# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 08:17:16 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{S},6~{S})-5-fluoranyl-6-heptoxy-2-(hydroxymethyl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1F
#
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
 6KS  6KS  (2~{R},3~{S},4~{S},5~{S},6~{S})-5-fluoranyl-6-heptoxy-2-(hydroxymethyl)oxane-3,4-diol  D-saccharide  44  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 GRAND
;

data_comp_6KS
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
 6KS  C4   C  CH1   0   0.028  -3.4677   0.4647  -0.6263
 6KS  C5   C  CH1   0  -0.015  -2.3166   1.2314   0.0287
 6KS  C6   C  CH2   0  -0.158  -2.7517   2.6073   0.4869
 6KS  C3   C  CH1   0  -0.034  -3.0251  -0.9642  -0.9254
 6KS  CAR  C  CH3   0  -0.662   8.4355   0.0749  -0.1665
 6KS  CAQ  C  CH2   0  -0.420   7.1306  -0.5368  -0.6571
 6KS  CAP  C  CH2   0  -0.407   5.9054   0.0277   0.0515
 6KS  CAO  C  CH2   0  -0.411   4.5985  -0.5924  -0.4256
 6KS  CAN  C  CH2   0  -0.426   3.3750  -0.0555   0.3063
 6KS  CAM  C  CH2   0  -0.462   2.0760  -0.6947  -0.1703
 6KS  CAL  C  CH2   0  -0.135   0.8836  -0.2075   0.6264
 6KS  O1   O  O2    0  -0.507  -0.2895  -0.8276   0.1227
 6KS  C1   C  CH1   0   0.211  -1.3929  -0.7627   0.9613
 6KS  O5   O  O2    0  -0.499  -1.8529   0.5376   1.1758
 6KS  C2   C  CH1   0   0.136  -2.4760  -1.6265   0.3256
 6KS  F2   F  F     0  -0.377  -3.4981  -1.7652   1.2610
 6KS  O3   O  OH1   0  -0.672  -4.1293  -1.6570  -1.4543
 6KS  O4   O  OH1   0  -0.673  -3.8181   1.1423  -1.8077
 6KS  O6   O  OH1   0  -0.668  -1.6318   3.2955   0.9889
 6KS  H1   H  HCH1  0   0.216  -4.3157   0.4358   0.0750
 6KS  H2   H  HCH1  0   0.229  -1.5093   1.3421  -0.7098
 6KS  H3   H  HCH2  0   0.211  -3.2006   3.1298  -0.3644
 6KS  H4   H  HCH2  0   0.196  -3.5374   2.4938   1.2467
 6KS  H5   H  HCH1  0   0.235  -2.2044  -0.9137  -1.6531
 6KS  H6   H  HCH3  0   0.226   9.2974  -0.3544  -0.6785
 6KS  H7   H  HCH3  0   0.216   8.4547   1.1532  -0.3349
 6KS  H8   H  HCH3  0   0.216   8.5693  -0.0911   0.9041
 6KS  H9   H  HCH2  0   0.211   7.0321  -0.3757  -1.7352
 6KS  H10  H  HCH2  0   0.210   7.1594  -1.6218  -0.5159
 6KS  H11  H  HCH2  0   0.207   6.0076  -0.1294   1.1310
 6KS  H12  H  HCH2  0   0.207   5.8691   1.1132  -0.0934
 6KS  H13  H  HCH2  0   0.210   4.4853  -0.4206  -1.5016
 6KS  H14  H  HCH2  0   0.209   4.6464  -1.6793  -0.2965
 6KS  H15  H  HCH2  0   0.214   3.4934  -0.2279   1.3815
 6KS  H16  H  HCH2  0   0.215   3.3195   1.0305   0.1769
 6KS  H17  H  HCH2  0   0.225   1.9264  -0.4728  -1.2312
 6KS  H18  H  HCH2  0   0.222   2.1503  -1.7827  -0.0804
 6KS  H19  H  HCH2  0   0.205   1.0144  -0.4583   1.6876
 6KS  H20  H  HCH2  0   0.212   0.8017   0.8833   0.5596
 6KS  H21  H  HCH1  0   0.247  -1.1475  -1.1440   1.9624
 6KS  H22  H  HCH1  0   0.241  -2.0884  -2.6254   0.1071
