# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 11:00:41 2019
#
#   Ligand name: 2,6-dideoxy-4-O-methyl-alpha-D-lyxo-hexopyranose
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@@H](C)O[C@H](O)C[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
1GL        1GL '2,6-dideoxy-4-O-methyl-alpha-D-lyxo-hexopyranose' d-saccharide 25 11 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_1GL
#
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
1GL         O1     O   OH1    0    .      -2.0604   -1.8618   -1.0007
1GL         C1     C   CH1    0    .      -0.6971   -1.8618   -1.0007
1GL         C2     C   CH2    0    .      -0.2058   -1.8618    0.4335
1GL         C3     C   CH1    0    .      -0.5180   -0.5950    1.1271
1GL         O3     O   OH1    0    .       0.1194   -0.6071    2.4362
1GL         C4     C   CH1    0    .      -0.0307    0.5998    0.3629
1GL         O4     O   O2     0    .       1.4049    0.5971    0.3638
1GL         CME    C   CH3    0    .       1.9760    1.5691    1.2049
1GL         C5     C   CH1    0    .      -0.5225    0.5959   -1.0798
1GL         O5     O   O2     0    .      -0.2099   -0.6619   -1.7661
1GL         C6     C   CH3    0    .       0.1313    1.7300   -1.8201
1GL         HO1    H   HOH1   0    .      -2.3748   -2.5566   -1.5552
1GL         H1     H   HCH1   0    .      -0.3406   -2.7587   -1.4926
1GL         H21    H   HCH2   0    .       0.8676   -2.0074    0.4362
1GL         H22    H   HCH2   0    .      -0.6784   -2.6785    0.9658
1GL         H3     H   HCH1   0    .      -1.5914   -0.5182    1.2523
1GL         HO3    H   HOH1   0    .      -0.5194   -0.8239    3.0950
1GL         H4     H   HCH1   0    .      -0.3869    1.4982    0.8523
1GL        HM41    H   HCH3   0    .       2.8315    1.1458    1.7173
1GL        HM42    H   HCH3   0    .       2.2941    2.4180    0.6118
1GL        HM43    H   HCH3   0    .       1.2424    1.8924    1.9336
1GL         H5     H   HCH1   0    .      -1.5963    0.7393   -1.0839
1GL         H61    H   HCH3   0    .       1.1813    1.5077   -1.9669
1GL         H62    H   HCH3   0    .      -0.3489    1.8573   -2.7828
1GL         H63    H   HCH3   0    .       0.0324    2.6420   -1.2438
#
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
1GL   O1      C1    single        1.363 0.020     1.363
1GL   O1      HO1   single        0.850 0.020     0.980
1GL   C1      C2    single        1.516 0.020     1.516
1GL   C1      O5    single        1.504 0.020     1.504
1GL   C1      H1    single        0.970 0.020     1.090
1GL   C2      C3    single        1.478 0.020     1.478
1GL   C2      H21   single        0.970 0.020     1.090
1GL   C2      H22   single        0.970 0.020     1.090
1GL   C3      O3    single        1.456 0.020     1.456
1GL   C3      C4    single        1.500 0.020     1.500
1GL   C3      H3    single        0.970 0.020     1.090
1GL   O3      HO3   single        0.850 0.020     0.980
1GL   C4      O4    single        1.436 0.020     1.436
1GL   C4      C5    single        1.524 0.020     1.524
1GL   C4      H4    single        0.970 0.020     1.090
1GL   O4      CME   single        1.407 0.020     1.407
1GL   CME    HM41   single        0.970 0.020     1.090
1GL   CME    HM42   single        0.970 0.020     1.090
1GL   CME    HM43   single        0.970 0.020     1.090
1GL   C5      O5    single        1.467 0.020     1.467
1GL   C5      C6    single        1.504 0.020     1.504
1GL   C5      H5    single        0.970 0.020     1.090
1GL   C6      H61   single        0.970 0.020     1.090
1GL   C6      H62   single        0.970 0.020     1.090
1GL   C6      H63   single        0.970 0.020     1.090
#
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
1GL   HO1     O1      C1          109.48 3.000
1GL   H1      C1      O5          108.83 3.000
1GL   H1      C1      C2          108.84 3.000
1GL   O5      C1      C2          112.11 3.000
1GL   H1      C1      O1          109.22 3.000
1GL   O5      C1      O1          108.90 3.000
1GL   C2      C1      O1          108.91 3.000
1GL   H22     C2      H21         109.25 3.000
1GL   H22     C2      C3          108.88 3.000
1GL   H21     C2      C3          108.87 3.000
1GL   H22     C2      C1          108.87 3.000
1GL   H21     C2      C1          108.87 3.000
1GL   C3      C2      C1          112.06 3.000
1GL   H3      C3      C4          108.93 3.000
1GL   H3      C3      O3          109.30 3.000
1GL   C4      C3      O3          108.82 3.000
1GL   H3      C3      C2          108.93 3.000
1GL   C4      C3      C2          112.03 3.000
1GL   O3      C3      C2          108.81 3.000
1GL   HO3     O3      C3          109.48 3.000
1GL   H4      C4      C5          108.88 3.000
1GL   H4      C4      O4          109.27 3.000
1GL   C5      C4      O4          108.86 3.000
1GL   H4      C4      C3          108.88 3.000
1GL   C5      C4      C3          112.06 3.000
1GL   O4      C4      C3          108.85 3.000
1GL   CME     O4      C4          113.90 3.000
1GL  HM43     CME    HM42         109.47 3.000
1GL  HM43     CME    HM41         109.47 3.000
1GL  HM42     CME    HM41         109.47 3.000
1GL  HM43     CME     O4          109.48 3.000
1GL  HM42     CME     O4          109.47 3.000
1GL  HM41     CME     O4          109.48 3.000
1GL   H5      C5      C6          109.22 3.000
1GL   H5      C5      O5          108.85 3.000
1GL   C6      C5      O5          108.89 3.000
1GL   H5      C5      C4          108.85 3.000
1GL   C6      C5      C4          108.89 3.000
1GL   O5      C5      C4          112.11 3.000
1GL   C5      O5      C1          112.15 3.000
1GL   H63     C6      H62         109.47 3.000
1GL   H63     C6      H61         109.47 3.000
1GL   H62     C6      H61         109.47 3.000
1GL   H63     C6      C5          109.47 3.000
1GL   H62     C6      C5          109.47 3.000
1GL   H61     C6      C5          109.48 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
1GL Var_01        HM41     CME     O4      C4          139.52  30.0 3
#
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
1GL chir_01   C1      O1      C2      O5    positiv
1GL chir_02   C3      O3      C4      C2    negativ
1GL chir_03   C4      O4      C5      C3    negativ
1GL chir_04   C5      O5      C4      C6    negativ
