# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:38:01 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  18  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.509  -2.3921  -0.2524   0.0398
 2HG  O1   O  O     0  -0.436  -3.1586   0.1197  -0.8113
 2HG  C2   C  CH1   0  -0.069  -1.1337   0.5028   0.4387
 2HG  O2   O  OH1   0  -0.589  -2.5313  -1.3779   0.7242
 2HG  C3   C  CH2   0  -0.471   0.1031  -0.2389  -0.0800
 2HG  O3   O  OH1   0  -0.650  -1.1960   1.8307   0.0085
 2HG  C4   C  CH2   0  -0.577   1.3819   0.4328   0.3903
 2HG  O4   O  O     0  -0.444   2.6503  -1.1880  -0.8635
 2HG  C5   C  C     0   0.551   2.6254  -0.2529  -0.1028
 2HG  O5   O  OH1   0  -0.596   3.7233   0.3027   0.4002
 2HG  H2   H  HCH1  0   0.276  -1.0916   0.5328   1.5321
 2HG  HO2  H  HOH1  0   0.486  -3.3172  -1.8586   0.4233
 2HG  H3   H  HCH2  0   0.259   0.0780  -1.2719   0.2697
 2HG  H3A  H  HCH2  0   0.252   0.0701  -0.2761  -1.1727
 2HG  HO3  H  HOH1  0   0.449  -1.2709   1.8463  -0.9523
 2HG  H4   H  HCH2  0   0.288   1.4202   1.4757   0.0640
 2HG  H4A  H  HCH2  0   0.281   1.4180   0.4646   1.4834
 2HG  HO5  H  HOH1  0   0.479   4.5092  -0.1535   0.0644

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   double  1.204  0.020  1.204
 2HG  C1  C2   single  1.521  0.020  1.521
 2HG  C1  O2   single  1.325  0.020  1.325
 2HG  C2  C3   single  1.533  0.020  1.533
 2HG  C2  O3   single  1.397  0.020  1.397
 2HG  C3  C4   single  1.519  0.020  1.519
 2HG  C4  C5   single  1.503  0.020  1.503
 2HG  O4  C5   double  1.206  0.020  1.206
 2HG  C5  O5   single  1.329  0.020  1.329
 2HG  C2  H2   single  0.970  0.020  1.090
 2HG  O2  HO2  single  0.850  0.020  0.980
 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
 2HG  O5  HO5  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
 2HG  O2   C1  C2  111.92  3.000
 2HG  O2   C1  O1  124.11  3.000
 2HG  C2   C1  O1  123.95  3.000
 2HG  H2   C2  O3  106.45  3.000
 2HG  H2   C2  C3  108.68  3.000
 2HG  O3   C2  C3  113.06  3.000
 2HG  H2   C2  C1  107.91  3.000
 2HG  O3   C2  C1  110.75  3.000
 2HG  C3   C2  C1  109.80  3.000
 2HG  HO2  O2  C1  110.26  3.000
 2HG  H3A  C3  H3  106.70  3.000
 2HG  H3A  C3  C4  110.47  3.000
 2HG  H3   C3  C4  109.81  3.000
 2HG  H3A  C3  C2  109.28  3.000
 2HG  H3   C3  C2  109.34  3.000
 2HG  C4   C3  C2  111.14  3.000
 2HG  HO3  O3  C2  109.02  3.000
 2HG  H4A  C4  H4  105.62  3.000
 2HG  H4A  C4  C5  108.28  3.000
 2HG  H4   C4  C5  107.95  3.000
 2HG  H4A  C4  C3  110.48  3.000
 2HG  H4   C4  C3  111.03  3.000
 2HG  C5   C4  C3  113.15  3.000
 2HG  O5   C5  O4  123.08  3.000
 2HG  O5   C5  C4  111.62  3.000
 2HG  O4   C5  C4  125.30  3.000
 2HG  HO5  O5  C5  110.00  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  CONST_01  HO2  O2  C1  O1     0.00   0.0  0
 2HG  CONST_02  HO5  O5  C5  C4   180.00   0.0  0
 2HG  Var_01    C5   C4  C3  C2  -179.54  30.0  3
 2HG  Var_02    O4   C5  C4  C3     4.60  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-1  HO2  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
 2HG  plan-2  HO5  0.020