 6KS  H23  H  HOH1  0   0.461  -3.8110  -2.4014  -1.9738
 6KS  H24  H  HOH1  0   0.454  -4.5357   0.6564  -2.2274
 6KS  H25  H  HOH1  0   0.456  -1.9202   4.1724   1.2575

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
 6KS  CAR  CAQ  single  1.522  0.020  1.522
 6KS  CAQ  CAP  single  1.524  0.020  1.524
 6KS  CAP  CAO  single  1.523  0.020  1.523
 6KS  CAO  CAN  single  1.523  0.020  1.523
 6KS  CAN  CAM  single  1.524  0.020  1.524
 6KS  CAM  CAL  single  1.514  0.020  1.514
 6KS  CAL  O1   single  1.419  0.020  1.419
 6KS  O1   C1   single  1.387  0.020  1.387
 6KS  C1   O5   single  1.396  0.020  1.396
 6KS  C1   C2   single  1.524  0.020  1.524
 6KS  O5   C5   single  1.418  0.020  1.418
 6KS  C5   C6   single  1.514  0.020  1.514
 6KS  C5   C4   single  1.530  0.020  1.530
 6KS  C2   C3   single  1.518  0.020  1.518
 6KS  C2   F2   single  1.392  0.020  1.392
 6KS  C3   C4   single  1.525  0.020  1.525
 6KS  C3   O3   single  1.407  0.020  1.407
 6KS  C6   O6   single  1.407  0.020  1.407
 6KS  O4   C4   single  1.406  0.020  1.406
 6KS  C4   H1   single  0.970  0.020  1.090
 6KS  C5   H2   single  0.970  0.020  1.090
 6KS  C6   H3   single  0.970  0.020  1.090
 6KS  C6   H4   single  0.970  0.020  1.090
 6KS  C3   H5   single  0.970  0.020  1.090
 6KS  CAR  H6   single  0.970  0.020  1.090
 6KS  CAR  H7   single  0.970  0.020  1.090
 6KS  CAR  H8   single  0.970  0.020  1.090
 6KS  CAQ  H9   single  0.970  0.020  1.090
 6KS  CAQ  H10  single  0.970  0.020  1.090
 6KS  CAP  H11  single  0.970  0.020  1.090
 6KS  CAP  H12  single  0.970  0.020  1.090
 6KS  CAO  H13  single  0.970  0.020  1.090
 6KS  CAO  H14  single  0.970  0.020  1.090
 6KS  CAN  H15  single  0.970  0.020  1.090
 6KS  CAN  H16  single  0.970  0.020  1.090
 6KS  CAM  H17  single  0.970  0.020  1.090
 6KS  CAM  H18  single  0.970  0.020  1.090
 6KS  CAL  H19  single  0.970  0.020  1.090
 6KS  CAL  H20  single  0.970  0.020  1.090
 6KS  C1   H21  single  0.970  0.020  1.090
 6KS  C2   H22  single  0.970  0.020  1.090
 6KS  O3   H23  single  0.850  0.020  0.980
 6KS  O4   H24  single  0.850  0.020  0.980
 6KS  O6   H25  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
 6KS  H1   C4   O4   110.85  3.000
 6KS  H1   C4   C3   108.89  3.000
 6KS  O4   C4   C3   111.03  3.000
 6KS  H1   C4   C5   108.66  3.000
 6KS  O4   C4   C5   107.80  3.000
 6KS  C3   C4   C5   109.57  3.000
 6KS  H2   C5   O5   110.63  3.000
 6KS  H2   C5   C6   108.83  3.000
 6KS  O5   C5   C6   107.08  3.000
 6KS  H2   C5   C4   108.37  3.000
 6KS  C6   C5   C4   111.63  3.000
 6KS  O5   C5   C4   110.30  3.000
 6KS  H4   C6   H3   107.08  3.000
 6KS  H4   C6   O6   111.90  3.000
 6KS  H3   C6   O6   111.73  3.000
 6KS  H4   C6   C5   108.71  3.000
 6KS  H3   C6   C5   108.43  3.000
 6KS  O6   C6   C5   108.89  3.000
 6KS  H5   C3   O3   111.11  3.000
 6KS  H5   C3   C2   107.21  3.000
