# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:18:47 2020
#   Inital geometry file: a 35 line input string
#   Ligand name: 3-hydroxy-2-oxopropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(=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
 3PY  3PY  '3-hydroxy-2-oxopropanoic acid'  ligand  11  7  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3PY
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
 3PY  C1   C  C     0   0.474   0.2455  -0.0090  -1.1473
 3PY  O1   O  O     0  -0.404   1.4272  -0.0218  -1.3683
 3PY  O2   O  OH1   0  -0.567  -0.7090  -0.0132  -2.0481
 3PY  C2   C  C     0   0.261  -0.3180   0.0146   0.2791
 3PY  O3   O  O     0  -0.335  -1.5016   0.0194   0.4700
 3PY  C3   C  CH2   0  -0.240   0.7176   0.0271   1.3636
 3PY  O4   O  OH1   0  -0.655   0.0718   0.0470   2.5978
 3PY  HO2  H  HOH1  0   0.495  -0.3319  -0.0275  -2.9419
 3PY  H31  H  HCH2  0   0.253   1.3664   0.8996   1.1999
 3PY  H32  H  HCH2  0   0.253   1.3610  -0.8537   1.2249
 3PY  HO4  H  HOH1  0   0.467   0.7452   0.0738   3.2833

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
 3PY  C1  O1   double  1.202  0.020  1.202
 3PY  C1  O2   single  1.312  0.020  1.312
 3PY  C1  C2   single  1.534  0.020  1.534
 3PY  O2  HO2  single  0.850  0.020  0.980
 3PY  C2  O3   double  1.199  0.020  1.199
 3PY  C2  C3   single  1.500  0.020  1.500
 3PY  C3  O4   single  1.393  0.020  1.393
 3PY  C3  H31  single  0.970  0.020  1.090
 3PY  C3  H32  single  0.970  0.020  1.090
 3PY  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
 3PY  C2   C1  O2   111.79  3.000
 3PY  C2   C1  O1   122.15  3.000
 3PY  O2   C1  O1   126.06  3.000
 3PY  HO2  O2  C1   110.47  3.000
 3PY  C3   C2  O3   124.51  3.000
 3PY  C3   C2  C1   114.77  3.000
 3PY  O3   C2  C1   120.72  3.000
 3PY  H32  C3  H31  105.76  3.000
 3PY  H32  C3  O4   113.23  3.000
 3PY  H31  C3  O4   113.22  3.000
 3PY  H32  C3  C2   107.83  3.000
 3PY  H31  C3  C2   107.85  3.000
 3PY  O4   C3  C2   108.70  3.000
 3PY  HO4  O4  C3   107.90  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
 3PY  CONST_01  HO2  O2  C1  O1     0.00   0.0  0
 3PY  Var_01    O4   C3  C2  C1  -179.95  30.0  3
 3PY  Var_02    O3   C2  C1  O1  -179.58  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
 3PY  plan-1  C1   0.020
 3PY  plan-1  C2   0.020
 3PY  plan-1  O3   0.020
 3PY  plan-1  C3   0.020
 3PY  plan-2  C1   0.020
 3PY  plan-2  O1   0.020
 3PY  plan-2  O2   0.020
 3PY  plan-2  C2   0.020
 3PY  plan-2  HO2  0.020

