# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 21:00:32 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-Se-methyl-5-seleno-beta-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
 8GG  8GG  5-Se-methyl-5-seleno-beta-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_8GG
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
 8GG  O4'  O   O2    0  -0.505   0.8132   0.5248  -0.9683
 8GG  C5'  C   CH2   0  -0.600  -0.6738  -0.6375   0.5659
 8GG  C4'  C   CH1   0  -0.005   0.4143  -0.7543  -0.4896
 8GG  C3'  C   CH1   0  -0.006   1.6892  -1.3964   0.0490
 8GG  O3'  O   OH1   0  -0.668   2.3804  -1.9679  -1.0324
 8GG  C2'  C   CH1   0  -0.057   2.4114  -0.1741   0.6019
 8GG  O2'  O   OH1   0  -0.666   3.7811  -0.4222   0.7377
 8GG  C1'  C   CH1   0   0.285   2.0542   0.9148  -0.4136
 8GG  O1'  O   OH1   0  -0.660   1.9678   2.1396   0.2270
 8GG  SE   SE  SE    0   0.038  -2.0670   0.5854  -0.0699
 8GG  CS   C   CH3   0  -0.805  -3.5200  -0.1084   1.0347
 8GG  H1   H   HCH2  0   0.275  -1.1218  -1.6198   0.7324
 8GG  H2   H   HCH2  0   0.265  -0.2884  -0.2794   1.5235
 8GG  H3   H   HCH1  0   0.259   0.0234  -1.3290  -1.3350
 8GG  H4   H   HCH1  0   0.244   1.4756  -2.1370   0.8306
 8GG  H5   H   HOH1  0   0.453   3.2768  -2.1752  -0.7475
 8GG  H6   H   HCH1  0   0.229   1.9564   0.0937   1.5659
 8GG  H7   H   HOH1  0   0.462   4.2027   0.3486   1.1302
 8GG  H8   H   HCH1  0   0.206   2.7964   0.9517  -1.2220
 8GG  H9   H   HOH1  0   0.463   2.0172   2.8472  -0.4238
 8GG  H10  H   HCH3  0   0.262  -3.6840  -1.1672   0.8384
 8GG  H11  H   HCH3  0   0.262  -3.3115   0.0370   2.0937
 8GG  H12  H   HCH3  0   0.268  -4.4260   0.4406   0.7793

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
 8GG  O3'  C3'  single  1.405  0.020  1.405
 8GG  C3'  C2'  single  1.524  0.020  1.524
 8GG  C3'  C4'  single  1.526  0.020  1.526
 8GG  O2'  C2'  single  1.399  0.020  1.399
 8GG  C5'  C4'  single  1.520  0.020  1.520
 8GG  C5'  SE   single  1.960  0.020  1.960
 8GG  C2'  C1'  single  1.531  0.020  1.531
 8GG  C4'  O4'  single  1.423  0.020  1.423
 8GG  CS   SE   single  1.953  0.020  1.953
 8GG  C1'  O4'  single  1.414  0.020  1.414
 8GG  C1'  O1'  single  1.385  0.020  1.385
 8GG  C5'  H1   single  0.970  0.020  1.090
 8GG  C5'  H2   single  0.970  0.020  1.090
 8GG  C4'  H3   single  0.970  0.020  1.090
 8GG  C3'  H4   single  0.970  0.020  1.090
 8GG  O3'  H5   single  0.850  0.020  0.980
 8GG  C2'  H6   single  0.970  0.020  1.090
 8GG  O2'  H7   single  0.850  0.020  0.980
 8GG  C1'  H8   single  0.970  0.020  1.090
 8GG  O1'  H9   single  0.850  0.020  0.980
 8GG  CS   H10  single  0.970  0.020  1.090
 8GG  CS   H11  single  0.970  0.020  1.090
 8GG  CS   H12  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
 8GG  C1'  O4'  C4'  111.22  3.000
 8GG  H2   C5'  H1   107.80  3.000
 8GG  H2   C5'  SE   109.31  3.000
 8GG  H1   C5'  SE   108.60  3.000
 8GG  H2   C5'  C4'  112.41  3.000
 8GG  H1   C5'  C4'  109.28  3.000
 8GG  SE   C5'  C4'  109.36  3.000
 8GG  H3   C4'  C3'  110.49  3.000
 8GG  H3   C4'  C5'  108.72  3.000
 8GG  C3'  C4'  C5'  112.66  3.000
 8GG  H3   C4'  O4'  108.20  3.000
 8GG  C5'  C4'  O4'  111.42  3.000
 8GG  C3'  C4'  O4'  105.24  3.000
 8GG  H4   C3'  C2'  112.03  3.000
 8GG  H4   C3'  O3'  111.67  3.000
 8GG  C2'  C3'  O3'  111.87  3.000
 8GG  H4   C3'  C4'  111.88  3.000
 8GG  C2'  C3'  C4'  100.75  3.000
 8GG  O3'  C3'  C4'  108.10  3.000
 8GG  H5   O3'  C3'  108.53  3.000
 8GG  H6   C2'  C1'  108.17  3.000
 8GG  H6   C2'  O2'  111.31  3.000
 8GG  C1'  C2'  O2'  114.77  3.000
 8GG  H6   C2'  C3'  108.51  3.000
 8GG  C1'  C2'  C3'  102.67  3.000
 8GG  O2'  C2'  C3'  110.92  3.000
 8GG  H7   O2'  C2'  109.06  3.000
 8GG  H8   C1'  O1'  110.67  3.000
 8GG  H8   C1'  C2'  110.76  3.000
 8GG  O1'  C1'  C2'  109.68  3.000
 8GG  H8   C1'  O4'  108.28  3.000
 8GG  O1'  C1'  O4'  111.75  3.000
 8GG  C2'  C1'  O4'  105.59  3.000
 8GG  H9   O1'  C1'  109.52  3.000
 8GG  CS   SE   C5'   97.11  3.000
 8GG  H12  CS   H11  108.65  3.000
 8GG  H12  CS   H10  108.81  3.000
 8GG  H11  CS   H10  109.50  3.000
 8GG  H12  CS   SE   107.89  3.000
 8GG  H11  CS   SE   111.11  3.000
 8GG  H10  CS   SE   110.82  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
 8GG  Var_01  H10  CS   SE  C5'  -58.46  30.0  3
 8GG  Var_02  H1   C5'  SE  CS    37.07  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
 8GG  chir_01  C4'  C3'  C5'  O4'  negativ
 8GG  chir_02  C3'  O3'  C2'  C4'  negativ
 8GG  chir_03  C2'  O2'  C1'  C3'  negativ
 8GG  chir_04  C1'  O1'  O4'  C2'  positiv

