# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:01:53 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 2,5-dioxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)CCC=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
 DO4  DO4  '2,5-dioxopentanoic acid  '  ligand  14  9  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DO4
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
 DO4  O3   O  O      0  -0.382  -3.9807  -0.2960   0.3700
 DO4  C5   C  C1     0   0.191  -2.9878  -0.3483  -0.3131
 DO4  C4   C  CH2    0  -0.547  -1.7663   0.4951  -0.1319
 DO4  C3   C  CH2    0  -0.566  -0.5135  -0.3717  -0.0885
 DO4  C2   C  C      0   0.245   0.7657   0.4249  -0.0707
 DO4  O5   O  O      0  -0.392   0.7665   1.6321  -0.1013
 DO4  C1   C  C      0   0.351   2.1010  -0.3749  -0.0135
 DO4  O1   O  O      0  -0.576   1.9800  -1.6064   0.0943
 DO4  O2   O  OC    -1  -0.580   3.1327   0.3054  -0.0842
 DO4  H5   H  H      0   0.182  -2.9273  -1.0540  -1.1627
 DO4  H41  H  HCH2   0   0.269  -1.7160   1.1656  -0.9975
 DO4  H42  H  HCH2   0   0.257  -1.8643   1.1124   0.7614
 DO4  H31  H  HCH2   0   0.278  -0.5232  -1.0275   0.7866
 DO4  H32  H  HCH2   0   0.271  -0.4758  -1.0509  -0.9468

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
 DO4  O3  C5   double  1.206  0.020  1.206
 DO4  C5  C4   single  1.495  0.020  1.495
 DO4  C5  H5   single  0.930  0.020  1.080
 DO4  C4  C3   single  1.524  0.020  1.524
 DO4  C4  H41  single  0.970  0.020  1.090
 DO4  C4  H42  single  0.970  0.020  1.090
 DO4  C3  C2   single  1.507  0.020  1.507
 DO4  C3  H31  single  0.970  0.020  1.090
 DO4  C3  H32  single  0.970  0.020  1.090
 DO4  C2  O5   double  1.208  0.020  1.208
 DO4  C2  C1   single  1.558  0.020  1.558
 DO4  C1  O1   deloc   1.242  0.020  1.242
 DO4  C1  O2   deloc   1.238  0.020  1.238

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
 DO4  H5   C5  C4   114.09  3.000
 DO4  H5   C5  O3   120.51  3.000
 DO4  C4   C5  O3   125.40  3.000
 DO4  H42  C4  H41  107.75  3.000
 DO4  H42  C4  C3   111.87  3.000
 DO4  H41  C4  C3   109.43  3.000
 DO4  H42  C4  C5   110.19  3.000
 DO4  H41  C4  C5   106.67  3.000
 DO4  C3   C4  C5   110.74  3.000
 DO4  H32  C3  H31  104.81  3.000
 DO4  H32  C3  C2   107.93  3.000
 DO4  H31  C3  C2   108.37  3.000
 DO4  H32  C3  C4   111.02  3.000
 DO4  H31  C3  C4   110.89  3.000
 DO4  C2   C3  C4   113.42  3.000
 DO4  C1   C2  O5   120.91  3.000
 DO4  C1   C2  C3   117.17  3.000
 DO4  O5   C2  C3   121.92  3.000
 DO4  O2   C1  O1   129.13  3.000
 DO4  O2   C1  C2   115.49  3.000
 DO4  O1   C1  C2   115.39  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
 DO4  Var_01  C3  C4  C5  O3  129.02  30.0  3
 DO4  Var_02  C2  C3  C4  C5  173.21  30.0  3
 DO4  Var_03  O5  C2  C3  C4   -0.64  30.0  3
 DO4  Var_04  O1  C1  C2  C3   -4.19  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
 DO4  plan-1  C3  0.020
 DO4  plan-1  C2  0.020
 DO4  plan-1  O5  0.020
 DO4  plan-1  C1  0.020
 DO4  plan-2  C2  0.020
 DO4  plan-2  C1  0.020
 DO4  plan-2  O1  0.020
 DO4  plan-2  O2  0.020
 DO4  plan-3  O3  0.020
 DO4  plan-3  C5  0.020
 DO4  plan-3  C4  0.020
 DO4  plan-3  H5  0.020

