# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 06:37:04 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  13  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   0.500   0.0984   0.0383  -1.2100
 DGY  O1    O  OH1   0  -0.588   1.3106  -0.3354  -1.5910
 DGY  O2    O  O     0  -0.433  -0.6786   0.6303  -1.9131
 DGY  C2    C  CH1   0  -0.099  -0.1940  -0.3543   0.2308
 DGY  O3    O  OH1   0  -0.646  -1.5532  -0.2304   0.5151
 DGY  C3    C  CH2   0  -0.166   0.6939   0.4511   1.1786
 DGY  O4    O  OH1   0  -0.664   0.4352   0.0110   2.4868
 DGY  H1    H  HOH1  0   0.486   1.4789  -0.0556  -2.5042
 DGY  H2    H  HCH1  0   0.278   0.0545  -1.4147   0.3458
 DGY  H3    H  HOH1  0   0.449  -1.8249   0.6838   0.3760
 DGY  H3C1  H  HCH2  0   0.208   0.4724   1.5212   1.0550
 DGY  H3C2  H  HCH2  0   0.216   1.7434   0.3060   0.9002
 DGY  H4    H  HOH1  0   0.459   1.0006   0.5091   3.0840

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    single  1.324  0.020  1.324
 DGY  C1  O2    double  1.204  0.020  1.204
 DGY  C1  C2    single  1.522  0.020  1.522
 DGY  O1  H1    single  0.850  0.020  0.980
 DGY  C2  O3    single  1.394  0.020  1.394
 DGY  C2  C3    single  1.528  0.020  1.528
 DGY  C2  H2    single  0.970  0.020  1.090
 DGY  O3  H3    single  0.850  0.020  0.980
 DGY  C3  O4    single  1.404  0.020  1.404
 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    123.78  3.000
 DGY  C2    C1  O1    112.05  3.000
 DGY  O2    C1  O1    124.17  3.000
 DGY  H1    O1  C1    110.39  3.000
 DGY  H2    C2  C3    108.26  3.000
 DGY  H2    C2  O3    106.61  3.000
 DGY  C3    C2  O3    113.15  3.000
 DGY  H2    C2  C1    107.80  3.000
 DGY  C3    C2  C1    109.86  3.000
 DGY  O3    C2  C1    110.95  3.000
 DGY  H3    O3  C2    109.25  3.000
 DGY  H3C2  C3  H3C1  107.05  3.000
 DGY  H3C2  C3  O4    111.82  3.000
 DGY  H3C1  C3  O4    111.87  3.000
 DGY  H3C2  C3  C2    109.22  3.000
 DGY  H3C1  C3  C2    109.03  3.000
 DGY  O4    C3  C2    107.79  3.000
 DGY  H4    O4  C3    107.93  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
 DGY  CONST_01  H1  O1  C1  O2  0.00  0.0  0

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
 DGY  plan-1  H1  0.020

