# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 01:02:07 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1,5-anhydro-D-arabino-hex-1-enitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC=C(O)[C@@H](O)[C@@H]1O
#
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
 LCN  LCN  1,5-anhydro-D-arabino-hex-1-enitol  D-saccharide  21  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 PERFECT
;

data_comp_LCN
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
 LCN  C1   C  C1    0  -0.107  -0.5544  -1.7048   0.1999
 LCN  C2   C  C     0   0.211  -1.5282  -0.8485  -0.1014
 LCN  O2   O  OH1   0  -0.639  -2.8227  -1.1951  -0.3217
 LCN  C3   C  CH1   0  -0.037  -1.2764   0.6247  -0.2619
 LCN  O3   O  OH1   0  -0.666  -2.2141   1.4062   0.4447
 LCN  C4   C  CH1   0   0.013   0.1065   0.9719   0.2796
 LCN  O4   O  OH1   0  -0.669   0.5390   2.2274  -0.1757
 LCN  C5   C  CH1   0  -0.017   1.1070  -0.0872  -0.1740
 LCN  O5   O  O2    0  -0.469   0.7473  -1.3428   0.3780
 LCN  C6   C  CH2   0  -0.161   2.5200   0.2195   0.2726
 LCN  O6   O  OH1   0  -0.670   3.3676  -0.8036  -0.1928
 LCN  H1   H  H     0   0.268  -0.7165  -2.7697   0.3281
 LCN  H3   H  HCH1  0   0.237  -1.2985   0.8764  -1.3330
 LCN  H4   H  HCH1  0   0.221   0.0586   0.9418   1.3797
 LCN  H5   H  HCH1  0   0.231   1.0768  -0.1588  -1.2729
 LCN  H6   H  HCH2  0   0.216   2.8059   1.1954  -0.1306
 LCN  H6A  H  HCH2  0   0.197   2.5408   0.3014   1.3686
 LCN  HO2  H  HOH1  0   0.468  -2.9429  -2.1442  -0.2042
 LCN  HO3  H  HOH1  0   0.460  -3.0436   1.4098  -0.0422
 LCN  HO4  H  HOH1  0   0.456  -0.0938   2.8895   0.1219
 LCN  HO6  H  HOH1  0   0.458   4.2710  -0.5643   0.0318

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
 LCN  O5   C1   single  1.363  0.020  1.363
 LCN  H1   C1   single  0.930  0.020  1.080
 LCN  C1   C2   double  1.331  0.020  1.331
 LCN  C2   C3   single  1.503  0.020  1.503
 LCN  C2   O2   single  1.358  0.020  1.358
 LCN  HO2  O2   single  0.850  0.020  0.980
 LCN  C4   C3   single  1.525  0.020  1.525
 LCN  H3   C3   single  0.970  0.020  1.090
 LCN  C3   O3   single  1.410  0.020  1.410
 LCN  O3   HO3  single  0.850  0.020  0.980
 LCN  C5   C4   single  1.526  0.020  1.526
 LCN  C4   O4   single  1.404  0.020  1.404
 LCN  C4   H4   single  0.970  0.020  1.090
 LCN  HO4  O4   single  0.850  0.020  0.980
 LCN  C6   C5   single  1.513  0.020  1.513
 LCN  H5   C5   single  0.970  0.020  1.090
 LCN  O5   C5   single  1.418  0.020  1.418
 LCN  H6   C6   single  0.970  0.020  1.090
 LCN  C6   H6A  single  0.970  0.020  1.090
 LCN  C6   O6   single  1.408  0.020  1.408
 LCN  HO6  O6   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
 LCN  H1   C1  O5  112.83  3.000
 LCN  H1   C1  C2  123.29  3.000
 LCN  O5   C1  C2  123.88  3.000
 LCN  C3   C2  O2  113.11  3.000
 LCN  O2   C2  C1  124.73  3.000
 LCN  C3   C2  C1  122.14  3.000
 LCN  HO2  O2  C2  110.51  3.000
 LCN  H3   C3  C4  108.16  3.000
 LCN  H3   C3  O3  110.34  3.000
 LCN  C4   C3  O3  107.39  3.000
 LCN  O3   C3  C2  112.22  3.000
 LCN  H3   C3  C2  108.95  3.000
 LCN  C4   C3  C2  109.70  3.000
 LCN  HO3  O3  C3  108.78  3.000
 LCN  H4   C4  C5  107.84  3.000
 LCN  H4   C4  O4  111.21  3.000
 LCN  C5   C4  O4  108.80  3.000
 LCN  H4   C4  C3  108.00  3.000
 LCN  O4   C4  C3  111.58  3.000
 LCN  C5   C4  C3  109.33  3.000
 LCN  HO4  O4  C4  108.19  3.000
 LCN  H5   C5  C6  109.46  3.000
 LCN  H5   C5  O5  108.89  3.000
 LCN  C6   C5  O5  107.54  3.000
 LCN  O5   C5  C4  109.42  3.000
 LCN  H5   C5  C4  108.89  3.000
 LCN  C6   C5  C4  112.57  3.000
 LCN  C5   O5  C1  115.25  3.000
 LCN  H6A  C6  H6  107.23  3.000
 LCN  H6A  C6  O6  111.87  3.000
 LCN  H6   C6  O6  111.66  3.000
 LCN  O6   C6  C5  108.50  3.000
 LCN  H6A  C6  C5  109.09  3.000
 LCN  H6   C6  C5  108.42  3.000
 LCN  HO6  O6  C6  107.92  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
 LCN  Var_01  O5  C1  C2  C3  -0.63  30.0  1

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
 LCN  chir_01  C3  C2  C4  O3  positiv
 LCN  chir_02  C4  O4  C5  C3  positiv
 LCN  chir_03  C5  O5  C6  C4  positiv

