# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 11:31:18 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 3,6-dideoxy-L-arabino-hexonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](O)C[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
 3LR  3LR  '3,6-dideoxy-L-arabino-hexonic acid'  L-saccharide  22  11  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3LR
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
 3LR  O1A  O  OC    -1  -0.597  -2.7789  -0.5163  -1.3342
 3LR  C1   C  C      0   0.393  -2.5589   0.0871  -0.2728
 3LR  O1B  O  O      0  -0.611  -3.2772   0.9590   0.2703
 3LR  C2   C  CH1    0  -0.075  -1.2583  -0.2454   0.4901
 3LR  O2   O  OH1    0  -0.703  -1.2240   0.4900   1.6899
 3LR  C3   C  CH2    0  -0.475  -0.0381   0.0533  -0.3776
 3LR  C4   C  CH1    0   0.024   1.2918  -0.2389   0.3098
 3LR  O4   O  OH1    0  -0.669   1.3808  -1.5915   0.7133
 3LR  C5   C  CH1    0   0.012   2.4910   0.1509  -0.5712
 3LR  C6   C  CH3    0  -0.679   3.8238  -0.2162   0.0642
 3LR  O5   O  OH1    0  -0.667   2.4425   1.5255  -0.9061
 3LR  H2   H  HCH1   0   0.195  -1.2721  -1.3209   0.7163
 3LR  HO2  H  HOH1   0   0.425  -2.0346   1.0292   1.6182
 3LR  H3   H  HCH2   0   0.217  -0.1042  -0.5424  -1.2946
 3LR  H3A  H  HCH2   0   0.225  -0.0609   1.1022  -0.6837
 3LR  H4   H  HCH1   0   0.215   1.3543   0.3465   1.2354
 3LR  HO4  H  HOH1   0   0.441   1.2541  -2.1454  -0.0650
 3LR  H5   H  HCH1   0   0.212   2.4006  -0.3800  -1.5271
 3LR  H6   H  HCH3   0   0.229   3.9182  -1.2913   0.2061
 3LR  H6A  H  HCH3   0   0.232   4.6487   0.1076  -0.5718
 3LR  H6B  H  HCH3   0   0.216   3.9434   0.2607   1.0412
 3LR  HO5  H  HOH1   0   0.441   2.5636   2.0350  -0.0973

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
 3LR  C1   O1A  deloc   1.241  0.020  1.241
 3LR  O1B  C1   deloc   1.253  0.020  1.253
 3LR  C2   C1   single  1.544  0.020  1.544
 3LR  O2   C2   single  1.408  0.020  1.408
 3LR  C2   C3   single  1.527  0.020  1.527
 3LR  C2   H2   single  0.970  0.020  1.090
 3LR  O2   HO2  single  0.850  0.020  0.980
 3LR  C4   C3   single  1.525  0.020  1.525
 3LR  C3   H3   single  0.970  0.020  1.090
 3LR  C3   H3A  single  0.970  0.020  1.090
 3LR  O4   C4   single  1.414  0.020  1.414
 3LR  C4   C5   single  1.538  0.020  1.538
 3LR  C4   H4   single  0.970  0.020  1.090
 3LR  O4   HO4  single  0.850  0.020  0.980
 3LR  O5   C5   single  1.416  0.020  1.416
 3LR  C5   C6   single  1.521  0.020  1.521
 3LR  C5   H5   single  0.970  0.020  1.090
 3LR  C6   H6   single  0.970  0.020  1.090
 3LR  C6   H6A  single  0.970  0.020  1.090
 3LR  C6   H6B  single  0.970  0.020  1.090
 3LR  O5   HO5  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
 3LR  C2   C1  O1B  114.73  3.000
 3LR  C2   C1  O1A  117.86  3.000
 3LR  O1B  C1  O1A  127.41  3.000
 3LR  H2   C2  C3   108.56  3.000
 3LR  H2   C2  O2   109.64  3.000
 3LR  C3   C2  O2   111.27  3.000
 3LR  H2   C2  C1   107.57  3.000
 3LR  C3   C2  C1   110.50  3.000
 3LR  O2   C2  C1   109.22  3.000
 3LR  HO2  O2  C2   101.87  3.000
 3LR  H3A  C3  H3   106.63  3.000
 3LR  H3A  C3  C4   109.16  3.000
 3LR  H3   C3  C4   109.00  3.000
 3LR  H3A  C3  C2   109.28  3.000
 3LR  H3   C3  C2   108.74  3.000
 3LR  C4   C3  C2   113.78  3.000
 3LR  H4   C4  C5   107.67  3.000
 3LR  H4   C4  O4   105.43  3.000
 3LR  C5   C4  O4   110.90  3.000
 3LR  H4   C4  C3   109.13  3.000
 3LR  C5   C4  C3   111.90  3.000
 3LR  O4   C4  C3   111.51  3.000
 3LR  HO4  O4  C4   108.12  3.000
 3LR  H5   C5  O5   105.12  3.000
 3LR  H5   C5  C6   108.62  3.000
 3LR  O5   C5  C6   111.29  3.000
 3LR  H5   C5  C4   108.18  3.000
 3LR  C6   C5  C4   112.49  3.000
 3LR  O5   C5  C4   110.79  3.000
 3LR  H6B  C6  H6A  107.98  3.000
 3LR  H6B  C6  H6   107.74  3.000
 3LR  H6A  C6  H6   107.67  3.000
 3LR  H6B  C6  C5   111.32  3.000
 3LR  H6A  C6  C5   110.32  3.000
 3LR  H6   C6  C5   111.64  3.000
 3LR  HO5  O5  C5   108.09  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
 3LR  chir_01  C2  C1  O2  C3  positiv
 3LR  chir_02  C4  O4  C5  C3  negativ
 3LR  chir_03  C5  O5  C4  C6  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
 3LR  plan-1  O1A  0.020
 3LR  plan-1  C1   0.020
 3LR  plan-1  O1B  0.020
 3LR  plan-1  C2   0.020

