# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 20:05:32 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
 AKG  AKG  '2-oxopentanedioic acid   '  ligand  14  10  .  2020-10-20  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AKG
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
 AKG  C1   C  C      0   0.343   2.4858  -0.3362   0.0129
 AKG  O1   O  O      0  -0.581   2.3389  -1.5706   0.0264
 AKG  O2   O  OC    -1  -0.587   3.5389   0.3169   0.0068
 AKG  C2   C  C      0   0.233   1.1712   0.5023   0.0022
 AKG  O5   O  O      0  -0.406   1.2263   1.7114  -0.0144
 AKG  C3   C  CH2    0  -0.536  -0.1308  -0.2483   0.0138
 AKG  C4   C  CH2    0  -0.581  -1.3695   0.6253   0.0026
 AKG  C5   C  C      0   0.415  -2.7067  -0.1382   0.0131
 AKG  O3   O  O      0  -0.609  -2.6731  -1.3835   0.0647
 AKG  O4   O  OC    -1  -0.634  -3.7350   0.5704  -0.0286
 AKG  H31  H  HCH2   0   0.247  -0.1275  -0.9345  -0.8381
 AKG  H32  H  HCH2   0   0.247  -0.1264  -0.9102   0.8847
 AKG  H41  H  HCH2   0   0.224  -1.3629   1.3013   0.8641
 AKG  H42  H  HCH2   0   0.223  -1.3621   1.2835  -0.8719

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
 AKG  C1  O1   deloc   1.243  0.020  1.243
 AKG  C1  O2   deloc   1.239  0.020  1.239
 AKG  C1  C2   single  1.559  0.020  1.559
 AKG  C2  O5   double  1.210  0.020  1.210
 AKG  C2  C3   single  1.503  0.020  1.503
 AKG  C3  C4   single  1.516  0.020  1.516
 AKG  C3  H31  single  0.970  0.020  1.090
 AKG  C3  H32  single  0.970  0.020  1.090
 AKG  C4  C5   single  1.540  0.020  1.540
 AKG  C4  H41  single  0.970  0.020  1.090
 AKG  C4  H42  single  0.970  0.020  1.090
 AKG  C5  O3   deloc   1.247  0.020  1.247
 AKG  C5  O4   deloc   1.249  0.020  1.249

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
 AKG  C2   C1  O2   115.65  3.000
 AKG  C2   C1  O1   115.75  3.000
 AKG  O2   C1  O1   128.59  3.000
 AKG  C3   C2  O5   122.57  3.000
 AKG  C3   C2  C1   117.50  3.000
 AKG  O5   C2  C1   119.93  3.000
 AKG  H32  C3  H31  103.91  3.000
 AKG  H32  C3  C4   110.97  3.000
 AKG  H31  C3  C4   110.99  3.000
 AKG  H32  C3  C2   107.75  3.000
 AKG  H31  C3  C2   107.74  3.000
 AKG  C4   C3  C2   114.84  3.000
 AKG  H42  C4  H41  104.91  3.000
 AKG  H42  C4  C5   108.03  3.000
 AKG  H41  C4  C5   107.82  3.000
 AKG  H42  C4  C3   110.30  3.000
 AKG  H41  C4  C3   110.18  3.000
 AKG  C5   C4  C3   115.08  3.000
 AKG  O4   C5  O3   126.16  3.000
 AKG  O4   C5  C4   115.67  3.000
 AKG  O3   C5  C4   118.17  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
 AKG  Var_01  C4  C3  C2  C1   179.99  30.0  3
 AKG  Var_02  O5  C2  C1  O1  -179.82  30.0  2
 AKG  Var_03  C5  C4  C3  C2   179.95  30.0  3
 AKG  Var_04  O3  C5  C4  C3     1.83  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
 AKG  plan-1  C1  0.020
 AKG  plan-1  C2  0.020
 AKG  plan-1  O5  0.020
 AKG  plan-1  C3  0.020
 AKG  plan-2  C1  0.020
 AKG  plan-2  O1  0.020
 AKG  plan-2  O2  0.020
 AKG  plan-2  C2  0.020
 AKG  plan-3  C4  0.020
 AKG  plan-3  C5  0.020
 AKG  plan-3  O3  0.020
 AKG  plan-3  O4  0.020

