# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 09:34:43 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 2-oxopentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=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
 2OG  2OG  '2-oxopentanedioic acid   '  ligand  14  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 GRAND
;

data_comp_2OG
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
 2OG  C1   C  C      0   0.318   0.3480   0.0210  -2.4626
 2OG  C2   C  C      0   0.178  -0.4893   0.0317  -1.1493
 2OG  C3   C  CH2    0  -0.496   0.2642   0.0202   0.1507
 2OG  C4   C  CH2    0  -0.587  -0.6042  -0.0017   1.3921
 2OG  C5   C  C      0   0.425   0.1678  -0.0240   2.7236
 2OG  O1   O  O      0  -0.393   1.5687   0.2135  -2.3257
 2OG  O2   O  OC    -1  -0.741  -0.2881  -0.1976  -3.5036
 2OG  O2'  O  O      0  -0.420  -1.6987   0.0478  -1.2023
 2OG  O3   O  O      0  -0.679   1.4133  -0.0539   2.6806
 2OG  O4   O  OC    -1  -0.681  -0.5345   0.0061   3.7569
 2OG  H31  H  HCH2   0   0.293   0.9340   0.8843   0.1560
 2OG  H32  H  HCH2   0   0.270   0.9434  -0.8377   0.1348
 2OG  H41  H  HCH2   0   0.280  -1.2694  -0.8713   1.3730
 2OG  H42  H  HCH2   0   0.233  -1.2733   0.8644   1.4021

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
 2OG  C1  C2   single  1.557  0.020  1.557
 2OG  C1  O1   deloc   1.243  0.020  1.243
 2OG  C1  O2   deloc   1.239  0.020  1.239
 2OG  C2  C3   single  1.503  0.020  1.503
 2OG  C2  O2'  double  1.211  0.020  1.211
 2OG  C3  C4   single  1.515  0.020  1.515
 2OG  C3  H31  single  0.970  0.020  1.090
 2OG  C3  H32  single  0.970  0.020  1.090
 2OG  C4  C5   single  1.539  0.020  1.539
 2OG  C4  H41  single  0.970  0.020  1.090
 2OG  C4  H42  single  0.970  0.020  1.090
 2OG  C5  O3   deloc   1.247  0.020  1.247
 2OG  C5  O4   deloc   1.250  0.020  1.250

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
 2OG  O2   C1  O1   128.58  3.000
 2OG  O2   C1  C2   115.69  3.000
 2OG  O1   C1  C2   115.72  3.000
 2OG  O2'  C2  C3   122.61  3.000
 2OG  O2'  C2  C1   120.01  3.000
 2OG  C3   C2  C1   117.38  3.000
 2OG  H32  C3  H31  103.85  3.000
 2OG  H32  C3  C4   110.87  3.000
 2OG  H31  C3  C4   111.01  3.000
 2OG  H32  C3  C2   107.74  3.000
 2OG  H31  C3  C2   107.78  3.000
 2OG  C4   C3  C2   114.93  3.000
 2OG  H42  C4  H41  104.91  3.000
 2OG  H42  C4  C5   108.07  3.000
 2OG  H41  C4  C5   107.95  3.000
 2OG  H42  C4  C3   110.27  3.000
 2OG  H41  C4  C3   110.20  3.000
 2OG  C5   C4  C3   114.93  3.000
 2OG  O4   C5  O3   126.20  3.000
 2OG  O4   C5  C4   115.66  3.000
 2OG  O3   C5  C4   118.14  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
 2OG  Var_01  C4  C3  C2  C1  -178.62  30.0  3
 2OG  Var_02  C5  C4  C3  C2   179.57  30.0  3
 2OG  Var_03  O1  C1  C2  C3   -10.79  30.0  2
 2OG  Var_04  O3  C5  C4  C3    -1.64  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
 2OG  plan-1  C1   0.020
 2OG  plan-1  C2   0.020
 2OG  plan-1  C3   0.020
 2OG  plan-1  O2'  0.020
 2OG  plan-2  C1   0.020
 2OG  plan-2  C2   0.020
 2OG  plan-2  O1   0.020
 2OG  plan-2  O2   0.020
 2OG  plan-3  C4   0.020
 2OG  plan-3  C5   0.020
 2OG  plan-3  O3   0.020
 2OG  plan-3  O4   0.020

