# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 07:09:57 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{R})-2-methyl-6-methylselanyl-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se][C@H]1O[C@@H](C)[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
 TFU  TFU  (2~{S},3~{S},4~{R},5~{S},6~{R})-2-methyl-6-methylselanyl-oxane-3,4,5-triol  L-saccharide  26  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TFU
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
 TFU  C1   C   CH1   0  -0.144  -0.3307  -0.0785   0.3606
 TFU  C2   C   CH1   0  -0.000   0.5190   1.1336  -0.0404
 TFU  O2   O   OH1   0  -0.667   0.0281   2.3200   0.5354
 TFU  C3   C   CH1   0   0.032   1.9356   0.9328   0.5009
 TFU  O3   O   OH1   0  -0.667   2.8045   1.9530   0.0878
 TFU  C4   C   CH1   0   0.001   2.5003  -0.4116   0.0692
 TFU  O4   O   OH1   0  -0.671   2.6960  -0.3895  -1.3234
 TFU  C5   C   CH1   0   0.018   1.5246  -1.5087   0.5025
 TFU  C6   C   CH3   0  -0.700   1.9686  -2.8978   0.0976
 TFU  O5   O   O2    0  -0.474   0.2465  -1.2762  -0.0724
 TFU  SE1  SE  SE    0   0.040  -2.1169   0.0486  -0.4176
 TFU  C7   C   CH3   0  -0.801  -2.9474  -1.3271   0.6899
 TFU  H1   H   HCH1  0   0.244  -0.4509  -0.0773   1.4567
 TFU  H2   H   HCH1  0   0.235   0.5650   1.2067  -1.1356
 TFU  HO2  H   HOH1  0   0.460  -0.6781   2.6759  -0.0119
 TFU  H3   H   HCH1  0   0.214   1.8629   0.9013   1.6004
 TFU  HO3  H   HOH1  0   0.450   2.4535   2.7895   0.4108
 TFU  H4   H   HCH1  0   0.234   3.4485  -0.5754   0.6018
 TFU  HO4  H   HOH1  0   0.457   3.2654  -1.1252  -1.5664
 TFU  H5   H   HCH1  0   0.214   1.4485  -1.4665   1.6004
 TFU  H63  H   HCH3  0   0.230   2.0281  -3.0049  -0.9863
 TFU  H62  H   HCH3  0   0.238   2.9510  -3.1141   0.5179
 TFU  H61  H   HCH3  0   0.249   1.2748  -3.6499   0.4721
 TFU  H72  H   HCH3  0   0.267  -2.5313  -2.3064   0.4637
 TFU  H7   H   HCH3  0   0.267  -2.8069  -1.1019   1.7462
 TFU  H71  H   HCH3  0   0.274  -4.0141  -1.3364   0.4706

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
 TFU  C6  C5   single  1.514  0.020  1.514
 TFU  C5  O5   single  1.421  0.020  1.421
 TFU  C5  C4   single  1.531  0.020  1.531
 TFU  O5  C1   single  1.398  0.020  1.398
 TFU  C7  SE1  single  1.952  0.020  1.952
 TFU  C1  SE1  single  1.952  0.020  1.952
 TFU  C1  C2   single  1.534  0.020  1.534
 TFU  C4  O4   single  1.406  0.020  1.406
 TFU  C4  C3   single  1.521  0.020  1.521
 TFU  C3  C2   single  1.530  0.020  1.530
 TFU  C3  O3   single  1.402  0.020  1.402
 TFU  C2  O2   single  1.407  0.020  1.407
 TFU  C1  H1   single  0.970  0.020  1.090
 TFU  C2  H2   single  0.970  0.020  1.090
 TFU  O2  HO2  single  0.850  0.020  0.980
 TFU  C3  H3   single  0.970  0.020  1.090
 TFU  O3  HO3  single  0.850  0.020  0.980
 TFU  C4  H4   single  0.970  0.020  1.090
 TFU  O4  HO4  single  0.850  0.020  0.980
 TFU  C5  H5   single  0.970  0.020  1.090
 TFU  C6  H63  single  0.970  0.020  1.090
 TFU  C6  H62  single  0.970  0.020  1.090
 TFU  C6  H61  single  0.970  0.020  1.090
 TFU  C7  H72  single  0.970  0.020  1.090
 TFU  C7  H7   single  0.970  0.020  1.090
 TFU  C7  H71  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
 TFU  H1   C1   SE1  107.24  3.000
 TFU  H1   C1   O5   110.72  3.000
 TFU  SE1  C1   O5   108.06  3.000
 TFU  H1   C1   C2   108.63  3.000
 TFU  SE1  C1   C2   110.56  3.000
 TFU  O5   C1   C2   111.55  3.000
 TFU  H2   C2   C3   108.83  3.000
 TFU  H2   C2   O2   111.49  3.000
 TFU  C3   C2   O2   106.79  3.000
 TFU  H2   C2   C1   109.66  3.000
 TFU  O2   C2   C1   111.48  3.000
 TFU  C3   C2   C1   108.47  3.000
 TFU  HO2  O2   C2   109.59  3.000
 TFU  H3   C3   C4   106.40  3.000
 TFU  H3   C3   O3   110.82  3.000
 TFU  C4   C3   O3   109.23  3.000
 TFU  H3   C3   C2   107.20  3.000
 TFU  O3   C3   C2   111.97  3.000
 TFU  C4   C3   C2   111.07  3.000
 TFU  HO3  O3   C3   107.90  3.000
 TFU  H4   C4   C5   107.80  3.000
 TFU  H4   C4   O4   111.22  3.000
 TFU  C5   C4   O4   112.35  3.000
 TFU  H4   C4   C3   108.32  3.000
 TFU  O4   C4   C3   108.60  3.000
 TFU  C5   C4   C3   108.45  3.000
 TFU  HO4  O4   C4   108.71  3.000
 TFU  H5   C5   O5   109.57  3.000
 TFU  H5   C5   C6   108.79  3.000
 TFU  O5   C5   C6   107.81  3.000
 TFU  H5   C5   C4   107.38  3.000
 TFU  O5   C5   C4   109.97  3.000
 TFU  C6   C5   C4   113.27  3.000
 TFU  H61  C6   H62  107.71  3.000
 TFU  H61  C6   H63  107.97  3.000
 TFU  H62  C6   H63  108.33  3.000
 TFU  H61  C6   C5   110.78  3.000
 TFU  H62  C6   C5   110.08  3.000
 TFU  H63  C6   C5   111.83  3.000
 TFU  C5   O5   C1   112.72  3.000
 TFU  C7   SE1  C1    96.73  3.000
 TFU  H71  C7   H7   108.87  3.000
 TFU  H71  C7   H72  108.97  3.000
 TFU  H7   C7   H72  109.78  3.000
 TFU  H71  C7   SE1  107.97  3.000
 TFU  H7   C7   SE1  110.47  3.000
 TFU  H72  C7   SE1  110.72  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
 TFU  Var_01  H72  C7  SE1  C1  -66.72  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
 TFU  chir_01  C1  O5  SE1  C2  positiv
 TFU  chir_02  C2  O2  C1   C3  positiv
 TFU  chir_03  C3  O3  C2   C4  negativ
 TFU  chir_04  C4  O4  C5   C3  positiv
 TFU  chir_05  C5  O5  C4   C6  positiv

