# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 07:40:04 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S},3~{R},4~{S},5~{R},6~{R})-4-fluoranyl-2-heptoxy-6-(hydroxymethyl)oxane-3,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](F)[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
 6KH  6KH  (2~{S},3~{R},4~{S},5~{R},6~{R})-4-fluoranyl-2-heptoxy-6-(hydroxymethyl)oxane-3,5-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 OK
;

data_comp_6KH
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
 6KH  C4   C  CH1   0  -0.021  -3.4206   0.5040  -0.6508
 6KH  C5   C  CH1   0  -0.017  -2.2744   1.2732   0.0171
 6KH  C6   C  CH2   0  -0.158  -2.7190   2.6532   0.4545
 6KH  C3   C  CH1   0   0.177  -2.9736  -0.9273  -0.8943
 6KH  CAR  C  CH3   0  -0.662   8.4466   0.1386  -0.1774
 6KH  CAQ  C  CH2   0  -0.420   7.1466  -0.4896  -0.6598
 6KH  CAP  C  CH2   0  -0.407   5.9184   0.0650   0.0512
 6KH  CAO  C  CH2   0  -0.411   4.6154  -0.5705  -0.4165
 6KH  CAN  C  CH2   0  -0.426   3.3906  -0.0352   0.3142
 6KH  CAM  C  CH2   0  -0.462   2.0928  -0.6852  -0.1508
 6KH  CAL  C  CH2   0  -0.135   0.8992  -0.1730   0.6284
 6KH  O1   O  O2    0  -0.505  -0.2756  -0.8010   0.1402
 6KH  C1   C  CH1   0   0.233  -1.3784  -0.7166   0.9796
 6KH  O5   O  O2    0  -0.496  -1.8225   0.5934   1.1742
 6KH  O6   O  OH1   0  -0.668  -1.6042   3.3539   0.9507
 6KH  O4   O  OH1   0  -0.671  -3.7205   1.1571  -1.8610
 6KH  F3   F  F     0  -0.377  -4.0361  -1.6567  -1.4259
 6KH  C2   C  CH1   0  -0.060  -2.4866  -1.5901   0.3784
 6KH  O2   O  OH1   0  -0.669  -3.5711  -1.6873   1.2643
 6KH  H1   H  HCH1  0   0.231  -4.2876   0.5039   0.0238
 6KH  H2   H  HCH1  0   0.230  -1.4600   1.3793  -0.7146
 6KH  H3   H  HCH2  0   0.211  -3.1683   3.1617  -0.4048
 6KH  H4   H  HCH2  0   0.196  -3.5056   2.5444   1.2140
 6KH  H5   H  HCH1  0   0.226  -2.1718  -0.9332  -1.6377
 6KH  H6   H  HCH3  0   0.215   8.5877  -0.0226   0.8931
 6KH  H7   H  HCH3  0   0.226   9.3111  -0.2824  -0.6920
 6KH  H8   H  HCH3  0   0.216   8.4527   1.2166  -0.3494
 6KH  H9   H  HCH2  0   0.211   7.0421  -0.3342  -1.7382
 6KH  H10  H  HCH2  0   0.210   7.1880  -1.5736  -0.5140
 6KH  H11  H  HCH2  0   0.206   6.0268  -0.0855   1.1312
 6KH  H12  H  HCH2  0   0.207   5.8698   1.1493  -0.0990
 6KH  H13  H  HCH2  0   0.210   4.4979  -0.4087  -1.4936
 6KH  H14  H  HCH2  0   0.209   4.6724  -1.6558  -0.2782
 6KH  H15  H  HCH2  0   0.214   3.5133  -0.1964   1.3907
 6KH  H16  H  HCH2  0   0.215   3.3280   1.0492   0.1745
 6KH  H17  H  HCH2  0   0.225   1.9479  -0.4904  -1.2178
 6KH  H18  H  HCH2  0   0.222   2.1639  -1.7708  -0.0326
 6KH  H19  H  HCH2  0   0.203   1.0268  -0.3932   1.6969
 6KH  H20  H  HCH2  0   0.210   0.8236   0.9162   0.5308
 6KH  H21  H  HCH1  0   0.239  -1.1260  -1.0790   1.9871
 6KH  H22  H  HOH1  0   0.456  -1.8980   4.2330   1.2058
