# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:38:12 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  16  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.487   2.4055  -0.3649  -0.0009
 AKG  O1   O  O     0  -0.403   2.3763  -1.5661   0.0181
 AKG  O2   O  OH1   0  -0.570   3.4877   0.3796  -0.0036
 AKG  C2   C  C     0   0.296   1.1289   0.4923  -0.0272
 AKG  O5   O  O     0  -0.345   1.2189   1.6904  -0.0492
 AKG  C3   C  CH2   0  -0.561  -0.1557  -0.2732  -0.0236
 AKG  C4   C  CH2   0  -0.583  -1.3732   0.6291  -0.0441
 AKG  C5   C  C     0   0.559  -2.6605  -0.1490  -0.0389
 AKG  O3   O  O     0  -0.442  -2.7473  -1.3510  -0.0110
 AKG  O4   O  OH1   0  -0.595  -3.7158   0.6569  -0.0680
 AKG  HO2  H  HOH1  0   0.494   4.2818  -0.1772   0.0106
 AKG  H31  H  HCH2  0   0.297  -0.1497  -0.9496  -0.8833
 AKG  H32  H  HCH2  0   0.296  -0.1598  -0.9264   0.8540
 AKG  H41  H  HCH2  0   0.294  -1.3797   1.3009   0.8184
 AKG  H42  H  HCH2  0   0.293  -1.3687   1.2763  -0.9251
 AKG  HO4  H  HOH1  0   0.481  -4.5321   0.1350  -0.0609

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   double  1.202  0.020  1.202
 AKG  C1  O2   single  1.314  0.020  1.314
 AKG  C1  C2   single  1.538  0.020  1.538
 AKG  O2  HO2  single  0.850  0.020  0.980
 AKG  C2  O5   double  1.202  0.020  1.202
 AKG  C2  C3   single  1.495  0.020  1.495
 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  1.504  0.020  1.504
 AKG  C4  H41  single  0.970  0.020  1.090
 AKG  C4  H42  single  0.970  0.020  1.090
 AKG  C5  O3   double  1.205  0.020  1.205
 AKG  C5  O4   single  1.328  0.020  1.328
 AKG  O4  HO4  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
 AKG  C2   C1  O2   111.59  3.000
 AKG  C2   C1  O1   122.50  3.000
 AKG  O2   C1  O1   125.91  3.000
 AKG  HO2  O2  C1   110.43  3.000
 AKG  C3   C2  O5   125.09  3.000
 AKG  C3   C2  C1   115.32  3.000
 AKG  O5   C2  C1   119.59  3.000
 AKG  H32  C3  H31  105.15  3.000
 AKG  H32  C3  C4   111.30  3.000
 AKG  H31  C3  C4   111.21  3.000
 AKG  H32  C3  C2   108.11  3.000
 AKG  H31  C3  C2   108.06  3.000
 AKG  C4   C3  C2   112.66  3.000
 AKG  H42  C4  H41  105.79  3.000
 AKG  H42  C4  C5   108.21  3.000
 AKG  H41  C4  C5   108.06  3.000
 AKG  H42  C4  C3   111.10  3.000
 AKG  H41  C4  C3   111.10  3.000
 AKG  C5   C4  C3   112.30  3.000
 AKG  O4   C5  O3   123.25  3.000
 AKG  O4   C5  C4   111.47  3.000
 AKG  O3   C5  C4   125.28  3.000
 AKG  HO4  O4  C5   110.02  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  CONST_01  HO2  O2  C1  O1     0.00   0.0  0
 AKG  CONST_02  HO4  O4  C5  C4   180.00   0.0  0
 AKG  Var_01    C4   C3  C2  C1   179.75  30.0  3
 AKG  Var_02    O5   C2  C1  O1  -179.80  30.0  2
 AKG  Var_03    C5   C4  C3  C2  -179.94  30.0  3
 AKG  Var_04    O3   C5  C4  C3     0.57  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-2  HO2  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
 AKG  plan-3  HO4  0.020

