# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 07:26:57 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (4S,5R,6R)-4,5-dihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-5,6-dihydro-4H-pyran-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H]1OC(=C[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
 KFN  KFN  '(4S,5R,6R)-4,5-dihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-5,6-dihydro-4H-pyran-2-carboxylic acid'  D-saccharide  30  17  .  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_KFN
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
 KFN  C10   C  C      0   0.373   2.0672  -2.2950   0.1870
 KFN  C2    C  C1     0  -0.416   2.5506   0.1196  -0.3641
 KFN  C3    C  CH1    0   0.022   2.1634   1.5614  -0.5043
 KFN  C4    C  CH1    0   0.031   0.8167   1.7865   0.1661
 KFN  C5    C  CH1    0   0.003  -0.1236   0.6690  -0.2767
 KFN  C6    C  CH1    0  -0.046  -1.5362   0.8086   0.2832
 KFN  C7    C  CH1    0  -0.013  -2.4719  -0.3135  -0.2087
 KFN  C9    C  CH2    0  -0.161  -3.9005  -0.0490   0.2399
 KFN  O4    O  OH1    0  -0.676   0.2379   3.0148  -0.1964
 KFN  O9    O  OC    -1  -0.593   1.1446  -3.0657   0.4963
 KFN  O8    O  O      0  -0.591   3.2711  -2.5700   0.0317
 KFN  O3    O  OH1    0  -0.676   3.0961   2.4303   0.1123
 KFN  O5    O  O2     0  -0.484   0.3639  -0.5881   0.1652
 KFN  C20   C  C      0   0.179   1.6816  -0.8341  -0.0258
 KFN  O6    O  OH1    0  -0.664  -1.5288   0.8853   1.6900
 KFN  O7    O  OH1    0  -0.661  -2.3909  -0.4793  -1.6063
 KFN  O10   O  OH1    0  -0.671  -4.7019  -1.1497  -0.1211
 KFN  H2    H  H      0   0.249   3.5810  -0.1607  -0.5373
 KFN  H3    H  HCH1   0   0.218   2.0591   1.8209  -1.5684
 KFN  H4    H  HCH1   0   0.210   0.9602   1.7172   1.2546
 KFN  HA    H  HOH1   0   0.455   3.8846   2.4684  -0.4372
 KFN  H5    H  HCH1   0   0.236  -0.1706   0.6719  -1.3740
 KFN  HB    H  HOH1   0   0.453   0.8544   3.7163   0.0381
 KFN  H6    H  HCH1   0   0.248  -1.9352   1.7656  -0.0696
 KFN  H7    H  HCH1   0   0.234  -2.1393  -1.2641   0.2227
 KFN  HC    H  HOH1   0   0.445  -1.1364   0.0754   2.0355
 KFN  H91C  H  HCH2   0   0.207  -3.9145   0.1230   1.3213
 KFN  H92C  H  HCH2   0   0.189  -4.2530   0.8805  -0.2343
 KFN  HD    H  HOH1   0   0.444  -2.7584   0.3037  -2.0316
 KFN  H10   H  HOH1   0   0.454  -5.5915  -0.9872   0.2038

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
 KFN  C10  O9    deloc   1.241  0.020  1.241
 KFN  C10  O8    deloc   1.245  0.020  1.245
 KFN  C10  C20   single  1.526  0.020  1.526
 KFN  C2   C3    single  1.499  0.020  1.499
 KFN  C2   C20   double  1.334  0.020  1.334
 KFN  C3   C4    single  1.521  0.020  1.521
 KFN  C3   O3    single  1.416  0.020  1.416
 KFN  C4   C5    single  1.526  0.020  1.526
 KFN  C4   O4    single  1.405  0.020  1.405
 KFN  C5   C6    single  1.526  0.020  1.526
 KFN  C5   O5    single  1.419  0.020  1.419
 KFN  C6   C7    single  1.542  0.020  1.542
 KFN  C6   O6    single  1.409  0.020  1.409
 KFN  C7   C9    single  1.521  0.020  1.521
 KFN  C7   O7    single  1.410  0.020  1.410
