# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 21:08:26 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2S,3S,4R,5S,6R)-5-methoxy-2-methyl-6-methylselanyl-oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)[C@H](O)[C@H](C)O[C@@H]1[Se]C
#
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
 6YR  6YR  (2S,3S,4R,5S,6R)-5-methoxy-2-methyl-6-methylselanyl-oxane-3,4-diol  L-saccharide  29  13  .  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_6YR
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
 6YR  O4    O   OH1   0  -0.670   2.7058   0.6627   1.3160
 6YR  C4    C   CH1   0  -0.015   2.5163   0.7258  -0.0755
 6YR  C3    C   CH1   0   0.032   2.0672  -0.6516  -0.5639
 6YR  O3    O   OH1   0  -0.663   2.9332  -1.6808  -0.1664
 6YR  C2    C   CH1   0   0.045   0.6660  -0.9785  -0.0479
 6YR  O2    O   O2    0  -0.496   0.1727  -2.1519  -0.6406
 6YR  C7    C   CH3   0  -0.407   0.1501  -3.2862   0.1946
 6YR  C5    C   CH1   0   0.018   1.4627   1.7599  -0.4762
 6YR  C6    C   CH3   0  -0.701   1.7840   3.1614  -0.0027
 6YR  O5    O   O2    0  -0.473   0.2004   1.3948   0.0638
 6YR  C1    C   CH1   0  -0.138  -0.2642   0.1756  -0.4333
 6YR  SE    SE  SE    0   0.048  -2.0529  -0.1385   0.2851
 6YR  C8    C   CH3   0  -0.803  -2.8902   1.4255  -0.5288
 6YR  HO4   H   HOH1  0   0.456   3.1761   1.4517   1.6006
 6YR  H4    H   HCH1  0   0.229   3.4526   0.9872  -0.5928
 6YR  H3    H   HCH1  0   0.215   2.0046  -0.5910  -1.6619
 6YR  H5    H   HCH1  0   0.214   1.4065   1.7639  -1.5762
 6YR  HO3   H   HOH1  0   0.453   3.7794  -1.5558  -0.6080
 6YR  H2    H   HCH1  0   0.235   0.6960  -1.0685   1.0474
 6YR  H1    H   HCH1  0   0.246  -0.3508   0.2150  -1.5317
 6YR  H71C  H   HCH3  0   0.215   1.1523  -3.6137   0.4820
 6YR  H72C  H   HCH3  0   0.208  -0.4303  -3.1116   1.1073
 6YR  H73C  H   HCH3  0   0.231  -0.3295  -4.0906  -0.3622
 6YR  H61C  H   HCH3  0   0.238   2.7529   3.4739  -0.3930
 6YR  H62C  H   HCH3  0   0.249   1.0380   3.8711  -0.3594
 6YR  H63C  H   HCH3  0   0.230   1.8154   3.2265   1.0858
 6YR  H81C  H   HCH3  0   0.267  -2.4781   2.3460  -0.1217
 6YR  H82C  H   HCH3  0   0.264  -2.7558   1.4101  -1.6099
 6YR  H83C  H   HCH3  0   0.271  -3.9559   1.3858  -0.3083

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
 6YR  O4  C4    single  1.406  0.020  1.406
 6YR  C4  C3    single  1.529  0.020  1.529
 6YR  C4  C5    single  1.530  0.020  1.530
 6YR  C3  O3    single  1.403  0.020  1.403
 6YR  C3  C2    single  1.529  0.020  1.529
 6YR  C2  O2    single  1.404  0.020  1.404
 6YR  C2  C1    single  1.532  0.020  1.532
 6YR  O2  C7    single  1.409  0.020  1.409
 6YR  C5  C6    single  1.514  0.020  1.514
 6YR  C5  O5    single  1.421  0.020  1.421
 6YR  O5  C1    single  1.396  0.020  1.396
 6YR  C1  SE    single  1.953  0.020  1.953
 6YR  SE  C8    single  1.952  0.020  1.952
 6YR  O4  HO4   single  0.850  0.020  0.980
 6YR  C4  H4    single  0.970  0.020  1.090
