# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 06:56:06 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-2-heptoxy-6-(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](F)[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
 6K3  6K3  (2~{S},3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-2-heptoxy-6-(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 PERFECT
;

data_comp_6K3
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
 6K3  C4   C  CH1   0   0.174  -3.4581   0.4748  -0.5770
 6K3  C5   C  CH1   0  -0.061  -2.3189   1.2364   0.0952
 6K3  C6   C  CH2   0  -0.159  -2.7666   2.5974   0.5834
 6K3  C3   C  CH1   0  -0.020  -3.0294  -0.9390  -0.9336
 6K3  CAR  C  CH3   0  -0.662   8.4101   0.1810  -0.1707
 6K3  CAQ  C  CH2   0  -0.419   7.1142  -0.4472  -0.6640
 6K3  CAP  C  CH2   0  -0.407   5.8813   0.0962   0.0477
 6K3  CAO  C  CH2   0  -0.411   4.5823  -0.5366  -0.4344
 6K3  CAN  C  CH2   0  -0.426   3.3537  -0.0262   0.3078
 6K3  CAM  C  CH2   0  -0.462   2.0596  -0.6657  -0.1816
 6K3  CAL  C  CH2   0  -0.135   0.8659  -0.2118   0.6328
 6K3  O1   O  O2    0  -0.505  -0.3051  -0.8216   0.1138
 6K3  C1   C  CH1   0   0.241  -1.4079  -0.7889   0.9556
 6K3  O5   O  O2    0  -0.497  -1.8586   0.5098   1.2192
 6K3  O6   O  OH1   0  -0.667  -1.6504   3.2890   1.0860
 6K3  F4   F  F     0  -0.379  -3.7968   1.1436  -1.7573
 6K3  O3   O  OH1   0  -0.667  -4.0812  -1.6975  -1.4715
 6K3  C2   C  CH1   0  -0.029  -2.5096  -1.6392   0.3144
 6K3  O2   O  OH1   0  -0.668  -3.5857  -1.7948   1.2042
 6K3  H1   H  HCH1  0   0.224  -4.3501   0.4644   0.0570
 6K3  H2   H  HCH1  0   0.235  -1.5135   1.3702  -0.6413
 6K3  H3   H  HCH2  0   0.211  -3.2302   3.1307  -0.2542
 6K3  H4   H  HCH2  0   0.200  -3.5435   2.4600   1.3479
 6K3  H5   H  HCH1  0   0.238  -2.1941  -0.8641  -1.6432
 6K3  H6   H  HCH3  0   0.216   8.4140   1.2603  -0.3348
 6K3  H7   H  HCH3  0   0.215   8.5466   0.0125   0.8992
 6K3  H8   H  HCH3  0   0.226   9.2782  -0.2340  -0.6842
 6K3  H9   H  HCH2  0   0.211   7.0132  -0.2820  -1.7412
 6K3  H10  H  HCH2  0   0.210   7.1586  -1.5323  -0.5281
 6K3  H11  H  HCH2  0   0.206   5.9849  -0.0670   1.1264
 6K3  H12  H  HCH2  0   0.207   5.8311   1.1821  -0.0895
 6K3  H13  H  HCH2  0   0.210   4.4640  -0.3523  -1.5077
 6K3  H14  H  HCH2  0   0.209   4.6458  -1.6243  -0.3192
 6K3  H15  H  HCH2  0   0.214   3.4739  -0.2196   1.3793
 6K3  H16  H  HCH2  0   0.215   3.2884   1.0618   0.2009
 6K3  H17  H  HCH2  0   0.225   1.9038  -0.4168  -1.2357
 6K3  H18  H  HCH2  0   0.221   2.1446  -1.7550  -0.1214
 6K3  H19  H  HCH2  0   0.204   1.0025  -0.4948   1.6852
 6K3  H20  H  HCH2  0   0.210   0.7787   0.8805   0.6014
 6K3  H21  H  HCH1  0   0.240  -1.1505  -1.1981   1.9440
 6K3  H22  H  HOH1  0   0.457  -1.9406   4.1654   1.3541
 6K3  H23  H  HOH1  0   0.456  -4.2721  -1.3699  -2.3556
