# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:03:19 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-deoxy-2-fluoro-alpha-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](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
 GAF  GAF  2-deoxy-2-fluoro-alpha-D-galactopyranose  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_GAF
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
 GAF  C1    C  CH1   0   0.195   1.4431  -0.4761  -0.3551
 GAF  C2    C  CH1   0   0.163   0.3835  -0.4765  -1.4526
 GAF  F2    F  F     0  -0.376   0.9981  -0.2590  -2.6833
 GAF  C3    C  CH1   0  -0.036  -0.6695   0.5910  -1.2105
 GAF  O3    O  OH1   0  -0.673  -1.7203   0.5241  -2.1431
 GAF  C4    C  CH1   0  -0.017  -1.2698   0.3863   0.1813
 GAF  O4    O  OH1   0  -0.671  -1.9885  -0.8202   0.2666
 GAF  C5    C  CH1   0  -0.014  -0.1467   0.3616   1.2081
 GAF  O5    O  O2    0  -0.501   0.8171  -0.6320   0.8875
 GAF  C6    C  CH2   0  -0.157  -0.6490   0.0841   2.6093
 GAF  O6    O  OH1   0  -0.671   0.4054   0.3171   3.5137
 GAF  O1    O  OH1   0  -0.664   2.1735   0.7006  -0.4584
 GAF  H1C1  H  HCH1  0   0.244   2.0892  -1.3551  -0.4577
 GAF  H2    H  HCH1  0   0.227  -0.0851  -1.4630  -1.4896
 GAF  H3    H  HCH1  0   0.232  -0.1904   1.5796  -1.2263
 GAF  HA    H  HOH1  0   0.460  -1.3761   0.7123  -3.0218
 GAF  H4    H  HCH1  0   0.239  -1.9139   1.2492   0.4039
 GAF  HB    H  HOH1  0   0.455  -2.6914  -0.8014  -0.3910
 GAF  H5    H  HCH1  0   0.235   0.3152   1.3577   1.2058
 GAF  H6C1  H  HCH2  0   0.207  -1.0212  -0.9443   2.6766
 GAF  H6C2  H  HCH2  0   0.202  -1.5008   0.7493   2.8018
 GAF  H6    H  HOH1  0   0.456   0.0995   0.0816   4.3940
 GAF  H1    H  HOH1  0   0.466   2.9687   0.6255   0.0802

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
 GAF  C1  C2    single  1.526  0.020  1.526
 GAF  C1  O5    single  1.400  0.020  1.400
 GAF  C1  O1    single  1.389  0.020  1.389
 GAF  C1  H1C1  single  0.970  0.020  1.090
 GAF  C2  F2    single  1.393  0.020  1.393
 GAF  C2  C3    single  1.519  0.020  1.519
 GAF  C2  H2    single  0.970  0.020  1.090
 GAF  C3  O3    single  1.406  0.020  1.406
 GAF  C3  C4    single  1.529  0.020  1.529
 GAF  C3  H3    single  0.970  0.020  1.090
 GAF  O3  HA    single  0.850  0.020  0.980
 GAF  C4  O4    single  1.407  0.020  1.407
 GAF  C4  C5    single  1.522  0.020  1.522
 GAF  C4  H4    single  0.970  0.020  1.090
 GAF  O4  HB    single  0.850  0.020  0.980
 GAF  C5  O5    single  1.421  0.020  1.421
 GAF  C5  C6    single  1.514  0.020  1.514
 GAF  C5  H5    single  0.970  0.020  1.090
 GAF  C6  O6    single  1.408  0.020  1.408
 GAF  C6  H6C1  single  0.970  0.020  1.090
 GAF  C6  H6C2  single  0.970  0.020  1.090
 GAF  O6  H6    single  0.850  0.020  0.980
 GAF  O1  H1    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
 GAF  H1C1  C1  O1    111.26  3.000
 GAF  H1C1  C1  O5    104.92  3.000
 GAF  O1    C1  O5    113.30  3.000
 GAF  H1C1  C1  C2    110.00  3.000
 GAF  O1    C1  C2    108.18  3.000
 GAF  O5    C1  C2    109.14  3.000
 GAF  H2    C2  C3    110.03  3.000
 GAF  H2    C2  F2    107.47  3.000
 GAF  C3    C2  F2    109.70  3.000
 GAF  H2    C2  C1    108.81  3.000
 GAF  C3    C2  C1    111.51  3.000
 GAF  F2    C2  C1    109.22  3.000
 GAF  H3    C3  C4    107.74  3.000
 GAF  H3    C3  O3    111.04  3.000
 GAF  C4    C3  O3    107.69  3.000
 GAF  H3    C3  C2    109.13  3.000
 GAF  C4    C3  C2    108.85  3.000
 GAF  O3    C3  C2    112.26  3.000
 GAF  HA    O3  C3    109.21  3.000
 GAF  H4    C4  C5    107.96  3.000
 GAF  H4    C4  O4    111.19  3.000
 GAF  C5    C4  O4    108.80  3.000
 GAF  H4    C4  C3    108.00  3.000
 GAF  C5    C4  C3    109.06  3.000
 GAF  O4    C4  C3    111.74  3.000
 GAF  HB    O4  C4    108.35  3.000
 GAF  H5    C5  C6    107.92  3.000
 GAF  H5    C5  O5    110.40  3.000
 GAF  C6    C5  O5    107.80  3.000
 GAF  H5    C5  C4    107.11  3.000
 GAF  C6    C5  C4    112.49  3.000
 GAF  O5    C5  C4    111.08  3.000
 GAF  C5    O5  C1    115.19  3.000
 GAF  H6C2  C6  H6C1  107.12  3.000
 GAF  H6C2  C6  O6    111.59  3.000
 GAF  H6C1  C6  O6    111.72  3.000
 GAF  H6C2  C6  C5    107.97  3.000
 GAF  H6C1  C6  C5    109.96  3.000
 GAF  O6    C6  C5    108.40  3.000
 GAF  H6    O6  C6    108.02  3.000
 GAF  H1    O1  C1    109.06  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
 GAF  chir_01  C1  C2  O5  O1  positiv
 GAF  chir_02  C2  F2  C3  C1  positiv
 GAF  chir_03  C3  O3  C2  C4  positiv
 GAF  chir_04  C4  O4  C3  C5  positiv
 GAF  chir_05  C5  O5  C4  C6  negativ

