# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 21:39:58 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 4,5-dioxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)C=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
 HKV  HKV  '4,5-dioxopentanoic acid  '  ligand  14  9  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HKV
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
 HKV  O4    O  OC    -1  -0.627  -2.8536  -0.5673   2.6419
 HKV  C5    C  C      0   0.422  -1.9065  -0.8018   1.8644
 HKV  O3    O  O      0  -0.606  -1.8766  -1.6697   0.9707
 HKV  C4    C  CH2    0  -0.585  -0.6562   0.0791   2.0526
 HKV  C3    C  CH2    0  -0.578   0.4353  -0.1518   1.0290
 HKV  C2    C  C      0   0.313   1.6597   0.6774   1.2073
 HKV  O5    O  O      0  -0.362   1.8528   1.4877   2.0776
 HKV  C1    C  C1     0   0.108   2.7605   0.4418   0.1607
 HKV  O2    O  O      0  -0.331   3.8085   1.0219   0.2181
 HKV  HA    H  HCH2   0   0.238  -0.2660  -0.0934   3.0608
 HKV  H3C1  H  HCH2   0   0.277   0.0719   0.0233   0.0086
 HKV  H3C2  H  HCH2   0   0.277   0.7575  -1.2005   1.0148
 HKV  H1    H  H      0   0.218   2.5316  -0.2858  -0.6355
 HKV  H41   H  HCH2   0   0.235  -0.9670   1.1279   2.0400

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
 HKV  O4  C5    deloc   1.248  0.020  1.248
 HKV  C5  O3    deloc   1.246  0.020  1.246
 HKV  C5  C4    single  1.541  0.020  1.541
 HKV  C4  H41   single  0.970  0.020  1.090
 HKV  C4  C3    single  1.514  0.020  1.514
 HKV  C4  HA    single  0.970  0.020  1.090
 HKV  C3  C2    single  1.490  0.020  1.490
 HKV  C3  H3C1  single  0.970  0.020  1.090
 HKV  C3  H3C2  single  0.970  0.020  1.090
 HKV  C2  O5    double  1.205  0.020  1.205
 HKV  C2  C1    single  1.537  0.020  1.537
 HKV  C1  O2    double  1.199  0.020  1.199
 HKV  C1  H1    single  0.930  0.020  1.080

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
 HKV  C4    C5  O3    117.79  3.000
 HKV  C4    C5  O4    115.62  3.000
 HKV  O3    C5  O4    126.59  3.000
 HKV  H41   C4  HA    105.24  3.000
 HKV  HA    C4  C3    109.98  3.000
 HKV  H41   C4  C3    110.07  3.000
 HKV  HA    C4  C5    108.16  3.000
 HKV  C3    C4  C5    114.53  3.000
 HKV  H41   C4  C5    108.43  3.000
 HKV  H3C2  C3  H3C1  103.75  3.000
 HKV  H3C2  C3  C2    106.99  3.000
 HKV  H3C1  C3  C2    107.14  3.000
 HKV  H3C2  C3  C4    111.48  3.000
 HKV  H3C1  C3  C4    111.45  3.000
 HKV  C2    C3  C4    115.27  3.000
 HKV  C1    C2  O5    118.70  3.000
 HKV  C1    C2  C3    114.96  3.000
 HKV  O5    C2  C3    126.34  3.000
 HKV  H1    C1  O2    122.36  3.000
 HKV  H1    C1  C2    116.37  3.000
 HKV  O2    C1  C2    121.27  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
 HKV  Var_01  C3  C4  C5  O4  -175.46  30.0  3
 HKV  Var_02  C2  C3  C4  C5  -179.15  30.0  3
 HKV  Var_03  O5  C2  C3  C4     0.47  30.0  3
 HKV  Var_04  O2  C1  C2  C3  -177.92  30.0  2

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
 HKV  plan-1  C3  0.020
 HKV  plan-1  C2  0.020
 HKV  plan-1  O5  0.020
 HKV  plan-1  C1  0.020
 HKV  plan-2  O4  0.020
 HKV  plan-2  C5  0.020
 HKV  plan-2  O3  0.020
 HKV  plan-2  C4  0.020
 HKV  plan-3  C2  0.020
 HKV  plan-3  C1  0.020
 HKV  plan-3  O2  0.020
 HKV  plan-3  H1  0.020