 6K3  H24  H  HCH1  0   0.243  -2.0805  -2.6086   0.0286
 6K3  H25  H  HOH1  0   0.458  -3.3012  -2.3461   1.9399

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
 6K3  CAR  CAQ  single  1.522  0.020  1.522
 6K3  CAQ  CAP  single  1.524  0.020  1.524
 6K3  CAP  CAO  single  1.523  0.020  1.523
 6K3  CAO  CAN  single  1.523  0.020  1.523
 6K3  CAN  CAM  single  1.524  0.020  1.524
 6K3  CAM  CAL  single  1.515  0.020  1.515
 6K3  CAL  O1   single  1.419  0.020  1.419
 6K3  O1   C1   single  1.388  0.020  1.388
 6K3  C1   O5   single  1.400  0.020  1.400
 6K3  C1   C2   single  1.532  0.020  1.532
 6K3  C5   O5   single  1.415  0.020  1.415
 6K3  C5   C6   single  1.514  0.020  1.514
 6K3  C5   C4   single  1.526  0.020  1.526
 6K3  C3   C2   single  1.522  0.020  1.522
 6K3  C3   C4   single  1.520  0.020  1.520
 6K3  C3   O3   single  1.404  0.020  1.404
 6K3  C2   O2   single  1.405  0.020  1.405
 6K3  F4   C4   single  1.398  0.020  1.398
 6K3  C6   O6   single  1.406  0.020  1.406
 6K3  C4   H1   single  0.970  0.020  1.090
 6K3  C5   H2   single  0.970  0.020  1.090
 6K3  C6   H3   single  0.970  0.020  1.090
 6K3  C6   H4   single  0.970  0.020  1.090
 6K3  C3   H5   single  0.970  0.020  1.090
 6K3  CAR  H6   single  0.970  0.020  1.090
 6K3  CAR  H7   single  0.970  0.020  1.090
 6K3  CAR  H8   single  0.970  0.020  1.090
 6K3  CAQ  H9   single  0.970  0.020  1.090
 6K3  CAQ  H10  single  0.970  0.020  1.090
 6K3  CAP  H11  single  0.970  0.020  1.090
 6K3  CAP  H12  single  0.970  0.020  1.090
 6K3  CAO  H13  single  0.970  0.020  1.090
 6K3  CAO  H14  single  0.970  0.020  1.090
 6K3  CAN  H15  single  0.970  0.020  1.090
 6K3  CAN  H16  single  0.970  0.020  1.090
 6K3  CAM  H17  single  0.970  0.020  1.090
 6K3  CAM  H18  single  0.970  0.020  1.090
 6K3  CAL  H19  single  0.970  0.020  1.090
 6K3  CAL  H20  single  0.970  0.020  1.090
 6K3  C1   H21  single  0.970  0.020  1.090
 6K3  O6   H22  single  0.850  0.020  0.980
 6K3  O3   H23  single  0.850  0.020  0.980
 6K3  C2   H24  single  0.970  0.020  1.090
 6K3  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
 6K3  H1   C4   F4   107.23  3.000
 6K3  H1   C4   C3   110.92  3.000
 6K3  F4   C4   C3   108.37  3.000
 6K3  H1   C4   C5   110.97  3.000
 6K3  F4   C4   C5   108.29  3.000
 6K3  C3   C4   C5   110.91  3.000
 6K3  H2   C5   O5   110.87  3.000
 6K3  H2   C5   C6   108.85  3.000
 6K3  O5   C5   C6   107.56  3.000
 6K3  H2   C5   C4   108.21  3.000
 6K3  C6   C5   C4   111.71  3.000
 6K3  O5   C5   C4   109.66  3.000
 6K3  H4   C6   H3   107.07  3.000
 6K3  H4   C6   O6   111.97  3.000
 6K3  H3   C6   O6   111.70  3.000
 6K3  H4   C6   C5   108.73  3.000
 6K3  H3   C6   C5   108.44  3.000
 6K3  O6   C6   C5   108.83  3.000
 6K3  H5   C3   C2   107.53  3.000
 6K3  H5   C3   O3   111.04  3.000