 6KH  H23  H  HOH1  0   0.459  -4.5710   0.8408  -2.1798
 6KH  H24  H  HCH1  0   0.247  -2.0678  -2.5772   0.1431
 6KH  H25  H  HOH1  0   0.460  -3.3098  -2.2332   2.0124

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
 6KH  O6   C6   single  1.407  0.020  1.407
 6KH  CAR  CAQ  single  1.522  0.020  1.522
 6KH  O5   C1   single  1.397  0.020  1.397
 6KH  O5   C5   single  1.416  0.020  1.416
 6KH  CAP  CAQ  single  1.524  0.020  1.524
 6KH  CAP  CAO  single  1.523  0.020  1.523
 6KH  CAN  CAM  single  1.524  0.020  1.524
 6KH  CAN  CAO  single  1.523  0.020  1.523
 6KH  CAL  CAM  single  1.515  0.020  1.515
 6KH  CAL  O1   single  1.419  0.020  1.419
 6KH  C1   O1   single  1.388  0.020  1.388
 6KH  C1   C2   single  1.534  0.020  1.534
 6KH  C6   C5   single  1.514  0.020  1.514
 6KH  O2   C2   single  1.404  0.020  1.404
 6KH  C5   C4   single  1.533  0.020  1.533
 6KH  C2   C3   single  1.515  0.020  1.515
 6KH  C4   C3   single  1.519  0.020  1.519
 6KH  C4   O4   single  1.407  0.020  1.407
 6KH  C3   F3   single  1.394  0.020  1.394
 6KH  C4   H1   single  0.970  0.020  1.090
 6KH  C5   H2   single  0.970  0.020  1.090
 6KH  C6   H3   single  0.970  0.020  1.090
 6KH  C6   H4   single  0.970  0.020  1.090
 6KH  C3   H5   single  0.970  0.020  1.090
 6KH  CAR  H6   single  0.970  0.020  1.090
 6KH  CAR  H7   single  0.970  0.020  1.090
 6KH  CAR  H8   single  0.970  0.020  1.090
 6KH  CAQ  H9   single  0.970  0.020  1.090
 6KH  CAQ  H10  single  0.970  0.020  1.090
 6KH  CAP  H11  single  0.970  0.020  1.090
 6KH  CAP  H12  single  0.970  0.020  1.090
 6KH  CAO  H13  single  0.970  0.020  1.090
 6KH  CAO  H14  single  0.970  0.020  1.090
 6KH  CAN  H15  single  0.970  0.020  1.090
 6KH  CAN  H16  single  0.970  0.020  1.090
 6KH  CAM  H17  single  0.970  0.020  1.090
 6KH  CAM  H18  single  0.970  0.020  1.090
 6KH  CAL  H19  single  0.970  0.020  1.090
 6KH  CAL  H20  single  0.970  0.020  1.090
 6KH  C1   H21  single  0.970  0.020  1.090
 6KH  O6   H22  single  0.850  0.020  0.980
 6KH  O4   H23  single  0.850  0.020  0.980
 6KH  C2   H24  single  0.970  0.020  1.090
 6KH  O2   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
 6KH  H1   C4   O4   111.09  3.000
 6KH  H1   C4   C3   109.30  3.000
 6KH  O4   C4   C3   111.23  3.000
 6KH  H1   C4   C5   108.81  3.000
 6KH  O4   C4   C5   107.52  3.000
 6KH  C3   C4   C5   108.82  3.000
 6KH  H2   C5   O5   110.70  3.000
 6KH  H2   C5   C6   108.76  3.000
 6KH  O5   C5   C6   107.17  3.000
 6KH  H2   C5   C4   108.18  3.000
 6KH  C6   C5   C4   111.31  3.000
 6KH  O5   C5   C4   110.71  3.000
 6KH  H4   C6   H3   107.14  3.000
 6KH  H4   C6   O6   111.88  3.000
 6KH  H3   C6   O6   111.75  3.000
 6KH  H4   C6   C5   108.64  3.000
 6KH  H3   C6   C5   108.48  3.000
 6KH  O6   C6   C5   108.84  3.000
 6KH  H5   C3   C2   109.45  3.000
 6KH  H5   C3   F3   107.27  3.000
