# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 08:44:17 2022
#   Inital geometry file: a 33 line input string
#   Ligand name: 2-oxopropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 PYR  PYR  '2-oxopropanoic acid      '  ligand  9  6  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PYR
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
 PYR  C1   C  C      0   0.327  35.5855  3.0568  6.6962
 PYR  O1   O  O      0  -0.580  34.6047  3.6861  6.2758
 PYR  O2   O  OC    -1  -0.576  36.4926  2.4970  6.0565
 PYR  C2   C  C      0   0.238  35.7150  2.9514  8.2453
 PYR  O3   O  O      0  -0.393  35.0237  3.6243  8.9753
 PYR  C3   C  CH3    0  -0.757  36.7411  1.9910  8.7814
 PYR  H31  H  HCH3   0   0.237  36.7209  1.9568  9.8692
 PYR  H32  H  HCH3   0   0.250  36.5690  0.9878  8.3883
 PYR  H33  H  HCH3   0   0.254  37.7396  2.2801  8.4514

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
 PYR  C1  O1   deloc   1.239  0.020  1.239
 PYR  C1  O2   deloc   1.243  0.020  1.243
 PYR  C1  C2   single  1.558  0.020  1.558
 PYR  C2  O3   double  1.210  0.020  1.210
 PYR  C2  C3   single  1.504  0.020  1.504
 PYR  C3  H31  single  0.970  0.020  1.090
 PYR  C3  H32  single  0.970  0.020  1.090
 PYR  C3  H33  single  0.970  0.020  1.090

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
 PYR  C2   C1  O2   114.86  3.000
 PYR  C2   C1  O1   115.95  3.000
 PYR  O2   C1  O1   129.19  3.000
 PYR  C3   C2  O3   122.00  3.000
 PYR  C3   C2  C1   117.02  3.000
 PYR  O3   C2  C1   120.98  3.000
 PYR  H33  C3  H32  106.21  3.000
 PYR  H33  C3  H31  109.13  3.000
 PYR  H32  C3  H31  109.16  3.000
 PYR  H33  C3  C2   110.33  3.000
 PYR  H32  C3  C2   110.55  3.000
 PYR  H31  C3  C2   111.32  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
 PYR  Var_01  O3   C2  C1  O1   -11.48  30.0  2
 PYR  Var_02  H31  C3  C2  C1  -177.33  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
 PYR  plan-1  C1  0.020
 PYR  plan-1  C2  0.020
 PYR  plan-1  O3  0.020
 PYR  plan-1  C3  0.020
 PYR  plan-2  C1  0.020
 PYR  plan-2  O1  0.020
 PYR  plan-2  O2  0.020
 PYR  plan-2  C2  0.020

