# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:29:53 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: alpha-D-threo-hexo-2,5-diulo-5,1-pyranosyl fluoride
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]1(F)OCC(=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
 AFR  AFR  'alpha-D-threo-hexo-2,5-diulo-5,1-pyranosyl fluoride'  D-saccharide  21  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 (reasonable std)
;

data_comp_AFR
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
 AFR  F1   F  F     0  -0.327   1.0108  -0.2334  -1.7142
 AFR  C5   C  CT    0   0.673   1.0142  -0.2422  -0.3218
 AFR  C4   C  CH1   0  -0.050   0.1349   0.9133   0.1578
 AFR  O4   O  OH1   0  -0.697   0.6561   2.1093  -0.3519
 AFR  C6   C  CH2   0  -0.262   2.4689  -0.1259   0.1041
 AFR  O6   O  OH1   0  -0.690   2.5214  -0.0743   1.5044
 AFR  O5   O  O2    0  -0.550   0.5346  -1.4531   0.1189
 AFR  C1   C  CH2   0  -0.282  -0.7938  -1.7979  -0.2255
 AFR  C2   C  C     0   0.359  -1.7774  -0.6903   0.0716
 AFR  O2   O  O     0  -0.293  -2.8821  -0.8985   0.5065
 AFR  C3   C  CH1   0  -0.119  -1.3106   0.7018  -0.2919
 AFR  O3   O  OH1   0  -0.656  -2.1008   1.6988   0.2761
 AFR  H4   H  HCH1  0   0.286   0.1562   0.9041   1.2548
 AFR  H61  H  HCH2  0   0.238   3.0112  -0.9912  -0.2989
 AFR  H62  H  HCH2  0   0.256   2.8892   0.7700  -0.3610
 AFR  HO4  H  HOH1  0   0.447   0.4028   2.8256   0.2343
 AFR  H3   H  HCH1  0   0.251  -1.3389   0.7414  -1.3955
 AFR  H6   H  HOH1  0   0.459   3.3908   0.2412   1.7574
 AFR  H11  H  HCH2  0   0.202  -0.8796  -2.0632  -1.2868
 AFR  H12  H  HCH2  0   0.305  -1.0519  -2.6837   0.3526
 AFR  HO3  H  HOH1  0   0.451  -3.0260   1.4687   0.1448

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
 AFR  F1  C5   single  1.392  0.020  1.392
 AFR  C5  C4   single  1.529  0.020  1.529
 AFR  C5  C6   single  1.520  0.020  1.520
 AFR  C5  O5   single  1.375  0.020  1.375
 AFR  C4  O4   single  1.401  0.020  1.401
 AFR  C4  C3   single  1.529  0.020  1.529
 AFR  C6  O6   single  1.402  0.020  1.402
 AFR  O5  C1   single  1.415  0.020  1.415
 AFR  C1  C2   single  1.511  0.020  1.511
 AFR  C2  O2   double  1.205  0.020  1.205
 AFR  C2  C3   single  1.513  0.020  1.513
 AFR  C3  O3   single  1.393  0.020  1.393
 AFR  C4  H4   single  0.970  0.020  1.090
 AFR  C6  H61  single  0.970  0.020  1.090
 AFR  C6  H62  single  0.970  0.020  1.090
 AFR  O4  HO4  single  0.850  0.020  0.980
 AFR  C3  H3   single  0.970  0.020  1.090
 AFR  O6  H6   single  0.850  0.020  0.980
 AFR  C1  H11  single  0.970  0.020  1.090
 AFR  C1  H12  single  0.970  0.020  1.090
 AFR  O3  HO3  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
 AFR  O5   C5  C6   108.14  3.000
 AFR  O5   C5  C4   111.37  3.000
 AFR  C6   C5  C4   113.87  3.000
 AFR  O5   C5  F1   108.98  3.000
 AFR  C6   C5  F1   106.38  3.000
 AFR  C4   C5  F1   107.91  3.000
 AFR  H4   C4  C3   108.14  3.000
 AFR  H4   C4  O4   111.33  3.000
 AFR  C3   C4  O4   111.28  3.000
 AFR  H4   C4  C5   107.22  3.000
 AFR  C3   C4  C5   110.30  3.000
 AFR  O4   C4  C5   108.49  3.000
 AFR  HO4  O4  C4   108.48  3.000
 AFR  H62  C6  H61  107.45  3.000
 AFR  H62  C6  O6   112.35  3.000
 AFR  H61  C6  O6   112.15  3.000
 AFR  H62  C6  C5   108.14  3.000
 AFR  H61  C6  C5   108.03  3.000
 AFR  O6   C6  C5   108.56  3.000
 AFR  H6   O6  C6   108.03  3.000
 AFR  C1   O5  C5   117.65  3.000
 AFR  H12  C1  H11  107.36  3.000
 AFR  H12  C1  C2   109.73  3.000
 AFR  H11  C1  C2   108.46  3.000
 AFR  H12  C1  O5   106.95  3.000
 AFR  H11  C1  O5   111.58  3.000
 AFR  C2   C1  O5   112.62  3.000
 AFR  C3   C2  O2   121.90  3.000
 AFR  C3   C2  C1   115.25  3.000
 AFR  O2   C2  C1   122.75  3.000
 AFR  H3   C3  O3   111.54  3.000
 AFR  H3   C3  C2   105.38  3.000
 AFR  O3   C3  C2   112.68  3.000
 AFR  H3   C3  C4   108.25  3.000
 AFR  O3   C3  C4   108.50  3.000
 AFR  C2   C3  C4   110.39  3.000
 AFR  HO3  O3  C3   108.57  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
 AFR  Var_01  C2  C1  O5  C5  -49.22  30.0  1
 AFR  Var_02  C3  C2  C1  O5   42.09  30.0  1

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
 AFR  chir_01  C5  C4  C6  O5  negativ
 AFR  chir_02  C4  O4  C5  C3  positiv
 AFR  chir_03  C3  O3  C4  C2  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 AFR  plan-1  C1  0.020
 AFR  plan-1  C2  0.020
 AFR  plan-1  O2  0.020
 AFR  plan-1  C3  0.020

