# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:22:49 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H]1O[C@@](O)([C@H](F)[C@H](O)[C@H]1O)C(O)=O
#
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
 FKD  FKD  '3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid'  L-saccharide  33  19  .  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_FKD
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
 FKD  O2   O  OH1    0  -0.678   1.4230   1.0081   1.7340
 FKD  C1   C  C      0   0.375   1.8095   2.2029  -0.3660
 FKD  F1   F  F      0  -0.380   2.4874  -0.2975  -1.3749
 FKD  C2   C  CT     0   0.306   1.3804   0.8786   0.3418
 FKD  C3   C  CH1    0   0.152   2.3638  -0.2424   0.0123
 FKD  C4   C  CH1    0  -0.033   1.8624  -1.5847   0.5157
 FKD  O4   O  OH1    0  -0.675   2.6860  -2.6491   0.0961
 FKD  C5   C  CH1    0   0.037   0.4522  -1.8570   0.0086
 FKD  O5   O  OH1    0  -0.677  -0.0985  -3.0025   0.6139
 FKD  C6   C  CH1    0   0.007  -0.4507  -0.6757   0.3641
 FKD  O6   O  O2     0  -0.513   0.1007   0.5383  -0.1064
 FKD  C7   C  CH1    0  -0.033  -1.8248  -0.7726  -0.3005
 FKD  O7   O  OH1    0  -0.670  -1.7051  -0.6721  -1.7011
 FKD  C8   C  CH1    0  -0.017  -2.8111   0.2718   0.2559
 FKD  O8   O  OH1    0  -0.661  -2.9194   0.1713   1.6584
 FKD  C9   C  CH2    0  -0.160  -4.1677   0.1452  -0.4199
 FKD  O9   O  OH1    0  -0.672  -5.0164   1.1581   0.0702
 FKD  O1A  O  O      0  -0.574   0.9864   2.7613  -1.1020
 FKD  O1B  O  OC    -1  -0.604   2.9647   2.5682  -0.0833
 FKD  HO2  H  HOH1   0   0.456   0.9373   1.7964   2.0012
 FKD  H3   H  HCH1   0   0.229   3.3489  -0.0120   0.4234
 FKD  H4   H  HCH1   0   0.231   1.8247  -1.5309   1.6117
 FKD  HO4  H  HOH1   0   0.458   3.4414  -2.7095   0.6882
 FKD  H5   H  HCH1   0   0.211   0.4855  -1.9687  -1.0840
 FKD  HO5  H  HOH1   0   0.452   0.4649  -3.7530   0.3992
 FKD  H6   H  HCH1   0   0.228  -0.5790  -0.6583   1.4527
 FKD  H7   H  HCH1   0   0.241  -2.2329  -1.7685  -0.0942
 FKD  HO7  H  HOH1   0   0.445  -1.1567   0.1004  -1.8854
 FKD  H8   H  HCH1   0   0.232  -2.4152   1.2742   0.0598
 FKD  HO8  H  HOH1   0   0.443  -3.3087  -0.6831   1.8765
 FKD  H9   H  HCH2   0   0.207  -4.0365   0.2191  -1.5038
 FKD  H9A  H  HCH2   0   0.185  -4.5757  -0.8574  -0.2146
 FKD  HO9  H  HOH1   0   0.454  -5.8455   1.1075  -0.4131

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
 FKD  O2   C2   single  1.399  0.020  1.399
 FKD  O2   HO2  single  0.850  0.020  0.980
 FKD  C2   C1   single  1.562  0.020  1.562
 FKD  O1A  C1   deloc   1.237  0.020  1.237
 FKD  C1   O1B  deloc   1.244  0.020  1.244
 FKD  C3   F1   single  1.394  0.020  1.394
 FKD  O6   C2   single  1.398  0.020  1.398
 FKD  C2   C3   single  1.527  0.020  1.527
 FKD  C4   C3   single  1.519  0.020  1.519
 FKD  C3   H3   single  0.970  0.020  1.090
 FKD  C5   C4   single  1.523  0.020  1.523
 FKD  C4   O4   single  1.410  0.020  1.410
 FKD  C4   H4   single  0.970  0.020  1.090
 FKD  O4   HO4  single  0.850  0.020  0.980
 FKD  C6   C5   single  1.529  0.020  1.529
 FKD  O5   C5   single  1.408  0.020  1.408
 FKD  C5   H5   single  0.970  0.020  1.090
