# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:56:01 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  34  19  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.652   1.4223   0.9926   1.7820
 FKD  C1    C  C     0   0.505   1.7851   2.1552  -0.3116
 FKD  F1    F  F     0  -0.369   2.5969  -0.2145  -1.3104
 FKD  C2    C  CT    0   0.341   1.3949   0.8459   0.4032
 FKD  C3    C  CH1   0   0.152   2.4168  -0.2462   0.0678
 FKD  C4    C  CH1   0  -0.037   1.9012  -1.6141   0.4849
 FKD  O4    O  OH1   0  -0.668   2.7512  -2.6400   0.0367
 FKD  C5    C  CH1   0   0.046   0.5090  -1.8653  -0.0851
 FKD  O5    O  OH1   0  -0.674  -0.0459  -3.0480   0.4314
 FKD  C6    C  CH1   0  -0.003  -0.4103  -0.7164   0.3263
 FKD  O6    O  O2    0  -0.510   0.1427   0.5239  -0.0926
 FKD  C7    C  CH1   0  -0.041  -1.7919  -0.7997  -0.3192
 FKD  O7    O  OH1   0  -0.662  -1.7067  -0.7913  -1.7243
 FKD  C8    C  CH1   0  -0.017  -2.7391   0.3014   0.1968
 FKD  O8    O  OH1   0  -0.660  -2.7618   0.3383   1.6052
 FKD  C9    C  CH2   0  -0.161  -4.1333   0.1264  -0.3845
 FKD  O9    O  OH1   0  -0.671  -4.9375   1.2027   0.0385
 FKD  O1A   O  O     0  -0.405   1.1258   2.6978  -1.1531
 FKD  O1B   O  OH1   0  -0.585   2.9445   2.5949   0.1439
 FKD  HO2   H  HOH1  0   0.469   0.7636   1.6413   2.0613
 FKD  H3    H  HCH1  0   0.258   3.3806  -0.0335   0.5362
 FKD  H4    H  HCH1  0   0.244   1.8247  -1.6141   1.5802
 FKD  HO4   H  HOH1  0   0.463   3.4566  -2.7657   0.6784
 FKD  H5    H  HCH1  0   0.220   0.5730  -1.9029  -1.1808
 FKD  HO5   H  HOH1  0   0.455   0.5226  -3.7826   0.1781
 FKD  H6    H  HCH1  0   0.242  -0.5299  -0.7415   1.4152
 FKD  H7    H  HCH1  0   0.251  -2.2172  -1.7717  -0.0471
 FKD  HO7   H  HOH1  0   0.446  -1.2907   0.0334  -2.0007
 FKD  H8    H  HCH1  0   0.234  -2.3523   1.2772  -0.1180
 FKD  HO8   H  HOH1  0   0.445  -3.1742  -0.4704   1.9295
 FKD  H9    H  HCH2  0   0.207  -4.0646   0.0781  -1.4760
 FKD  H9A   H  HCH2  0   0.189  -4.5421  -0.8401  -0.0494
 FKD  HO9   H  HOH1  0   0.455  -5.8001   1.1078  -0.3743
 FKD  HO1B  H  HOH1  0   0.493   3.1997   3.4128  -0.3102

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  1.387  0.020  1.387
 FKD  O2   HO2   single  0.850  0.020  0.980
 FKD  C2   C1    single  1.542  0.020  1.542
 FKD  O1A  C1    double  1.199  0.020  1.199
 FKD  C1   O1B   single  1.321  0.020  1.321
 FKD  C3   F1    single  1.390  0.020  1.390
 FKD  O6   C2    single  1.385  0.020  1.385
 FKD  C2   C3    single  1.533  0.020  1.533
 FKD  C4   C3    single  1.520  0.020  1.520
 FKD  C3   H3    single  0.970  0.020  1.090
 FKD  C5   C4    single  1.525  0.020  1.525
 FKD  C4   O4    single  1.406  0.020  1.406
 FKD  C4   H4    single  0.970  0.020  1.090
 FKD  O4   HO4   single  0.850  0.020  0.980
 FKD  C6   C5    single  1.528  0.020  1.528
 FKD  O5   C5    single  1.405  0.020  1.405