 6KS  O3   C3   C2   112.26  3.000
 6KS  H5   C3   C4   107.68  3.000
 6KS  O3   C3   C4   107.90  3.000
 6KS  C2   C3   C4   110.61  3.000
 6KS  H8   CAR  H7   107.42  3.000
 6KS  H8   CAR  H6   107.68  3.000
 6KS  H7   CAR  H6   107.61  3.000
 6KS  H8   CAR  CAQ  111.11  3.000
 6KS  H7   CAR  CAQ  111.25  3.000
 6KS  H6   CAR  CAQ  111.59  3.000
 6KS  H10  CAQ  H9   105.98  3.000
 6KS  H10  CAQ  CAP  109.17  3.000
 6KS  H9   CAQ  CAP  109.34  3.000
 6KS  H10  CAQ  CAR  109.52  3.000
 6KS  H9   CAQ  CAR  109.60  3.000
 6KS  CAP  CAQ  CAR  112.99  3.000
 6KS  H12  CAP  H11  105.99  3.000
 6KS  H12  CAP  CAO  109.48  3.000
 6KS  H11  CAP  CAO  109.28  3.000
 6KS  H12  CAP  CAQ  109.40  3.000
 6KS  H11  CAP  CAQ  109.27  3.000
 6KS  CAO  CAP  CAQ  113.17  3.000
 6KS  H14  CAO  H13  106.01  3.000
 6KS  H14  CAO  CAN  109.16  3.000
 6KS  H13  CAO  CAN  109.49  3.000
 6KS  H14  CAO  CAP  109.23  3.000
 6KS  H13  CAO  CAP  109.42  3.000
 6KS  CAN  CAO  CAP  113.27  3.000
 6KS  H16  CAN  H15  106.11  3.000
 6KS  H16  CAN  CAM  109.62  3.000
 6KS  H15  CAN  CAM  109.46  3.000
 6KS  H16  CAN  CAO  109.48  3.000
 6KS  H15  CAN  CAO  109.22  3.000
 6KS  CAM  CAN  CAO  112.73  3.000
 6KS  H18  CAM  H17  106.89  3.000
 6KS  H18  CAM  CAL  109.28  3.000
 6KS  H17  CAM  CAL  109.70  3.000
 6KS  H18  CAM  CAN  109.48  3.000
 6KS  H17  CAM  CAN  109.55  3.000
 6KS  CAL  CAM  CAN  111.81  3.000
 6KS  H20  CAL  H19  107.16  3.000
 6KS  H20  CAL  O1   110.58  3.000
 6KS  H19  CAL  O1   109.97  3.000
 6KS  H20  CAL  CAM  110.30  3.000
 6KS  H19  CAL  CAM  109.94  3.000
 6KS  O1   CAL  CAM  108.88  3.000
 6KS  C1   O1   CAL  114.99  3.000
 6KS  H21  C1   C2   110.00  3.000
 6KS  H21  C1   O5   104.88  3.000
 6KS  C2   C1   O5   110.97  3.000
 6KS  H21  C1   O1   110.90  3.000
 6KS  C2   C1   O1   106.65  3.000
 6KS  O5   C1   O1   113.49  3.000
 6KS  C1   O5   C5   116.05  3.000
 6KS  H22  C2   F2   107.66  3.000
 6KS  H22  C2   C1   110.44  3.000
 6KS  F2   C2   C1   107.33  3.000
 6KS  H22  C2   C3   111.23  3.000
 6KS  F2   C2   C3   109.36  3.000
 6KS  C1   C2   C3   110.69  3.000
 6KS  H23  O3   C3   108.93  3.000
 6KS  H24  O4   C4   107.98  3.000
 6KS  H25  O6   C6   107.88  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
 6KS  Var_01  H19  CAL  O1   C1     43.01  30.0  1
 6KS  Var_02  CAO  CAP  CAQ  CAR  -179.38  30.0  3
 6KS  Var_03  CAN  CAO  CAP  CAQ   178.53  30.0  3
 6KS  Var_04  CAM  CAN  CAO  CAP  -179.39  30.0  3
 6KS  Var_05  CAL  CAM  CAN  CAO   176.60  30.0  3
 6KS  Var_06  O1   CAL  CAM  CAN   179.33  30.0  3
 6KS  Var_07  H6   CAR  CAQ  CAP   179.23  30.0  3

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
 6KS  chir_01  C4  C5  C3  O4  positiv
 6KS  chir_02  C5  O5  C4  C6  negativ
 6KS  chir_03  C3  O3  C4  C2  negativ
 6KS  chir_04  C1  O5  O1  C2  positiv
 6KS  chir_05  C2  F2  C3  C1  negativ

