# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 20:17:14 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (2S)-2-hydroxypentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CCC(O)=O)C(O)=O
#
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
 S2G  S2G  '(2S)-2-hydroxypentanedioic acid'  ligand  16  10  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S2G
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
 S2G  C1   C  C      0   0.393   2.3593  -0.2185   0.0214
 S2G  C3   C  CH2    0  -0.417  -0.1734  -0.1882  -0.0170
 S2G  C4   C  CH2    0  -0.581  -1.4572   0.5161   0.3890
 S2G  C5   C  C      0   0.409  -2.7644  -0.1989   0.0044
 S2G  O2   O  OC    -1  -0.598   2.5149  -1.3522   0.5014
 S2G  O1   O  O      0  -0.614   3.1289   0.3849  -0.7638
 S2G  O3   O  OH1    0  -0.704   1.1421   1.8486  -0.1662
 S2G  O5   O  OC    -1  -0.636  -3.8215   0.4044   0.2901
 S2G  C2   C  CH1    0  -0.080   1.0850   0.5633   0.4090
 S2G  O4   O  O      0  -0.611  -2.6818  -1.3120  -0.5519
 S2G  H2   H  HCH1   0   0.184   1.0721   0.6533   1.5073
 S2G  H3   H  HCH2   0   0.204  -0.1420  -1.1847   0.4262
 S2G  H3A  H  HCH2   0   0.198  -0.1535  -0.3334  -1.1025
 S2G  H4   H  HCH2   0   0.212  -1.4639   0.6669   1.4760
 S2G  H4A  H  HCH2   0   0.219  -1.4823   1.5251  -0.0344
 S2G  HO3  H  HOH1   0   0.423   1.9649   1.7970  -0.6885

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
 S2G  C1  O2   deloc   1.241  0.020  1.241
 S2G  C1  O1   deloc   1.254  0.020  1.254
 S2G  C1  C2   single  1.544  0.020  1.544
 S2G  C3  C4   single  1.520  0.020  1.520
 S2G  C3  C2   single  1.526  0.020  1.526
 S2G  C4  C5   single  1.539  0.020  1.539
 S2G  C5  O5   deloc   1.250  0.020  1.250
 S2G  C5  O4   deloc   1.247  0.020  1.247
 S2G  O3  C2   single  1.409  0.020  1.409
 S2G  C2  H2   single  0.970  0.020  1.090
 S2G  C3  H3   single  0.970  0.020  1.090
 S2G  C3  H3A  single  0.970  0.020  1.090
 S2G  C4  H4   single  0.970  0.020  1.090
 S2G  C4  H4A  single  0.970  0.020  1.090
 S2G  O3  HO3  single  0.850  0.020  0.980

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
 S2G  C2   C1  O1  114.83  3.000
 S2G  C2   C1  O2  117.96  3.000
 S2G  O1   C1  O2  127.21  3.000
 S2G  H3A  C3  H3  106.31  3.000
 S2G  H3A  C3  C2  109.08  3.000
 S2G  H3   C3  C2  108.22  3.000
 S2G  H3A  C3  C4  109.97  3.000
 S2G  H3   C3  C4  109.82  3.000
 S2G  C2   C3  C4  113.19  3.000
 S2G  H4A  C4  H4  104.86  3.000
 S2G  H4A  C4  C5  108.19  3.000
 S2G  H4   C4  C5  107.83  3.000
 S2G  H4A  C4  C3  110.07  3.000
 S2G  H4   C4  C3  109.48  3.000
 S2G  C5   C4  C3  115.82  3.000
 S2G  O4   C5  O5  126.06  3.000
 S2G  O4   C5  C4  118.03  3.000
 S2G  O5   C5  C4  115.90  3.000
 S2G  HO3  O3  C2  101.79  3.000
 S2G  H2   C2  O3  109.44  3.000
 S2G  H2   C2  C3  107.98  3.000
 S2G  O3   C2  C3  111.62  3.000
 S2G  H2   C2  C1  107.52  3.000
 S2G  O3   C2  C1  109.02  3.000
 S2G  C3   C2  C1  111.16  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
 S2G  Var_01  O5  C5  C4  C3  -177.25  30.0  3
 S2G  Var_02  C2  C3  C4  C5  -179.27  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
 S2G  chir_01  C2  C1  C3  O3  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
 S2G  plan-1  C1  0.020
 S2G  plan-1  O2  0.020
 S2G  plan-1  O1  0.020
 S2G  plan-1  C2  0.020
 S2G  plan-2  C4  0.020
 S2G  plan-2  C5  0.020
 S2G  plan-2  O5  0.020
 S2G  plan-2  O4  0.020

