# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:12:42 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-one (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC(=O)[C@H](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
 LGC  LGC  '(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-one (non-preferred name)'  D-saccharide  22  12  .  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_LGC
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
 LGC  C1    C  C     0   0.525   1.4946  -0.0540  -0.5795
 LGC  C2    C  CH1   0  -0.114   0.3628  -0.3368  -1.5584
 LGC  O5    O  O2    0  -0.443   1.2097   0.0316   0.7137
 LGC  O1    O  O     0  -0.427   2.6418   0.0103  -0.9318
 LGC  O2    O  OH1   0  -0.655   0.6721   0.1303  -2.8355
 LGC  C3    C  CH1   0   0.004  -0.9481   0.2837  -1.1076
 LGC  O3    O  OH1   0  -0.667  -2.0230  -0.1484  -1.8991
 LGC  C4    C  CH1   0  -0.009  -1.2212  -0.1659   0.3185
 LGC  O4    O  OH1   0  -0.664  -2.4057   0.3875   0.8243
 LGC  C5    C  CH1   0  -0.003  -0.0998   0.3101   1.2353
 LGC  C6    C  CH2   0  -0.152  -0.1761  -0.3379   2.6006
 LGC  O6    O  OH1   0  -0.668   0.8023   0.2357   3.4297
 LGC  HC2   H  HCH1  0   0.268   0.2354  -1.4323  -1.5456
 LGC  HO2   H  HOH1  0   0.463   1.4030  -0.3847  -3.1921
 LGC  HC3   H  HCH1  0   0.241  -0.8561   1.3804  -1.1252
 LGC  HO3   H  HOH1  0   0.463  -1.9768   0.2889  -2.7550
 LGC  HC4   H  HCH1  0   0.229  -1.2590  -1.2673   0.3338
 LGC  HO4   H  HOH1  0   0.460  -3.1324   0.1157   0.2534
 LGC  HC5   H  HCH1  0   0.262  -0.1790   1.3982   1.3396
 LGC  HC61  H  HCH2  0   0.206  -0.0358  -1.4213   2.4849
 LGC  HC62  H  HCH2  0   0.222  -1.1870  -0.1808   2.9904
 LGC  HO6   H  HOH1  0   0.460   0.6700  -0.0966   4.3218

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
 LGC  C1  C2    single  1.523  0.020  1.523
 LGC  C1  O5    single  1.327  0.020  1.327
 LGC  C1  O1    double  1.202  0.020  1.202
 LGC  C2  O2    single  1.395  0.020  1.395
 LGC  C2  C3    single  1.519  0.020  1.519
 LGC  C2  HC2   single  0.970  0.020  1.090
 LGC  O5  C5    single  1.437  0.020  1.437
 LGC  O2  HO2   single  0.850  0.020  0.980
 LGC  C3  O3    single  1.403  0.020  1.403
 LGC  C3  C4    single  1.520  0.020  1.520
 LGC  C3  HC3   single  0.970  0.020  1.090
 LGC  O3  HO3   single  0.850  0.020  0.980
 LGC  C4  O4    single  1.402  0.020  1.402
 LGC  C4  C5    single  1.525  0.020  1.525
 LGC  C4  HC4   single  0.970  0.020  1.090
 LGC  O4  HO4   single  0.850  0.020  0.980
 LGC  C5  C6    single  1.513  0.020  1.513
 LGC  C5  HC5   single  0.970  0.020  1.090
 LGC  C6  O6    single  1.405  0.020  1.405
 LGC  C6  HC61  single  0.970  0.020  1.090
 LGC  C6  HC62  single  0.970  0.020  1.090
 LGC  O6  HO6   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
 LGC  O1    C1  O5    119.16  3.000
 LGC  O1    C1  C2    122.07  3.000
 LGC  O5    C1  C2    118.61  3.000
 LGC  HC2   C2  C3    107.62  3.000
 LGC  HC2   C2  O2    111.65  3.000
 LGC  C3    C2  O2    109.05  3.000
 LGC  HC2   C2  C1    105.24  3.000
 LGC  C3    C2  C1    112.01  3.000
 LGC  O2    C2  C1    111.20  3.000
 LGC  C5    O5  C1    124.19  3.000
 LGC  HO2   O2  C2    109.18  3.000
 LGC  HC3   C3  C4    108.95  3.000
 LGC  HC3   C3  O3    111.21  3.000
 LGC  C4    C3  O3    107.49  3.000
 LGC  HC3   C3  C2    109.28  3.000
 LGC  C4    C3  C2    108.23  3.000
 LGC  O3    C3  C2    111.59  3.000
 LGC  HO3   O3  C3    108.97  3.000
 LGC  HC4   C4  C5    109.20  3.000
 LGC  HC4   C4  O4    111.13  3.000
 LGC  C5    C4  O4    106.34  3.000
 LGC  HC4   C4  C3    108.35  3.000
 LGC  C5    C4  C3    109.85  3.000
 LGC  O4    C4  C3    111.94  3.000
 LGC  HO4   O4  C4    108.19  3.000
 LGC  HC5   C5  C6    109.61  3.000
 LGC  HC5   C5  C4    108.31  3.000
 LGC  C6    C5  C4    111.82  3.000
 LGC  HC5   C5  O5    107.03  3.000
 LGC  C6    C5  O5    106.89  3.000
 LGC  C4    C5  O5    113.05  3.000
 LGC  HC62  C6  HC61  107.27  3.000
 LGC  HC62  C6  O6    111.99  3.000
 LGC  HC61  C6  O6    112.08  3.000
 LGC  HC62  C6  C5    107.84  3.000
 LGC  HC61  C6  C5    108.71  3.000
 LGC  O6    C6  C5    108.81  3.000
 LGC  HO6   O6  C6    108.10  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
 LGC  chir_01  C2  C1  O2  C3  positiv
 LGC  chir_02  C3  O3  C2  C4  positiv
 LGC  chir_03  C4  O4  C3  C5  negativ
 LGC  chir_04  C5  O5  C4  C6  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
 LGC  plan-1  C1  0.020
 LGC  plan-1  C2  0.020
 LGC  plan-1  O5  0.020
 LGC  plan-1  O1  0.020