 6YR  C3  H3    single  0.970  0.020  1.090
 6YR  C5  H5    single  0.970  0.020  1.090
 6YR  O3  HO3   single  0.850  0.020  0.980
 6YR  C2  H2    single  0.970  0.020  1.090
 6YR  C1  H1    single  0.970  0.020  1.090
 6YR  C7  H71C  single  0.970  0.020  1.090
 6YR  C7  H72C  single  0.970  0.020  1.090
 6YR  C7  H73C  single  0.970  0.020  1.090
 6YR  C6  H61C  single  0.970  0.020  1.090
 6YR  C6  H62C  single  0.970  0.020  1.090
 6YR  C6  H63C  single  0.970  0.020  1.090
 6YR  C8  H81C  single  0.970  0.020  1.090
 6YR  C8  H82C  single  0.970  0.020  1.090
 6YR  C8  H83C  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
 6YR  HO4   O4  C4    108.79  3.000
 6YR  H4    C4  C5    107.59  3.000
 6YR  H4    C4  C3    108.28  3.000
 6YR  C5    C4  C3    108.85  3.000
 6YR  H4    C4  O4    111.16  3.000
 6YR  C5    C4  O4    112.49  3.000
 6YR  C3    C4  O4    108.39  3.000
 6YR  H3    C3  C2    107.23  3.000
 6YR  H3    C3  O3    110.98  3.000
 6YR  C2    C3  O3    108.26  3.000
 6YR  H3    C3  C4    106.59  3.000
 6YR  C2    C3  C4    110.74  3.000
 6YR  O3    C3  C4    112.90  3.000
 6YR  HO3   O3  C3    108.51  3.000
 6YR  H2    C2  C1    109.20  3.000
 6YR  H2    C2  O2    111.21  3.000
 6YR  C1    C2  O2    108.06  3.000
 6YR  H2    C2  C3    109.20  3.000
 6YR  C1    C2  C3    108.09  3.000
 6YR  O2    C2  C3    110.99  3.000
 6YR  C7    O2  C2    115.35  3.000
 6YR  H73C  C7  H72C  108.06  3.000
 6YR  H73C  C7  H71C  108.47  3.000
 6YR  H72C  C7  H71C  108.34  3.000
 6YR  H73C  C7  O2    107.37  3.000
 6YR  H72C  C7  O2    111.97  3.000
 6YR  H71C  C7  O2    112.49  3.000
 6YR  H5    C5  O5    109.59  3.000
 6YR  H5    C5  C6    108.65  3.000
 6YR  O5    C5  C6    107.91  3.000
 6YR  H5    C5  C4    107.41  3.000
 6YR  O5    C5  C4    109.80  3.000
 6YR  C6    C5  C4    113.44  3.000
 6YR  H63C  C6  H62C  107.91  3.000
 6YR  H63C  C6  H61C  108.33  3.000
 6YR  H62C  C6  H61C  107.73  3.000
 6YR  H63C  C6  C5    111.93  3.000
 6YR  H62C  C6  C5    110.81  3.000
 6YR  H61C  C6  C5    110.00  3.000
 6YR  C1    O5  C5    112.62  3.000
 6YR  H1    C1  SE    107.47  3.000
 6YR  H1    C1  O5    110.46  3.000
 6YR  SE    C1  O5    108.31  3.000
 6YR  H1    C1  C2    108.99  3.000
 6YR  SE    C1  C2    110.03  3.000
 6YR  O5    C1  C2    111.49  3.000
 6YR  C8    SE  C1     96.35  3.000
 6YR  H83C  C8  H82C  108.73  3.000
 6YR  H83C  C8  H81C  109.01  3.000
 6YR  H82C  C8  H81C  109.67  3.000
 6YR  H83C  C8  SE    107.83  3.000
 6YR  H82C  C8  SE    110.46  3.000
 6YR  H81C  C8  SE    111.07  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
 6YR  Var_01  H71C  C7  O2  C2  -65.48  30.0  3
 6YR  Var_02  H81C  C8  SE  C1  -65.46  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
 6YR  chir_01  C4  O4  C3  C5  negativ
 6YR  chir_02  C3  O3  C2  C4  negativ
 6YR  chir_03  C2  O2  C3  C1  negativ
 6YR  chir_04  C5  O5  C4  C6  positiv
 6YR  chir_05  C1  SE  O5  C2  negativ

