# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:59:46 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: 2-deoxy-2,2-difluoro-alpha-D-arabino-hexopyranosyl fluoride
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](F)C(F)(F)[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
 TW7  TW7  '2-deoxy-2,2-difluoro-alpha-D-arabino-hexopyranosyl fluoride'  D-saccharide  22  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_TW7
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
 TW7  C1   C  CH1   0   0.338  25.1731  -30.1562  281.7556
 TW7  C2   C  CT    0   0.618  23.9539  -30.0693  280.8397
 TW7  F1   F  F     0  -0.192  25.0841  -31.3534  282.4441
 TW7  F21  F  F     0  -0.309  23.9130  -28.7969  280.3590
 TW7  F22  F  F     0  -0.415  22.8207  -30.2386  281.5712
 TW7  O4   O  OH1   0  -0.677  25.4394  -31.9366  278.0156
 TW7  C3   C  CH1   0  -0.018  23.9983  -31.0588  279.6820
 TW7  C4   C  CH1   0  -0.047  25.3395  -30.9128  278.9700
 TW7  C5   C  CH1   0   0.088  26.4800  -31.0436  279.9900
 TW7  C6   C  CH2   0  -0.262  27.8530  -30.8466  279.3890
 TW7  O3   O  OH1   0  -0.607  22.9658  -30.8150  278.7743
 TW7  O5   O  O2    0  -0.555  26.3319  -30.0880  281.0456
 TW7  O6   O  OH1   0  -0.710  27.9185  -29.5968  278.7493
 TW7  H1   H  HCH1  0   0.269  25.1756  -29.3447  282.4871
 TW7  H3   H  HCH1  0   0.169  23.9408  -32.0721  280.1047
 TW7  H4   H  HCH1  0   0.228  25.3806  -29.9234  278.4998
 TW7  H5   H  HCH1  0   0.234  26.4597  -32.0604  280.4025
 TW7  H61  H  HCH2  0   0.226  28.0338  -31.6772  278.6970
 TW7  H62  H  HCH2  0   0.270  28.5973  -30.9390  280.1904
 TW7  HO3  H  HOH1  0   0.475  22.1657  -31.2533  279.0783
 TW7  HO6  H  HOH1  0   0.447  28.7438  -29.5519  278.2594
 TW7  HO4  H  HOH1  0   0.432  25.9156  -31.6032  277.2509

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
 TW7  O4   C4   single  1.403  0.020  1.403
 TW7  O3   C3   single  1.396  0.020  1.396
 TW7  C4   C3   single  1.525  0.020  1.525
 TW7  C4   C5   single  1.536  0.020  1.536
 TW7  O6   C6   single  1.406  0.020  1.406
 TW7  C6   C5   single  1.512  0.020  1.512
 TW7  C3   C2   single  1.524  0.020  1.524
 TW7  C5   O5   single  1.432  0.020  1.432
 TW7  F21  C2   single  1.361  0.020  1.361
 TW7  C2   F22  single  1.359  0.020  1.359
 TW7  C2   C1   single  1.527  0.020  1.527
 TW7  O5   C1   single  1.361  0.020  1.361
 TW7  C1   F1   single  1.384  0.020  1.384
 TW7  C1   H1   single  0.970  0.020  1.090
 TW7  C3   H3   single  0.970  0.020  1.090
 TW7  C4   H4   single  0.970  0.020  1.090
 TW7  C5   H5   single  0.970  0.020  1.090
 TW7  C6   H61  single  0.970  0.020  1.090
 TW7  C6   H62  single  0.970  0.020  1.090
 TW7  O3   HO3  single  0.850  0.020  0.980
 TW7  O6   HO6  single  0.850  0.020  0.980
 TW7  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
 TW7  H1   C1  O5   108.07  3.000
 TW7  H1   C1  F1   108.03  3.000
 TW7  O5   C1  F1   110.96  3.000
 TW7  H1   C1  C2   111.17  3.000
 TW7  F1   C1  C2   107.23  3.000
 TW7  O5   C1  C2   111.35  3.000
 TW7  C3   C2  F22  110.63  3.000
 TW7  F22  C2  F21  106.35  3.000
 TW7  C3   C2  F21  109.86  3.000
 TW7  F22  C2  C1   109.61  3.000
 TW7  F21  C2  C1   106.80  3.000
 TW7  C3   C2  C1   113.30  3.000
 TW7  HO4  O4  C4   108.87  3.000
 TW7  H3   C3  O3   111.85  3.000
 TW7  H3   C3  C4   108.28  3.000
 TW7  O3   C3  C4   109.27  3.000
 TW7  H3   C3  C2   107.75  3.000
 TW7  C4   C3  C2   108.55  3.000
 TW7  O3   C3  C2   111.04  3.000
 TW7  H4   C4  C5   109.50  3.000
 TW7  H4   C4  C3   108.63  3.000
 TW7  C5   C4  C3   109.56  3.000
 TW7  H4   C4  O4   111.35  3.000
 TW7  C5   C4  O4   109.68  3.000
 TW7  C3   C4  O4   108.07  3.000
 TW7  H5   C5  O5   109.84  3.000
 TW7  H5   C5  C6   106.68  3.000
 TW7  O5   C5  C6   107.46  3.000
 TW7  H5   C5  C4   108.35  3.000
 TW7  O5   C5  C4   110.86  3.000
 TW7  C6   C5  C4   113.54  3.000
 TW7  H62  C6  H61  106.58  3.000
 TW7  H62  C6  O6   112.06  3.000
 TW7  H61  C6  O6   112.26  3.000
 TW7  H62  C6  C5   108.34  3.000
 TW7  H61  C6  C5   107.58  3.000
 TW7  O6   C6  C5   109.83  3.000
 TW7  HO3  O3  C3   109.28  3.000
 TW7  C5   O5  C1   116.06  3.000
 TW7  HO6  O6  C6   108.28  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
 TW7  chir_01  C1  C2  O5  F1  positiv
 TW7  chir_02  C3  O3  C2  C4  positiv
 TW7  chir_03  C4  O4  C5  C3  positiv
 TW7  chir_04  C5  O5  C6  C4  positiv