 6KH  C2   C3   F3   109.66  3.000
 6KH  H5   C3   C4   109.25  3.000
 6KH  F3   C3   C4   109.26  3.000
 6KH  C2   C3   C4   111.84  3.000
 6KH  H8   CAR  H7   107.61  3.000
 6KH  H8   CAR  H6   107.43  3.000
 6KH  H7   CAR  H6   107.66  3.000
 6KH  H8   CAR  CAQ  111.24  3.000
 6KH  H7   CAR  CAQ  111.59  3.000
 6KH  H6   CAR  CAQ  111.11  3.000
 6KH  H10  CAQ  H9   105.99  3.000
 6KH  H10  CAQ  CAP  109.20  3.000
 6KH  H9   CAQ  CAP  109.34  3.000
 6KH  H10  CAQ  CAR  109.52  3.000
 6KH  H9   CAQ  CAR  109.59  3.000
 6KH  CAP  CAQ  CAR  112.97  3.000
 6KH  H12  CAP  H11  105.99  3.000
 6KH  H12  CAP  CAO  109.44  3.000
 6KH  H11  CAP  CAO  109.27  3.000
 6KH  H12  CAP  CAQ  109.39  3.000
 6KH  H11  CAP  CAQ  109.28  3.000
 6KH  CAO  CAP  CAQ  113.22  3.000
 6KH  H14  CAO  H13  106.02  3.000
 6KH  H14  CAO  CAN  109.23  3.000
 6KH  H13  CAO  CAN  109.48  3.000
 6KH  H14  CAO  CAP  109.27  3.000
 6KH  H13  CAO  CAP  109.40  3.000
 6KH  CAN  CAO  CAP  113.19  3.000
 6KH  H16  CAN  H15  106.11  3.000
 6KH  H16  CAN  CAM  109.56  3.000
 6KH  H15  CAN  CAM  109.42  3.000
 6KH  H16  CAN  CAO  109.43  3.000
 6KH  H15  CAN  CAO  109.25  3.000
 6KH  CAM  CAN  CAO  112.86  3.000
 6KH  H18  CAM  H17  106.89  3.000
 6KH  H18  CAM  CAL  109.34  3.000
 6KH  H17  CAM  CAL  109.69  3.000
 6KH  H18  CAM  CAN  109.56  3.000
 6KH  H17  CAM  CAN  109.53  3.000
 6KH  CAL  CAM  CAN  111.70  3.000
 6KH  H20  CAL  H19  107.09  3.000
 6KH  H20  CAL  O1   110.62  3.000
 6KH  H19  CAL  O1   110.01  3.000
 6KH  H20  CAL  CAM  110.15  3.000
 6KH  H19  CAL  CAM  109.94  3.000
 6KH  O1   CAL  CAM  109.02  3.000
 6KH  C1   O1   CAL  115.01  3.000
 6KH  H21  C1   C2   109.71  3.000
 6KH  H21  C1   O5   104.73  3.000
 6KH  C2   C1   O5   111.04  3.000
 6KH  H21  C1   O1   110.57  3.000
 6KH  C2   C1   O1   107.60  3.000
 6KH  O5   C1   O1   113.18  3.000
 6KH  C1   O5   C5   115.97  3.000
 6KH  H22  O6   C6   107.87  3.000
 6KH  H23  O4   C4   108.71  3.000
 6KH  H24  C2   O2   111.57  3.000
 6KH  H24  C2   C1   108.69  3.000
 6KH  O2   C2   C1   110.50  3.000
 6KH  H24  C2   C3   109.63  3.000
 6KH  O2   C2   C3   108.18  3.000
 6KH  C1   C2   C3   108.20  3.000
 6KH  H25  O2   C2   108.67  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
 6KH  Var_01  H19  CAL  O1   C1     42.45  30.0  1
 6KH  Var_02  CAO  CAP  CAQ  CAR  -179.38  30.0  1
 6KH  Var_03  CAN  CAO  CAP  CAQ   178.86  30.0  3
 6KH  Var_04  CAM  CAN  CAO  CAP  -179.48  30.0  1
 6KH  Var_05  CAL  CAM  CAN  CAO   177.82  30.0  3
 6KH  Var_06  O1   CAL  CAM  CAN   179.31  30.0  1
 6KH  Var_07  H6   CAR  CAQ  CAP    59.16  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
 6KH  chir_01  C4  C5  C3  O4  positiv
 6KH  chir_02  C5  O5  C4  C6  negativ
 6KH  chir_03  C3  F3  C4  C2  negativ
 6KH  chir_04  C1  O1  O5  C2  negativ
 6KH  chir_05  C2  O2  C1  C3  positiv