 FKD  C5   H5    single  0.970  0.020  1.090
 FKD  O5   HO5   single  0.850  0.020  0.980
 FKD  C6   C7    single  1.527  0.020  1.527
 FKD  C6   O6    single  1.421  0.020  1.421
 FKD  C6   H6    single  0.970  0.020  1.090
 FKD  C8   C7    single  1.541  0.020  1.541
 FKD  C7   O7    single  1.408  0.020  1.408
 FKD  C7   H7    single  0.970  0.020  1.090
 FKD  O7   HO7   single  0.850  0.020  0.980
 FKD  O8   C8    single  1.409  0.020  1.409
 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
 FKD  O1B  HO1B  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   110.19  3.000
 FKD  O1B   C1   O1A  125.04  3.000
 FKD  O1B   C1   C2   110.18  3.000
 FKD  O1A   C1   C2   124.79  3.000
 FKD  O6    C2   C3   111.03  3.000
 FKD  C3    C2   C1   109.57  3.000
 FKD  O6    C2   C1   105.09  3.000
 FKD  C3    C2   O2   106.24  3.000
 FKD  O6    C2   O2   113.48  3.000
 FKD  C1    C2   O2   111.47  3.000
 FKD  H3    C3   C4   110.90  3.000
 FKD  H3    C3   C2   110.83  3.000
 FKD  C4    C3   C2   110.79  3.000
 FKD  H3    C3   F1   107.84  3.000
 FKD  C4    C3   F1   109.66  3.000
 FKD  C2    C3   F1   106.68  3.000
 FKD  H4    C4   C5   108.01  3.000
 FKD  H4    C4   O4   111.12  3.000
 FKD  C5    C4   O4   108.21  3.000
 FKD  H4    C4   C3   107.30  3.000
 FKD  O4    C4   C3   111.36  3.000
 FKD  C5    C4   C3   110.81  3.000
 FKD  HO4   O4   C4   109.03  3.000
 FKD  H5    C5   C6   109.23  3.000
 FKD  H5    C5   O5   111.16  3.000
 FKD  C6    C5   O5   107.24  3.000
 FKD  H5    C5   C4   108.99  3.000
 FKD  O5    C5   C4   111.22  3.000
 FKD  C6    C5   C4   108.95  3.000
 FKD  HO5   O5   C5   108.20  3.000
 FKD  H6    C6   C7   108.66  3.000
 FKD  H6    C6   O6   110.82  3.000
 FKD  C7    C6   O6   105.97  3.000
 FKD  H6    C6   C5   108.42  3.000
 FKD  O6    C6   C5   110.05  3.000
 FKD  C7    C6   C5   112.92  3.000
 FKD  C6    O6   C2   116.70  3.000
 FKD  H7    C7   C8   108.19  3.000
 FKD  H7    C7   O7   106.07  3.000
 FKD  C8    C7   O7   111.53  3.000
 FKD  H7    C7   C6   107.14  3.000
 FKD  O7    C7   C6   111.52  3.000
 FKD  C8    C7   C6   112.05  3.000
 FKD  HO7   O7   C7   108.50  3.000
 FKD  H8    C8   C9   108.44  3.000
 FKD  H8    C8   O8   105.64  3.000
 FKD  C9    C8   O8   111.74  3.000
 FKD  H8    C8   C7   108.84  3.000
 FKD  C9    C8   C7   110.68  3.000
 FKD  O8    C8   C7   111.29  3.000
 FKD  HO8   O8   C8   108.74  3.000
 FKD  H9A   C9   H9   106.73  3.000
 FKD  H9A   C9   O9   111.54  3.000
 FKD  H9    C9   O9   111.65  3.000
 FKD  H9A   C9   C8   108.96  3.000
 FKD  H9    C9   C8   109.19  3.000
 FKD  O9    C9   C8   108.70  3.000
 FKD  HO9   O9   C9   107.93  3.000
 FKD  HO1B  O1B  C1   110.50  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
 FKD  CONST_01  HO1B  O1B  C1  C2  180.00  0.0  0

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
 FKD  plan-1  HO1B  0.020

