# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 19:58:09 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-Se-methyl-5-seleno-alpha-D-ribofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se]C[C@H]1O[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
 8GA  8GA  5-Se-methyl-5-seleno-alpha-D-ribofuranose  D-saccharide  23  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_8GA
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
 8GA  CS   C   CH3   0  -0.803   3.7638   0.4108   0.5097
 8GA  C5'  C   CH2   0  -0.599   0.8428   0.5973   0.7459
 8GA  C4'  C   CH1   0   0.046  -0.4897   0.2911   0.1021
 8GA  O4'  O   O2    0  -0.516  -0.8606  -1.0485   0.3810
 8GA  C1'  C   CH1   0   0.282  -2.2619  -1.1618   0.5754
 8GA  O1'  O   OH1   0  -0.663  -2.8181  -2.0835  -0.2929
 8GA  C2'  C   CH1   0  -0.102  -2.8427   0.2321   0.3055
 8GA  O2'  O   OH1   0  -0.665  -3.1532   0.4281  -1.0465
 8GA  C3'  C   CH1   0   0.031  -1.6496   1.1166   0.6584
 8GA  O3'  O   OH1   0  -0.661  -1.6462   2.3988   0.1101
 8GA  SE   SE  SE    0   0.031   2.1954  -0.6971   0.1579
 8GA  H1   H   HCH3  0   0.262   3.7477   1.3118  -0.1024
 8GA  H2   H   HCH3  0   0.263   3.8173   0.6870   1.5617
 8GA  H3   H   HCH3  0   0.269   4.6501  -0.1703   0.2563
 8GA  H4   H   HCH2  0   0.274   1.1682   1.5950   0.4442
 8GA  H5   H   HCH2  0   0.262   0.7632   0.5755   1.8352
 8GA  H6   H   HCH1  0   0.226  -0.4131   0.4530  -0.9822
 8GA  H7   H   HCH1  0   0.214  -2.4342  -1.4559   1.6178
 8GA  H8   H   HOH1  0   0.470  -2.7620  -2.9645   0.0897
 8GA  H9   H   HCH1  0   0.241  -3.7100   0.4195   0.9522
 8GA  H10  H   HOH1  0   0.452  -3.7520  -0.2743  -1.3215
 8GA  H11  H   HCH1  0   0.226  -1.5649   1.1436   1.7552
 8GA  H12  H   HOH1  0   0.459  -2.2974   2.9345   0.5733

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
 8GA  O3'  C3'  single  1.395  0.020  1.395
 8GA  C3'  C2'  single  1.527  0.020  1.527
 8GA  C3'  C4'  single  1.528  0.020  1.528
 8GA  O2'  C2'  single  1.401  0.020  1.401
 8GA  C2'  C1'  single  1.534  0.020  1.534
 8GA  C5'  C4'  single  1.511  0.020  1.511
 8GA  C5'  SE   single  1.962  0.020  1.962
 8GA  C4'  O4'  single  1.418  0.020  1.418
 8GA  CS   SE   single  1.952  0.020  1.952
 8GA  C1'  O4'  single  1.419  0.020  1.419
 8GA  C1'  O1'  single  1.383  0.020  1.383
 8GA  CS   H1   single  0.970  0.020  1.090
 8GA  CS   H2   single  0.970  0.020  1.090
 8GA  CS   H3   single  0.970  0.020  1.090
 8GA  C5'  H4   single  0.970  0.020  1.090
 8GA  C5'  H5   single  0.970  0.020  1.090
 8GA  C4'  H6   single  0.970  0.020  1.090
 8GA  C1'  H7   single  0.970  0.020  1.090
 8GA  O1'  H8   single  0.850  0.020  0.980
 8GA  C2'  H9   single  0.970  0.020  1.090
 8GA  O2'  H10  single  0.850  0.020  0.980
 8GA  C3'  H11  single  0.970  0.020  1.090
 8GA  O3'  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
 8GA  H3   CS   H2   108.66  3.000
 8GA  H3   CS   H1   108.81  3.000
 8GA  H2   CS   H1   109.50  3.000
 8GA  H3   CS   SE   107.99  3.000
 8GA  H2   CS   SE   110.94  3.000
 8GA  H1   CS   SE   110.87  3.000
 8GA  H5   C5'  H4   108.39  3.000
 8GA  H5   C5'  SE   109.63  3.000
 8GA  H4   C5'  SE   108.33  3.000
 8GA  H5   C5'  C4'  110.89  3.000
 8GA  H4   C5'  C4'  109.28  3.000
 8GA  SE   C5'  C4'  110.27  3.000
 8GA  H6   C4'  C3'  109.41  3.000
 8GA  H6   C4'  O4'  110.58  3.000
 8GA  C3'  C4'  O4'  103.89  3.000
 8GA  H6   C4'  C5'  109.22  3.000
 8GA  O4'  C4'  C5'  109.77  3.000
 8GA  C3'  C4'  C5'  113.87  3.000
 8GA  C1'  O4'  C4'  111.14  3.000
 8GA  H7   C1'  C2'  110.58  3.000
 8GA  H7   C1'  O1'  110.78  3.000
 8GA  C2'  C1'  O1'  110.05  3.000
 8GA  H7   C1'  O4'  107.86  3.000
 8GA  O1'  C1'  O4'  111.36  3.000
 8GA  C2'  C1'  O4'  106.09  3.000
 8GA  H8   O1'  C1'  109.70  3.000
 8GA  H9   C2'  C3'  112.48  3.000
 8GA  H9   C2'  O2'  111.68  3.000
 8GA  C3'  C2'  O2'  108.37  3.000
 8GA  H9   C2'  C1'  110.52  3.000
 8GA  O2'  C2'  C1'  112.39  3.000
 8GA  C3'  C2'  C1'  100.95  3.000
 8GA  H10  O2'  C2'  108.14  3.000
 8GA  H11  C3'  O3'  111.66  3.000
 8GA  H11  C3'  C2'  107.74  3.000
 8GA  O3'  C3'  C2'  116.35  3.000
 8GA  H11  C3'  C4'  108.52  3.000
 8GA  C2'  C3'  C4'  101.31  3.000
 8GA  O3'  C3'  C4'  110.59  3.000
 8GA  H12  O3'  C3'  108.73  3.000
 8GA  C5'  SE   CS    97.20  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
 8GA  Var_01  C4'  C5'  SE  CS   157.00  30.0  2
 8GA  Var_02  H1   CS   SE  C5'  -62.22  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
 8GA  chir_01  C4'  C3'  C5'  O4'  negativ
 8GA  chir_02  C1'  O4'  O1'  C2'  positiv
 8GA  chir_03  C2'  O2'  C1'  C3'  negativ
 8GA  chir_04  C3'  O3'  C2'  C4'  negativ

