# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 12:41:41 2019
#
#   Ligand name: 6-thio-alpha-D-glucopyranose
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@H](CS)[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
SGD        SGD '6-thio-alpha-D-glucopyranose' saccharide 24 12 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_SGD
#
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
SGD         C1     C   CH1    0    .      -0.6982   -0.2709   -1.4151
SGD         O5     O   O2     0    .       0.8138   -0.2577   -1.3787
SGD         C2     C   CH1    0    .      -1.3016    0.8531   -0.5815
SGD         O2     O   OH1    0    .      -0.9897    2.1192   -1.2085
SGD         C3     C   CH1    0    .      -0.7756    0.8594    0.8145
SGD         O3     O   OH1    0    .      -1.2546   -0.3111    1.4954
SGD         C4     C   CH1    0    .       0.7496    0.8670    0.8516
SGD         O4     O   OH1    0    .       1.2218    2.1173    0.3514
SGD         C5     C   CH1    0    .       1.3439   -0.2519    0.0215
SGD         C6     C   CH2    0    .       1.0158   -1.5305    0.6546
SGD         S1     S   S2     0    .       2.0076   -2.8297   -0.0764
SGD         O1     O   OH1    0    .      -1.1086   -0.1366   -2.6957
SGD         H1     H   HCH1   0    .      -1.0525   -1.2420   -1.0197
SGD         H2     H   HCH1   0    .      -2.3787    0.7267   -0.5491
SGD         H3     H   HOH1   0    .      -1.8363    2.6139   -1.3960
SGD         H4     H   HCH1   0    .      -1.1287    1.7049    1.3013
SGD         H5     H   HOH1   0    .      -1.8931   -0.0522    2.1623
SGD         H6     H   HCH1   0    .       1.0681    0.7518    1.8551
SGD         H7     H   HOH1   0    .       1.8468    2.5303    1.0239
SGD         H8     H   HCH1   0    .       2.4015   -0.1345   -0.0075
SGD         H9     H   HCH2   0    .      -0.0731   -1.7560    0.4982
SGD         H10    H   HCH2   0    .       1.2188   -1.4738    1.6755
SGD         H11    H   HSH1   0    .       1.9676   -3.9262    0.7121
SGD         H12    H   HOH1   0    .      -1.1644   -0.9706   -3.0894
#
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
SGD   O1      C1    single        1.351 0.020     1.351
SGD   O2      C2    single        1.447 0.020     1.447
SGD   C1      C2    single        1.524 0.020     1.524
SGD   C1      O5    single        1.512 0.020     1.512
SGD   C2      C3    single        1.492 0.020     1.492
SGD   C3      O3    single        1.436 0.020     1.436
SGD   C3      C4    single        1.526 0.020     1.526
SGD   O5      C5    single        1.497 0.020     1.497
SGD   C5      C4    single        1.515 0.020     1.515
SGD   C5      C6    single        1.464 0.020     1.464
SGD   C4      O4    single        1.427 0.020     1.427
SGD   S1      C6    single        1.790 0.020     1.790
SGD   C1      H1    single        0.970 0.020     1.090
SGD   C2      H2    single        0.970 0.020     1.090
SGD   O2      H3    single        0.850 0.020     0.980
SGD   C3      H4    single        0.970 0.020     1.090
SGD   O3      H5    single        0.850 0.020     0.980
SGD   C4      H6    single        0.970 0.020     1.090
SGD   O4      H7    single        0.850 0.020     0.980
SGD   C5      H8    single        0.970 0.020     1.090
SGD   C6      H9    single        0.970 0.020     1.090
SGD   C6      H10   single        0.970 0.020     1.090
SGD   S1      H11   single        1.200 0.020     1.300
SGD   O1      H12   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
SGD   H1      C1      O1          109.18 3.000
SGD   H1      C1      C2          108.97 3.000
SGD   O1      C1      C2          108.95 3.000
SGD   H1      C1      O5          108.61 3.000
SGD   C2      C1      O5          112.10 3.000
SGD   O1      C1      O5          109.00 3.000
SGD   C5      O5      C1          112.12 3.000
SGD   H2      C2      C3          108.82 3.000
SGD   H2      C2      O2          109.20 3.000
SGD   C3      C2      O2          109.01 3.000
SGD   H2      C2      C1          108.88 3.000
SGD   C3      C2      C1          112.04 3.000
SGD   O2      C2      C1          108.85 3.000
SGD   H3      O2      C2          109.40 3.000
SGD   H4      C3      C4          108.95 3.000
SGD   H4      C3      O3          109.16 3.000
SGD   C4      C3      O3          109.02 3.000
SGD   H4      C3      C2          108.81 3.000
SGD   C4      C3      C2          112.04 3.000
SGD   O3      C3      C2          108.82 3.000
SGD   H5      O3      C3          109.37 3.000
SGD   H6      C4      C5          108.72 3.000
SGD   H6      C4      O4          109.15 3.000
SGD   C5      C4      O4          108.98 3.000
SGD   H6      C4      C3          108.85 3.000
SGD   O4      C4      C3          109.06 3.000
SGD   C5      C4      C3          112.04 3.000
SGD   H7      O4      C4          109.31 3.000
SGD   H8      C5      C6          109.31 3.000
SGD   H8      C5      C4          108.86 3.000
SGD   C6      C5      C4          108.67 3.000
SGD   H8      C5      O5          109.07 3.000
SGD   C6      C5      O5          108.77 3.000
SGD   C4      C5      O5          112.12 3.000
SGD   H10     C6      H9          109.64 3.000
SGD   H10     C6      S1          109.36 3.000
SGD   H9      C6      S1          109.54 3.000
SGD   H10     C6      C5          109.41 3.000
SGD   H9      C6      C5          109.42 3.000
SGD   S1      C6      C5          109.45 3.000
SGD   H11     S1      C6          109.52 3.000
SGD   H12     O1      C1          109.42 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
SGD chir_01   C1      O1      C2      O5    positiv
SGD chir_02   C2      O2      C1      C3    negativ
SGD chir_03   C3      O3      C2      C4    positiv
SGD chir_04   C4      O4      C5      C3    positiv
SGD chir_05   C5      O5      C4      C6    negativ
