# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 07:00:54 2020
#   Inital geometry file: a 36 line input string
#   Ligand name: (2R)-2,3-dihydroxypropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](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
 DGY  DGY  '(2R)-2,3-dihydroxypropanoic acid'  ligand  12  7  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DGY
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
 DGY  C1    C  C      0   0.385   0.0582  -0.0525  -1.1407
 DGY  O1    O  OC    -1  -0.592   1.1988  -0.2767  -1.5722
 DGY  O2    O  O      0  -0.608  -0.9181   0.4167  -1.7681
 DGY  C2    C  CH1    0  -0.110  -0.2305  -0.3773   0.3443
 DGY  O3    O  OH1    0  -0.696  -1.5663  -0.0610   0.6425
 DGY  C3    C  CH2    0  -0.152   0.7292   0.3766   1.2452
 DGY  O4    O  OH1    0  -0.676   0.4848   0.0106   2.5871
 DGY  H2    H  HCH1   0   0.199  -0.0556  -1.4553   0.4895
 DGY  H3    H  HOH1   0   0.426  -1.8895   0.2758  -0.2147
 DGY  H3C1  H  HCH2   0   0.184   0.5928   1.4574   1.0938
 DGY  H3C2  H  HCH2   0   0.191   1.7529   0.1331   0.9427
 DGY  H4    H  HOH1   0   0.450   1.1291   0.4627   3.1386

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
 DGY  C1  O1    deloc   1.240  0.020  1.240
 DGY  C1  O2    deloc   1.252  0.020  1.252
 DGY  C1  C2    single  1.547  0.020  1.547
 DGY  C2  O3    single  1.405  0.020  1.405
 DGY  C2  C3    single  1.517  0.020  1.517
 DGY  C2  H2    single  0.970  0.020  1.090
 DGY  O3  H3    single  0.850  0.020  0.980
 DGY  C3  O4    single  1.412  0.020  1.412
 DGY  C3  H3C1  single  0.970  0.020  1.090
 DGY  C3  H3C2  single  0.970  0.020  1.090
 DGY  O4  H4    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
 DGY  C2    C1  O2    114.47  3.000
 DGY  C2    C1  O1    117.89  3.000
 DGY  O2    C1  O1    127.65  3.000
 DGY  H2    C2  C3    107.92  3.000
 DGY  H2    C2  O3    110.07  3.000
 DGY  C3    C2  O3    111.33  3.000
 DGY  H2    C2  C1    107.59  3.000
 DGY  C3    C2  C1    110.34  3.000
 DGY  O3    C2  C1    109.51  3.000
 DGY  H3    O3  C2    101.90  3.000
 DGY  H3C2  C3  H3C1  107.25  3.000
 DGY  H3C2  C3  O4    111.51  3.000
 DGY  H3C1  C3  O4    111.35  3.000
 DGY  H3C2  C3  C2    108.47  3.000
 DGY  H3C1  C3  C2    109.16  3.000
 DGY  O4    C3  C2    109.03  3.000
 DGY  H4    O4  C3    107.90  3.000

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DGY  chir_01  C2  C1  O3  C3  positiv

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
 DGY  plan-1  C1  0.020
 DGY  plan-1  O1  0.020
 DGY  plan-1  O2  0.020
 DGY  plan-1  C2  0.020

