# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 01:32:00 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (2R)-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
 2HG  2HG  '(2R)-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_2HG
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
 2HG  C1   C  C      0   0.393  -2.3718  -0.2524  -0.0196
 2HG  O1   O  O      0  -0.614  -3.1424   0.3565  -0.7999
 2HG  C2   C  CH1    0  -0.080  -1.1011   0.5304   0.3772
 2HG  O2   O  OC    -1  -0.598  -2.5249  -1.3909   0.4491
 2HG  C3   C  CH2    0  -0.418   0.1622  -0.2117  -0.0513
 2HG  O3   O  OH1    0  -0.704  -1.1617   1.8202  -0.1874
 2HG  C4   C  CH2    0  -0.580   1.4389   0.4913   0.3787
 2HG  O4   O  O      0  -0.611   2.6876  -1.2417  -0.7001
 2HG  C5   C  C      0   0.408   2.7544  -0.2092  -0.0040
 2HG  O5   O  OC    -1  -0.636   3.8022   0.3269   0.4178
 2HG  H2   H  HCH1   0   0.184  -1.0915   0.6115   1.4761
 2HG  H3   H  HCH2   0   0.204   0.1299  -1.2160   0.3755
 2HG  H3A  H  HCH2   0   0.198   0.1520  -0.3386  -1.1387
 2HG  HO3  H  HOH1   0   0.423  -1.9833   1.7680  -0.7119
 2HG  H4   H  HCH2   0   0.222   1.4632   1.5050  -0.0347
 2HG  H4A  H  HCH2   0   0.210   1.4320   0.6317   1.4663

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
 2HG  C1  O1   deloc   1.254  0.020  1.254
 2HG  C1  C2   single  1.544  0.020  1.544
 2HG  C1  O2   deloc   1.241  0.020  1.241
 2HG  C2  C3   single  1.527  0.020  1.527
 2HG  C2  O3   single  1.409  0.020  1.409
 2HG  C3  C4   single  1.520  0.020  1.520
 2HG  C4  C5   single  1.539  0.020  1.539
 2HG  O4  C5   deloc   1.247  0.020  1.247
 2HG  C5  O5   deloc   1.250  0.020  1.250
 2HG  C2  H2   single  0.970  0.020  1.090
 2HG  C3  H3   single  0.970  0.020  1.090
 2HG  C3  H3A  single  0.970  0.020  1.090
 2HG  O3  HO3  single  0.850  0.020  0.980
 2HG  C4  H4   single  0.970  0.020  1.090
 2HG  C4  H4A  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
 2HG  O2   C1  C2  118.01  3.000
 2HG  O2   C1  O1  127.20  3.000
 2HG  C2   C1  O1  114.79  3.000
 2HG  H2   C2  O3  109.42  3.000
 2HG  H2   C2  C3  107.97  3.000
 2HG  O3   C2  C3  111.59  3.000
 2HG  H2   C2  C1  107.50  3.000
 2HG  O3   C2  C1  109.01  3.000
 2HG  C3   C2  C1  111.25  3.000
 2HG  H3A  C3  H3  106.34  3.000
 2HG  H3A  C3  C4  110.03  3.000
 2HG  H3   C3  C4  109.87  3.000
 2HG  H3A  C3  C2  109.11  3.000
 2HG  H3   C3  C2  108.24  3.000
 2HG  C4   C3  C2  113.02  3.000
 2HG  HO3  O3  C2  101.68  3.000
 2HG  H4A  C4  H4  104.84  3.000
 2HG  H4A  C4  C5  108.08  3.000
 2HG  H4   C4  C5  107.97  3.000
 2HG  H4A  C4  C3  109.55  3.000
 2HG  H4   C4  C3  109.88  3.000
 2HG  C5   C4  C3  115.93  3.000
 2HG  O5   C5  O4  126.03  3.000
 2HG  O5   C5  C4  115.93  3.000
 2HG  O4   C5  C4  118.03  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
 2HG  Var_01  C5  C4  C3  C2  179.27  30.0  3
 2HG  Var_02  O4  C5  C4  C3    4.36  30.0  3

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
 2HG  chir_01  C2  C1  C3  O3  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
 2HG  plan-1  C1  0.020
 2HG  plan-1  O1  0.020
 2HG  plan-1  C2  0.020
 2HG  plan-1  O2  0.020
 2HG  plan-2  C4  0.020
 2HG  plan-2  O4  0.020
 2HG  plan-2  C5  0.020
 2HG  plan-2  O5  0.020

