# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:34:40 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 2,4-dioxopentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)CC(=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
 DHD  DHD  '2,4-dioxopentanedioic acid'  ligand  15  11  .  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_DHD
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
 DHD  C1   C  C     0   0.456   0.4053  -0.0059   2.5514
 DHD  C2   C  C     0   0.372  -0.4584   0.0212   1.2777
 DHD  C3   C  CH2   0  -0.716   0.3354   0.0397   0.0063
 DHD  C4   C  C     0   0.295  -0.4352  -0.0239  -1.2797
 DHD  C5   C  C     0   0.454   0.4554   0.0280  -2.5365
 DHD  O11  O  O     0  -0.428   1.6058  -0.0342   2.5074
 DHD  O12  O  OH1   0  -0.642  -0.3335  -0.0048   3.6340
 DHD  O51  O  OH1   0  -0.582  -0.2623  -0.0422  -3.6326
 DHD  O52  O  O     0  -0.264   1.6499   0.1435  -2.4779
 DHD  O4   O  O     0  -0.393  -1.6258  -0.0646  -1.3995
 DHD  O2   O  O     0  -0.190  -1.6528   0.0111   1.3695
 DHD  H31  H  HCH2  0   0.320   0.9844   0.9224  -0.0175
 DHD  H32  H  HCH2  0   0.321   1.0475  -0.7935   0.0262
 DHD  HO1  H  HOH1  0   0.509   0.2229  -0.0363   4.4280
 DHD  HO5  H  HOH1  0   0.489   0.3113  -0.0465  -4.4148

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
 DHD  C1   C2   single  1.539  0.020  1.539
 DHD  C1   O11  double  1.202  0.020  1.202
 DHD  C1   O12  single  1.311  0.020  1.311
 DHD  C2   C3   single  1.499  0.020  1.499
 DHD  C2   O2   double  1.198  0.020  1.198
 DHD  C3   C4   single  1.501  0.020  1.501
 DHD  C3   H31  single  0.970  0.020  1.090
 DHD  C3   H32  single  0.970  0.020  1.090
 DHD  C4   C5   single  1.541  0.020  1.541
 DHD  C4   O4   double  1.197  0.020  1.197
 DHD  C5   O51  single  1.312  0.020  1.312
 DHD  C5   O52  double  1.201  0.020  1.201
 DHD  O12  HO1  single  0.850  0.020  0.980
 DHD  O51  HO5  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
 DHD  O12  C1   O11  126.40  3.000
 DHD  O12  C1   C2   111.54  3.000
 DHD  O11  C1   C2   122.05  3.000
 DHD  O2   C2   C3   126.38  3.000
 DHD  O2   C2   C1   119.73  3.000
 DHD  C3   C2   C1   113.89  3.000
 DHD  H32  C3   H31  103.18  3.000
 DHD  H32  C3   C4   108.48  3.000
 DHD  H31  C3   C4   108.64  3.000
 DHD  H32  C3   C2   108.62  3.000
 DHD  H31  C3   C2   110.00  3.000
 DHD  C4   C3   C2   117.03  3.000
 DHD  O4   C4   C5   119.62  3.000
 DHD  O4   C4   C3   126.72  3.000
 DHD  C5   C4   C3   113.62  3.000
 DHD  O52  C5   O51  126.14  3.000
 DHD  O52  C5   C4   122.55  3.000
 DHD  O51  C5   C4   111.30  3.000
 DHD  HO1  O12  C1   110.66  3.000
 DHD  HO5  O51  C5   110.51  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
 DHD  CONST_01  HO1  O12  C1  C2  180.00   0.0  0
 DHD  CONST_02  HO5  O51  C5  C4  180.00   0.0  0
 DHD  Var_01    C4   C3   C2  C1  176.12  30.0  3
 DHD  Var_02    C5   C4   C3  C2  178.86  30.0  3
 DHD  Var_03    O11  C1   C2  C3   -1.29  30.0  2
 DHD  Var_04    O51  C5   C4  C3  179.45  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
 DHD  plan-1  C1   0.020
 DHD  plan-1  C2   0.020
 DHD  plan-1  C3   0.020
 DHD  plan-1  O2   0.020
 DHD  plan-2  C3   0.020
 DHD  plan-2  C4   0.020
 DHD  plan-2  C5   0.020
 DHD  plan-2  O4   0.020
 DHD  plan-3  C1   0.020
 DHD  plan-3  C2   0.020
 DHD  plan-3  O11  0.020
 DHD  plan-3  O12  0.020
 DHD  plan-3  HO1  0.020
 DHD  plan-4  C4   0.020
 DHD  plan-4  C5   0.020
 DHD  plan-4  O51  0.020
 DHD  plan-4  O52  0.020
 DHD  plan-4  HO5  0.020