 KFN  C9   O10   single  1.409  0.020  1.409
 KFN  O5   C20   single  1.354  0.020  1.354
 KFN  C2   H2    single  0.930  0.020  1.080
 KFN  C3   H3    single  0.970  0.020  1.090
 KFN  C4   H4    single  0.970  0.020  1.090
 KFN  O3   HA    single  0.850  0.020  0.980
 KFN  C5   H5    single  0.970  0.020  1.090
 KFN  O4   HB    single  0.850  0.020  0.980
 KFN  C6   H6    single  0.970  0.020  1.090
 KFN  C7   H7    single  0.970  0.020  1.090
 KFN  O6   HC    single  0.850  0.020  0.980
 KFN  C9   H91C  single  0.970  0.020  1.090
 KFN  C9   H92C  single  0.970  0.020  1.090
 KFN  O7   HD    single  0.850  0.020  0.980
 KFN  O10  H10   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
 KFN  C20   C10  O8    116.01  3.000
 KFN  C20   C10  O9    116.19  3.000
 KFN  O8    C10  O9    127.80  3.000
 KFN  H2    C2   C20   118.41  3.000
 KFN  H2    C2   C3    118.70  3.000
 KFN  C20   C2   C3    122.89  3.000
 KFN  H3    C3   O3    109.80  3.000
 KFN  H3    C3   C4    107.90  3.000
 KFN  O3    C3   C4    107.48  3.000
 KFN  H3    C3   C2    109.98  3.000
 KFN  O3    C3   C2    112.29  3.000
 KFN  C4    C3   C2    109.25  3.000
 KFN  H4    C4   O4    111.34  3.000
 KFN  H4    C4   C5    108.74  3.000
 KFN  O4    C4   C5    108.14  3.000
 KFN  H4    C4   C3    108.14  3.000
 KFN  O4    C4   C3    112.35  3.000
 KFN  C5    C4   C3    108.02  3.000
 KFN  H5    C5   O5    109.16  3.000
 KFN  H5    C5   C6    109.08  3.000
 KFN  O5    C5   C6    106.55  3.000
 KFN  H5    C5   C4    108.31  3.000
 KFN  O5    C5   C4    110.28  3.000
 KFN  C6    C5   C4    113.39  3.000
 KFN  H6    C6   O6    106.02  3.000
 KFN  H6    C6   C7    108.18  3.000
 KFN  O6    C6   C7    111.19  3.000
 KFN  H6    C6   C5    107.40  3.000
 KFN  O6    C6   C5    111.50  3.000
 KFN  C7    C6   C5    112.22  3.000
 KFN  H7    C7   O7    105.71  3.000
 KFN  H7    C7   C9    108.66  3.000
 KFN  O7    C7   C9    111.53  3.000
 KFN  H7    C7   C6    108.76  3.000
 KFN  O7    C7   C6    111.54  3.000
 KFN  C9    C7   C6    110.46  3.000
 KFN  H92C  C9   H91C  106.78  3.000
 KFN  H92C  C9   O10   111.53  3.000
 KFN  H91C  C9   O10   111.63  3.000
 KFN  H92C  C9   C7    108.69  3.000
 KFN  H91C  C9   C7    109.31  3.000
 KFN  O10   C9   C7    108.84  3.000
 KFN  HB    O4   C4    108.07  3.000
 KFN  HA    O3   C3    108.39  3.000
 KFN  C20   O5   C5    116.83  3.000
 KFN  O5    C20  C2    122.68  3.000
 KFN  O5    C20  C10   113.59  3.000
 KFN  C2    C20  C10   123.74  3.000
 KFN  HC    O6   C6    108.32  3.000
 KFN  HD    O7   C7    108.66  3.000
 KFN  H10   O10  C9    107.93  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
 KFN  Var_01  O5  C20  C2   C3     2.83  30.0  1
 KFN  Var_02  O9  C10  C20  C2  -179.83  30.0  2

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
 KFN  chir_01  C3  C2  C4  O3  negativ
 KFN  chir_02  C4  O4  C3  C5  positiv
 KFN  chir_03  C5  O5  C6  C4  negativ
 KFN  chir_04  C6  O6  C5  C7  negativ
 KFN  chir_05  C7  O7  C6  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
 KFN  plan-1  C10  0.020
 KFN  plan-1  O9   0.020
 KFN  plan-1  O8   0.020
 KFN  plan-1  C20  0.020

