# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:27:15 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  23  11  .  2023-02-15  2023-02-16
;
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  OH1   0  -0.591  -2.7726  -0.8037  -1.2750
 3LR  C1    C  C     0   0.505  -2.5863   0.0166  -0.2503
 3LR  O1B   O  O     0  -0.437  -3.3314   0.9202   0.0318
 3LR  C2    C  CH1   0  -0.058  -1.3085  -0.3015   0.5084
 3LR  O2    O  OH1   0  -0.652  -1.3091   0.3225   1.7589
 3LR  C3    C  CH2   0  -0.512  -0.0956   0.0743  -0.3497
 3LR  C4    C  CH1   0   0.028   1.2323  -0.2604   0.3260
 3LR  O4    O  OH1   0  -0.664   1.3044  -1.6274   0.6681
 3LR  C5    C  CH1   0   0.005   2.4267   0.1643  -0.5451
 3LR  C6    C  CH3   0  -0.681   3.7603  -0.2307   0.0702
 3LR  O5    O  OH1   0  -0.663   2.3729   1.5498  -0.8224
 3LR  HO1A  H  HOH1  0   0.485  -3.5758  -0.5579  -1.7582
 3LR  H2    H  HCH1  0   0.272  -1.2901  -1.3782   0.6982
 3LR  HO2   H  HOH1  0   0.448  -1.3385   1.2774   1.6318
 3LR  H3    H  HCH2  0   0.246  -0.1509  -0.4515  -1.3084
 3LR  H3A   H  HCH2  0   0.254  -0.1305   1.1426  -0.5789
 3LR  H4    H  HCH1  0   0.225   1.3011   0.2823   1.2756
 3LR  HO4   H  HOH1  0   0.444   1.2364  -2.1494  -0.1394
 3LR  H5    H  HCH1  0   0.218   2.3303  -0.3279  -1.5208
 3LR  H6    H  HCH3  0   0.233   3.8531  -1.3106   0.1697
 3LR  H6A   H  HCH3  0   0.236   4.5821   0.1155  -0.5579
 3LR  H6B   H  HCH3  0   0.219   3.8858   0.2077   1.0639
 3LR  HO5   H  HOH1  0   0.442   2.5344   2.0280  -0.0016

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   single  1.326  0.020  1.326
 3LR  O1A  HO1A  single  0.850  0.020  0.980
 3LR  O1B  C1    double  1.205  0.020  1.205
 3LR  C2   C1    single  1.520  0.020  1.520
 3LR  O2   C2    single  1.397  0.020  1.397
 3LR  C2   C3    single  1.533  0.020  1.533
 3LR  C2   H2    single  0.970  0.020  1.090
 3LR  O2   HO2   single  0.850  0.020  0.980
 3LR  C4   C3    single  1.527  0.020  1.527
 3LR  C3   H3    single  0.970  0.020  1.090
 3LR  C3   H3A   single  0.970  0.020  1.090
 3LR  O4   C4    single  1.411  0.020  1.411
 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  1.414  0.020  1.414
 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  HO1A  O1A  C1   110.18  3.000
 3LR  C2    C1   O1B  124.07  3.000
 3LR  C2    C1   O1A  111.99  3.000
 3LR  O1B   C1   O1A  123.93  3.000
 3LR  H2    C2   C3   108.98  3.000
 3LR  H2    C2   O2   106.52  3.000
 3LR  C3    C2   O2   113.07  3.000
 3LR  H2    C2   C1   107.88  3.000
 3LR  C3    C2   C1   109.54  3.000
 3LR  O2    C2   C1   110.67  3.000
 3LR  HO2   O2   C2   108.93  3.000
 3LR  H3A   C3   H3   106.51  3.000
 3LR  H3A   C3   C4   109.55  3.000
 3LR  H3    C3   C4   109.03  3.000
 3LR  H3A   C3   C2   109.38  3.000
 3LR  H3    C3   C2   109.43  3.000
 3LR  C4    C3   C2   112.75  3.000
 3LR  H4    C4   C5   107.77  3.000
 3LR  H4    C4   O4   105.45  3.000
 3LR  C5    C4   O4   111.42  3.000
 3LR  H4    C4   C3   109.24  3.000
 3LR  C5    C4   C3   111.36  3.000
 3LR  O4    C4   C3   111.35  3.000
 3LR  HO4   O4   C4   108.53  3.000
 3LR  H5    C5   O5   105.18  3.000
 3LR  H5    C5   C6   108.69  3.000
 3LR  O5    C5   C6   111.54  3.000
 3LR  H5    C5   C4   108.15  3.000
 3LR  C6    C5   C4   112.34  3.000
 3LR  O5    C5   C4   110.61  3.000
 3LR  H6B   C6   H6A  108.04  3.000
 3LR  H6B   C6   H6   107.76  3.000
 3LR  H6A   C6   H6   107.66  3.000
 3LR  H6B   C6   C5   111.36  3.000
 3LR  H6A   C6   C5   110.19  3.000
 3LR  H6    C6   C5   111.68  3.000
 3LR  HO5   O5   C5   108.23  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
 3LR  CONST_01  HO1A  O1A  C1  O1B  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
 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
 3LR  plan-1  HO1A  0.020