 6K3  C2   C3   O3   108.74  3.000
 6K3  H5   C3   C4   107.62  3.000
 6K3  O3   C3   C4   112.40  3.000
 6K3  C2   C3   C4   109.38  3.000
 6K3  H8   CAR  H7   107.65  3.000
 6K3  H8   CAR  H6   107.61  3.000
 6K3  H7   CAR  H6   107.43  3.000
 6K3  H8   CAR  CAQ  111.59  3.000
 6K3  H7   CAR  CAQ  111.12  3.000
 6K3  H6   CAR  CAQ  111.24  3.000
 6K3  H10  CAQ  H9   106.00  3.000
 6K3  H10  CAQ  CAP  109.17  3.000
 6K3  H9   CAQ  CAP  109.35  3.000
 6K3  H10  CAQ  CAR  109.53  3.000
 6K3  H9   CAQ  CAR  109.58  3.000
 6K3  CAP  CAQ  CAR  112.97  3.000
 6K3  H12  CAP  H11  105.98  3.000
 6K3  H12  CAP  CAO  109.45  3.000
 6K3  H11  CAP  CAO  109.28  3.000
 6K3  H12  CAP  CAQ  109.39  3.000
 6K3  H11  CAP  CAQ  109.28  3.000
 6K3  CAO  CAP  CAQ  113.20  3.000
 6K3  H14  CAO  H13  106.03  3.000
 6K3  H14  CAO  CAN  109.16  3.000
 6K3  H13  CAO  CAN  109.51  3.000
 6K3  H14  CAO  CAP  109.25  3.000
 6K3  H13  CAO  CAP  109.41  3.000
 6K3  CAN  CAO  CAP  113.23  3.000
 6K3  H16  CAN  H15  106.11  3.000
 6K3  H16  CAN  CAM  109.57  3.000
 6K3  H15  CAN  CAM  109.46  3.000
 6K3  H16  CAN  CAO  109.47  3.000
 6K3  H15  CAN  CAO  109.20  3.000
 6K3  CAM  CAN  CAO  112.81  3.000
 6K3  H18  CAM  H17  106.89  3.000
 6K3  H18  CAM  CAL  109.26  3.000
 6K3  H17  CAM  CAL  109.73  3.000
 6K3  H18  CAM  CAN  109.52  3.000
 6K3  H17  CAM  CAN  109.56  3.000
 6K3  CAL  CAM  CAN  111.76  3.000
 6K3  H20  CAL  H19  107.10  3.000
 6K3  H20  CAL  O1   110.62  3.000
 6K3  H19  CAL  O1   110.03  3.000
 6K3  H20  CAL  CAM  110.24  3.000
 6K3  H19  CAL  CAM  109.87  3.000
 6K3  O1   CAL  CAM  108.97  3.000
 6K3  C1   O1   CAL  115.09  3.000
 6K3  H21  C1   C2   109.74  3.000
 6K3  H21  C1   O5   104.55  3.000
 6K3  C2   C1   O5   111.23  3.000
 6K3  H21  C1   O1   110.50  3.000
 6K3  C2   C1   O1   107.73  3.000
 6K3  O5   C1   O1   113.08  3.000
 6K3  C1   O5   C5   115.56  3.000
 6K3  H22  O6   C6   107.97  3.000
 6K3  H23  O3   C3   108.47  3.000
 6K3  H24  C2   O2   111.50  3.000
 6K3  H24  C2   C1   108.53  3.000
 6K3  O2   C2   C1   110.31  3.000
 6K3  H24  C2   C3   109.04  3.000
 6K3  O2   C2   C3   107.97  3.000
 6K3  C1   C2   C3   109.47  3.000
 6K3  H25  O2   C2   108.73  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
 6K3  Var_01  H19  CAL  O1   C1     43.08  30.0  1
 6K3  Var_02  CAO  CAP  CAQ  CAR  -179.56  30.0  3
 6K3  Var_03  CAN  CAO  CAP  CAQ   178.16  30.0  3
 6K3  Var_04  CAM  CAN  CAO  CAP  -179.98  30.0  3
 6K3  Var_05  CAL  CAM  CAN  CAO   176.18  30.0  3
 6K3  Var_06  O1   CAL  CAM  CAN   178.97  30.0  3
 6K3  Var_07  H6   CAR  CAQ  CAP   -60.63  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
 6K3  chir_01  C4  C5  C3  F4  positiv
 6K3  chir_02  C5  O5  C4  C6  negativ
 6K3  chir_03  C3  O3  C4  C2  negativ
 6K3  chir_04  C1  O1  O5  C2  negativ
 6K3  chir_05  C2  O2  C1  C3  positiv