 FKD  O5   HO5  single  0.850  0.020  0.980
 FKD  C6   C7   single  1.529  0.020  1.529
 FKD  C6   O6   single  1.414  0.020  1.414
 FKD  C6   H6   single  0.970  0.020  1.090
 FKD  C8   C7   single  1.540  0.020  1.540
 FKD  C7   O7   single  1.409  0.020  1.409
 FKD  C7   H7   single  0.970  0.020  1.090
 FKD  O7   HO7  single  0.850  0.020  0.980
 FKD  O8   C8   single  1.410  0.020  1.410
 FKD  C8   C9   single  1.521  0.020  1.521
 FKD  C8   H8   single  0.970  0.020  1.090
 FKD  O8   HO8  single  0.850  0.020  0.980
 FKD  O9   C9   single  1.409  0.020  1.409
 FKD  C9   H9   single  0.970  0.020  1.090
 FKD  C9   H9A  single  0.970  0.020  1.090
 FKD  O9   HO9  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
 FKD  HO2  O2  C2   109.65  3.000
 FKD  O1B  C1  O1A  128.34  3.000
 FKD  O1B  C1  C2   113.65  3.000
 FKD  O1A  C1  C2   118.00  3.000
 FKD  O6   C2  C3   109.98  3.000
 FKD  C3   C2  C1   110.35  3.000
 FKD  O6   C2  C1   108.22  3.000
 FKD  C3   C2  O2   105.25  3.000
 FKD  O6   C2  O2   111.68  3.000
 FKD  C1   C2  O2   111.36  3.000
 FKD  H3   C3  C4   111.07  3.000
 FKD  H3   C3  C2   110.17  3.000
 FKD  C4   C3  C2   111.39  3.000
 FKD  H3   C3  F1   107.64  3.000
 FKD  C4   C3  F1   108.91  3.000
 FKD  C2   C3  F1   107.51  3.000
 FKD  H4   C4  C5   108.02  3.000
 FKD  H4   C4  O4   110.74  3.000
 FKD  C5   C4  O4   107.87  3.000
 FKD  H4   C4  C3   107.39  3.000
 FKD  O4   C4  C3   112.08  3.000
 FKD  C5   C4  C3   110.69  3.000
 FKD  HO4  O4  C4   108.85  3.000
 FKD  H5   C5  C6   109.13  3.000
 FKD  H5   C5  O5   110.90  3.000
 FKD  C6   C5  O5   107.32  3.000
 FKD  H5   C5  C4   108.73  3.000
 FKD  O5   C5  C4   111.38  3.000
 FKD  C6   C5  C4   109.35  3.000
 FKD  HO5  O5  C5   108.03  3.000
 FKD  H6   C6  C7   109.11  3.000
 FKD  H6   C6  O6   111.25  3.000
 FKD  C7   C6  O6   105.08  3.000
 FKD  H6   C6  C5   108.20  3.000
 FKD  O6   C6  C5   110.84  3.000
 FKD  C7   C6  C5   112.37  3.000
 FKD  C6   O6  C2   117.34  3.000
 FKD  H7   C7  C8   108.04  3.000
 FKD  H7   C7  O7   106.47  3.000
 FKD  C8   C7  O7   111.40  3.000
 FKD  H7   C7  C6   108.08  3.000
 FKD  O7   C7  C6   110.55  3.000
 FKD  C8   C7  C6   112.05  3.000
 FKD  HO7  O7  C7   107.16  3.000
 FKD  H8   C8  C9   108.60  3.000
 FKD  H8   C8  O8   105.72  3.000
 FKD  C9   C8  O8   111.55  3.000
 FKD  H8   C8  C7   108.93  3.000
 FKD  C9   C8  C7   110.75  3.000
 FKD  O8   C8  C7   111.10  3.000
 FKD  HO8  O8  C8   108.61  3.000
 FKD  H9A  C9  H9   106.88  3.000
 FKD  H9A  C9  O9   111.48  3.000
 FKD  H9   C9  O9   111.60  3.000
 FKD  H9A  C9  C8   108.86  3.000
 FKD  H9   C9  C8   109.12  3.000
 FKD  O9   C9  C8   108.83  3.000
 FKD  HO9  O9  C9   107.86  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
 FKD  chir_01  C2  C1  O6  C3  negativ
 FKD  chir_02  C3  F1  C4  C2  positiv
 FKD  chir_03  C4  O4  C3  C5  negativ
 FKD  chir_04  C5  O5  C4  C6  positiv
 FKD  chir_05  C6  O6  C7  C5  negativ
 FKD  chir_06  C7  O7  C8  C6  positiv
 FKD  chir_07  C8  O8  C7  C9  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
 FKD  plan-1  C1   0.020
 FKD  plan-1  C2   0.020
 FKD  plan-1  O1A  0.020
 FKD  plan-1  O1B  0.020

