# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:50:02 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-deoxy-3-fluoro-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](F)[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
 TUP  TUP  3-deoxy-3-fluoro-alpha-D-glucopyranose  D-saccharide  23  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 GRAND
;

data_comp_TUP
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
 TUP  F3   F  F     0  -0.376   8.6454  13.3817  12.3980
 TUP  C3   C  CH1   0   0.172   9.8440  13.1916  11.7137
 TUP  C2   C  CH1   0  -0.034  10.2943  11.7566  11.9075
 TUP  O2   O  OH1   0  -0.663   9.3342  10.9075  11.3431
 TUP  C1   C  CH1   0   0.211  11.6863  11.5592  11.2940
 TUP  O1   O  OH1   0  -0.660  11.5747  11.6614   9.9141
 TUP  O5   O  O2    0  -0.502  12.5861  12.4864  11.8392
 TUP  C5   C  CH1   0  -0.014  12.2416  13.8442  11.6178
 TUP  C6   C  CH2   0  -0.199  13.3649  14.7069  12.1494
 TUP  O6   O  OH1   0  -0.672  13.4487  14.5801  13.5486
 TUP  C4   C  CH1   0  -0.026  10.8807  14.1538  12.2586
 TUP  O4   O  OH1   0  -0.671  10.4708  15.4650  11.9593
 TUP  H3   H  HCH1  0   0.221   9.6494  13.4007  10.6565
 TUP  H2   H  HCH1  0   0.234  10.4009  11.5800  12.9876
 TUP  HO2  H  HOH1  0   0.457   9.5210  10.0054  11.6207
 TUP  H1   H  HCH1  0   0.239  12.0811  10.5796  11.5906
 TUP  HO1  H  HOH1  0   0.464  12.3919  11.3510   9.5092
 TUP  H5   H  HCH1  0   0.232  12.1707  14.0548  10.5421
 TUP  H61  H  HCH2  0   0.222  14.2965  14.4028  11.6546
 TUP  H62  H  HCH2  0   0.210  13.1742  15.7418  11.8410
 TUP  HO6  H  HOH1  0   0.460  14.1089  15.2024  13.8658
 TUP  H4   H  HCH1  0   0.236  10.9536  13.9960  13.3423
 TUP  HO4  H  HOH1  0   0.460  10.8234  16.0584  12.6281

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
 TUP  F3  C3   single  1.393  0.020  1.393
 TUP  C3  C2   single  1.516  0.020  1.516
 TUP  C3  C4   single  1.516  0.020  1.516
 TUP  C2  C1   single  1.534  0.020  1.534
 TUP  C2  O2   single  1.401  0.020  1.401
 TUP  C1  O1   single  1.388  0.020  1.388
 TUP  C1  O5   single  1.402  0.020  1.402
 TUP  O5  C5   single  1.418  0.020  1.418
 TUP  C5  C4   single  1.536  0.020  1.536
 TUP  C5  C6   single  1.513  0.020  1.513
 TUP  C6  O6   single  1.407  0.020  1.407
 TUP  C4  O4   single  1.406  0.020  1.406
 TUP  C3  H3   single  0.970  0.020  1.090
 TUP  C2  H2   single  0.970  0.020  1.090
 TUP  O2  HO2  single  0.850  0.020  0.980
 TUP  C1  H1   single  0.970  0.020  1.090
 TUP  O1  HO1  single  0.850  0.020  0.980
 TUP  C5  H5   single  0.970  0.020  1.090
 TUP  C6  H61  single  0.970  0.020  1.090
 TUP  C6  H62  single  0.970  0.020  1.090
 TUP  O6  HO6  single  0.850  0.020  0.980
 TUP  C4  H4   single  0.970  0.020  1.090
 TUP  O4  HO4  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
 TUP  H3   C3  C4   110.33  3.000
 TUP  H3   C3  C2   110.90  3.000
 TUP  C4   C3  C2   110.59  3.000
 TUP  H3   C3  F3   107.17  3.000
 TUP  C4   C3  F3   108.98  3.000
 TUP  C2   C3  F3   108.77  3.000
 TUP  H2   C2  C1   106.51  3.000
 TUP  H2   C2  O2   111.41  3.000
 TUP  C1   C2  O2   112.51  3.000
 TUP  H2   C2  C3   107.84  3.000
 TUP  O2   C2  C3   108.58  3.000
 TUP  C1   C2  C3   109.88  3.000
 TUP  HO2  O2  C2   108.60  3.000
 TUP  H1   C1  O5   104.73  3.000
 TUP  H1   C1  O1   111.31  3.000
 TUP  O5   C1  O1   112.91  3.000
 TUP  H1   C1  C2   109.47  3.000
 TUP  O5   C1  C2   109.98  3.000
 TUP  O1   C1  C2   108.37  3.000
 TUP  HO1  O1  C1   109.02  3.000
 TUP  C5   O5  C1   114.61  3.000
 TUP  H5   C5  C4   108.23  3.000
 TUP  H5   C5  C6   106.42  3.000
 TUP  C4   C5  C6   113.36  3.000
 TUP  H5   C5  O5   110.62  3.000
 TUP  C6   C5  O5   108.10  3.000
 TUP  C4   C5  O5   110.07  3.000
 TUP  H62  C6  H61  106.40  3.000
 TUP  H62  C6  O6   112.02  3.000
 TUP  H61  C6  O6   111.88  3.000
 TUP  H62  C6  C5   108.07  3.000
 TUP  H61  C6  C5   108.29  3.000
 TUP  O6   C6  C5   110.01  3.000
 TUP  HO6  O6  C6   108.10  3.000
 TUP  H4   C4  O4   111.33  3.000
 TUP  H4   C4  C5   108.92  3.000
 TUP  O4   C4  C5   110.95  3.000
 TUP  H4   C4  C3   108.00  3.000
 TUP  O4   C4  C3   108.42  3.000
 TUP  C5   C4  C3   109.16  3.000
 TUP  HO4  O4  C4   108.70  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
 TUP  chir_01  C3  F3  C2  C4  positiv
 TUP  chir_02  C2  O2  C1  C3  negativ
 TUP  chir_03  C1  O1  O5  C2  negativ
 TUP  chir_04  C5  O5  C6  C4  positiv
 TUP  chir_05  C4  O4  C5  C3  positiv

