# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 17:55:44 2020
#   Inital geometry file: a 34 line input string
#   Ligand name: (2R)-2,3-dihydroxypropanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)C=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
 3GR  3GR  (2R)-2,3-dihydroxypropanal  D-saccharide  12  6  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3GR
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
 3GR  C1    C  CH2   0  -0.166   0.7716   0.3071   0.9854
 3GR  O1    O  OH1   0  -0.667   0.4196  -0.2642   2.2211
 3GR  C2    C  CH1   0  -0.103  -0.2736  -0.0955  -0.0412
 3GR  O2    O  OH1   0  -0.654  -1.5731   0.3319   0.2727
 3GR  C3    C  C1    0   0.137   0.1021   0.3479  -1.4422
 3GR  O3    O  O     0  -0.369   1.2297   0.4733  -1.8450
 3GR  H1C1  H  HCH2  0   0.208   0.8192   1.4042   1.0415
 3GR  H1C2  H  HCH2  0   0.212   1.7521  -0.0372   0.6401
 3GR  H1    H  HOH1  0   0.458   1.0667   0.0189   2.8732
 3GR  H2    H  HCH1  0   0.279  -0.3180  -1.1926  -0.0810
 3GR  HA    H  HOH1  0   0.453  -1.5646   1.2855   0.4103
 3GR  H3    H  H     0   0.212  -0.7688   0.5377  -2.0972

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
 3GR  C1  O1    single  1.406  0.020  1.406
 3GR  C1  C2    single  1.519  0.020  1.519
 3GR  C1  H1C1  single  0.970  0.020  1.090
 3GR  C1  H1C2  single  0.970  0.020  1.090
 3GR  O1  H1    single  0.850  0.020  0.980
 3GR  C2  O2    single  1.404  0.020  1.404
 3GR  C2  C3    single  1.517  0.020  1.517
 3GR  C2  H2    single  0.970  0.020  1.090
 3GR  O2  HA    single  0.850  0.020  0.980
 3GR  C3  O3    double  1.204  0.020  1.204
 3GR  C3  H3    single  0.930  0.020  1.080

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
 3GR  H1C2  C1  H1C1  106.92  3.000
 3GR  H1C2  C1  C2    108.64  3.000
 3GR  H1C1  C1  C2    109.19  3.000
 3GR  H1C2  C1  O1    111.93  3.000
 3GR  H1C1  C1  O1    111.80  3.000
 3GR  C2    C1  O1    108.30  3.000
 3GR  H1    O1  C1    107.94  3.000
 3GR  H2    C2  C3    105.57  3.000
 3GR  H2    C2  O2    105.95  3.000
 3GR  C3    C2  O2    110.30  3.000
 3GR  H2    C2  C1    108.47  3.000
 3GR  C3    C2  C1    112.10  3.000
 3GR  O2    C2  C1    113.90  3.000
 3GR  HA    O2  C2    108.97  3.000
 3GR  H3    C3  O3    121.43  3.000
 3GR  H3    C3  C2    113.71  3.000
 3GR  O3    C3  C2    124.85  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
 3GR  chir_01  C2  C1  O2  C3  negativ

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
 3GR  plan-1  C2  0.020
 3GR  plan-1  C3  0.020
 3GR  plan-1  O3  0.020
 3GR  plan-1  H3  0.020

