4.5546  -0.6623   1.0446

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  1.503  0.020  1.503
 LPA  C1  O2   double  1.206  0.020  1.206
 LPA  C1  O1   single  1.331  0.020  1.331
 LPA  O1  HO1  single  0.850  0.020  0.980
 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  1.521  0.020  1.521
 LPA  C4  H4   single  0.970  0.020  1.090
 LPA  C4  H4A  single  0.970  0.020  1.090
 LPA  C6  C5   single  1.521  0.020  1.521
 LPA  C5  H5   single  0.970  0.020  1.090
 LPA  C5  H5A  single  0.970  0.020  1.090
 LPA  C7  C6   single  1.540  0.020  1.540
 LPA  C6  S6   single  1.851  0.020  1.851
 LPA  C6  H6   single  0.970  0.020  1.090
 LPA  S8  S6   single  2.079  0.020  2.079
 LPA  C8  C7   single  1.520  0.020  1.520
 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  125.38  3.000
 LPA  O2   C1  O1  122.86  3.000
 LPA  C2   C1  O1  111.76  3.000
 LPA  HO1  O1  C1  109.93  3.000
 LPA  H2A  C2  H2  105.32  3.000
 LPA  H2A  C2  C3  110.74  3.000
 LPA  H2   C2  C3  110.42  3.000
 LPA  H2A  C2  C1  108.13  3.000
 LPA  H2   C2  C1  107.82  3.000
 LPA  C3   C2  C1  114.00  3.000
 LPA  H3A  C3  H3  106.56  3.000
 LPA  H3A  C3  C4  109.44  3.000
 LPA  H3   C3  C4  109.45  3.000
 LPA  H3A  C3  C2  109.85  3.000
 LPA  H3   C3  C2  109.91  3.000
 LPA  C4   C3  C2  111.49  3.000
 LPA  H4A  C4  H4  106.34  3.000
 LPA  H4A  C4  C5  109.69  3.000
 LPA  H4   C4  C5  109.27  3.000
 LPA  H4A  C4  C3  109.25  3.000
 LPA  H4   C4  C3  109.46  3.000
 LPA  C5   C4  C3  112.64  3.000
 LPA  H5A  C5  H5  106.46  3.000
 LPA  H5A  C5  C6  107.50  3.000
 LPA  H5   C5  C6  108.86  3.000
 LPA  H5A  C5  C4  109.19  3.000
 LPA  H5   C5  C4  110.51  3.000
 LPA  C6   C5  C4  114.02  3.000
 LPA  H6   C6  C7  109.95  3.000
 LPA  H6   C6  S6  103.90  3.000
 LPA  C7   C6  S6  109.02  3.000
 LPA  H6   C6  C5  109.71  3.000
 LPA  S6   C6  C5  111.98  3.000
 LPA  C7   C6  C5  111.97  3.000
 LPA  S8   S6  C6   95.32  3.000
 LPA  H7A  C7  H7  107.32  3.000
 LPA  H7A  C7  C8  110.23  3.000
 LPA  H7   C7  C8  108.46  3.000
 LPA  H7A  C7  C6  109.35  3.000
 LPA  H7   C7  C6  108.76  3.000
 LPA  C8   C7  C6  112.57  3.000
 LPA  H8A  C8  H8  108.98  3.000
 LPA  H8A  C8  S8  109.38  3.000
 LPA  H8   C8  S8  108.08  3.000
 LPA  H8A  C8  C7  112.44  3.000
 LPA  H8   C8  C7  111.87  3.000
 LPA  S8   C8  C7  105.94  3.000
 LPA  C8   S8  S6   90.85  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  CONST_01  HO1  O1  C1  C2   180.00   0.0  0
 LPA  Var_01    S8   C8  C7  C6    46.49  30.0  1
 LPA  Var_02    C7   C8  S8  S6   -49.76  30.0  1
 LPA  Var_03    C6   C5  C4  C3   178.27  30.0  1
 LPA  Var_04    C4   C3  C2  C1   179.31  30.0  1
 LPA  Var_05    C3   C2  C1  O1   177.27  30.0  2
 LPA  Var_06    C5   C4  C3  C2  -179.38  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
 LPA  plan-1  HO1  0.020

