# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:29:40 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: 3-hydroxypentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(CC(O)=O)CC(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
 3HG  3HG  '3-hydroxypentanedioic acid'  ligand  16  10  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3HG
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
 3HG  O2   O  OH1    0  -0.678  -0.0097  -0.8898   1.1049
 3HG  O1   O  OC    -1  -0.624  -3.4834   0.3813   0.7360
 3HG  C1   C  C      0   0.407  -2.5656   0.0591  -0.0464
 3HG  O3   O  O      0  -0.620  -2.6111  -0.8493  -0.9015
 3HG  C2   C  CH2    0  -0.580  -1.2642   0.8764   0.0171
 3HG  C3   C  CH1    0   0.044  -0.0067   0.0187   0.0128
 3HG  C4   C  CH2    0  -0.579   1.2622   0.8598   0.0105
 3HG  C5   C  C      0   0.406   2.5510   0.0232  -0.0580
 3HG  O4   O  O      0  -0.621   2.5849  -0.8759  -0.9236
 3HG  O5   O  OC    -1  -0.623   3.4709   0.3202   0.7317
 3HG  HO2  H  HOH1   0   0.432  -0.0066  -0.3711   1.9163
 3HG  H21  H  HCH2   0   0.197  -1.2621   1.5310   0.8961
 3HG  H22  H  HCH2   0   0.220  -1.2336   1.5399  -0.8554
 3HG  H3   H  HCH1   0   0.202  -0.0127  -0.6066  -0.8817
 3HG  H41  H  HCH2   0   0.220   1.2366   1.5223  -0.8629
 3HG  H42  H  HCH2   0   0.196   1.2734   1.5154   0.8887

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
 3HG  O2  C3   single  1.421  0.020  1.421
 3HG  O2  HO2  single  0.850  0.020  0.980
 3HG  O1  C1   deloc   1.248  0.020  1.248
 3HG  C1  O3   deloc   1.248  0.020  1.248
 3HG  C1  C2   single  1.538  0.020  1.538
 3HG  C2  C3   single  1.522  0.020  1.522
 3HG  C2  H21  single  0.970  0.020  1.090
 3HG  C2  H22  single  0.970  0.020  1.090
 3HG  C3  C4   single  1.522  0.020  1.522
 3HG  C3  H3   single  0.970  0.020  1.090
 3HG  C4  C5   single  1.538  0.020  1.538
 3HG  C4  H41  single  0.970  0.020  1.090
 3HG  C4  H42  single  0.970  0.020  1.090
 3HG  C5  O4   deloc   1.248  0.020  1.248
 3HG  C5  O5   deloc   1.248  0.020  1.248

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
 3HG  HO2  O2  C3   107.66  3.000
 3HG  C2   C1  O3   116.47  3.000
 3HG  C2   C1  O1   117.33  3.000
 3HG  O3   C1  O1   126.18  3.000
 3HG  H22  C2  H21  106.06  3.000
 3HG  H22  C2  C3   108.40  3.000
 3HG  H21  C2  C3   109.71  3.000
 3HG  H22  C2  C1   108.19  3.000
 3HG  H21  C2  C1   110.62  3.000
 3HG  C3   C2  C1   113.54  3.000
 3HG  H3   C3  C4   108.66  3.000
 3HG  H3   C3  C2   108.70  3.000
 3HG  C4   C3  C2   112.16  3.000
 3HG  H3   C3  O2   105.29  3.000
 3HG  C4   C3  O2   110.87  3.000
 3HG  C2   C3  O2   110.88  3.000
 3HG  H42  C4  H41  106.09  3.000
 3HG  H42  C4  C5   110.64  3.000
 3HG  H41  C4  C5   108.22  3.000
 3HG  H42  C4  C3   109.74  3.000
 3HG  H41  C4  C3   108.39  3.000
 3HG  C5   C4  C3   113.45  3.000
 3HG  O5   C5  O4   126.16  3.000
 3HG  O5   C5  C4   117.38  3.000
 3HG  O4   C5  C4   116.45  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
 3HG  Var_01  C1  C2  C3  O2  -58.13  30.0  2
 3HG  Var_02  C5  C4  C3  O2   58.05  30.0  3
 3HG  Var_03  C3  C2  C1  O1  134.54  30.0  3
 3HG  Var_04  O4  C5  C4  C3   47.83  30.0  3

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
 3HG  plan-1  O1  0.020
 3HG  plan-1  C1  0.020
 3HG  plan-1  O3  0.020
 3HG  plan-1  C2  0.020
 3HG  plan-2  C4  0.020
 3HG  plan-2  C5  0.020
 3HG  plan-2  O4  0.020
 3HG  plan-2  O5  0.020

