# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:16:53 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1~{S},2~{S},3~{S},4~{S})-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1=C[C@H](O)[C@H](O)[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
 FDK  FDK  (1~{S},2~{S},3~{S},4~{S})-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol  ligand  24  12  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FDK
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
 FDK  OAC  O  OH1   0  -0.661   0.2764  -2.0945  -0.8516
 FDK  CAJ  C  CH1   0  -0.104   0.3125  -1.2360   0.2725
 FDK  CAL  C  CH1   0   0.047  -1.0967  -0.6952   0.5274
 FDK  OAE  O  OH1   0  -0.668  -2.0603  -1.7148   0.5268
 FDK  CAK  C  CH1   0   0.038  -1.4558   0.3233  -0.5443
 FDK  OAD  O  OH1   0  -0.670  -2.8064   0.6791  -0.3985
 FDK  CAI  C  CH1   0  -0.054  -0.5246   1.5305  -0.4302
 FDK  OAB  O  OH1   0  -0.664  -0.9299   2.3036   0.6856
 FDK  CAF  C  C1    0  -0.301   0.9108   1.1098  -0.2943
 FDK  CAH  C  C     0   0.037   1.2995  -0.1120   0.0573
 FDK  CAG  C  CH2   0  -0.169   2.7346  -0.4985   0.2460
 FDK  OAA  O  OH1   0  -0.663   3.5923   0.5711  -0.0420
 FDK  H1   H  HOH1  0   0.455   1.0355  -2.6828  -0.8150
 FDK  H2   H  HCH1  0   0.234   0.6184  -1.8021   1.1655
 FDK  H3   H  HCH1  0   0.217  -1.0673  -0.1840   1.5008
 FDK  H4   H  HOH1  0   0.448  -1.8368  -2.3442   1.2199
 FDK  H5   H  HCH1  0   0.215  -1.2753  -0.1248  -1.5323
 FDK  H6   H  HOH1  0   0.449  -3.0231   1.3200  -1.0830
 FDK  H7   H  HCH1  0   0.222  -0.6246   2.1281  -1.3490
 FDK  H8   H  HOH1  0   0.451  -0.3445   3.0646   0.7472
 FDK  H9   H  H     0   0.257   1.6504   1.8854  -0.4620
 FDK  H10  H  HCH2  0   0.217   2.8535  -0.8500   1.2823
 FDK  H11  H  HCH2  0   0.206   2.9542  -1.3696  -0.3895
 FDK  H12  H  HOH1  0   0.462   4.4965   0.2741   0.0926

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
 FDK  OAC  CAJ  single  1.415  0.020  1.415
 FDK  OAA  CAG  single  1.401  0.020  1.401
 FDK  CAG  CAH  single  1.498  0.020  1.498
 FDK  CAH  CAJ  single  1.511  0.020  1.511
 FDK  CAH  CAF  double  1.329  0.020  1.329
 FDK  CAJ  CAL  single  1.531  0.020  1.531
 FDK  CAF  CAI  single  1.502  0.020  1.502
 FDK  CAK  CAI  single  1.529  0.020  1.529
 FDK  CAK  CAL  single  1.522  0.020  1.522
 FDK  CAK  OAD  single  1.404  0.020  1.404
 FDK  CAI  OAB  single  1.417  0.020  1.417
 FDK  CAL  OAE  single  1.403  0.020  1.403
 FDK  OAC  H1   single  0.850  0.020  0.980
 FDK  CAJ  H2   single  0.970  0.020  1.090
 FDK  CAL  H3   single  0.970  0.020  1.090
 FDK  OAE  H4   single  0.850  0.020  0.980
 FDK  CAK  H5   single  0.970  0.020  1.090
 FDK  OAD  H6   single  0.850  0.020  0.980
 FDK  CAI  H7   single  0.970  0.020  1.090
 FDK  OAB  H8   single  0.850  0.020  0.980
 FDK  CAF  H9   single  0.930  0.020  1.080
 FDK  CAG  H10  single  0.970  0.020  1.090
 FDK  CAG  H11  single  0.970  0.020  1.090
 FDK  OAA  H12  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
 FDK  H1   OAC  CAJ  108.72  3.000
 FDK  H2   CAJ  CAH  108.46  3.000
 FDK  H2   CAJ  CAL  107.60  3.000
 FDK  CAH  CAJ  CAL  111.23  3.000
 FDK  H2   CAJ  OAC  109.85  3.000
 FDK  CAL  CAJ  OAC  108.85  3.000
 FDK  CAH  CAJ  OAC  110.78  3.000
 FDK  H3   CAL  CAK  108.57  3.000
 FDK  H3   CAL  OAE  110.89  3.000
 FDK  CAK  CAL  OAE  108.91  3.000
 FDK  H3   CAL  CAJ  106.68  3.000
 FDK  OAE  CAL  CAJ  112.06  3.000
 FDK  CAK  CAL  CAJ  109.66  3.000
 FDK  H4   OAE  CAL  108.38  3.000
 FDK  H5   CAK  CAI  106.79  3.000
 FDK  H5   CAK  OAD  110.75  3.000
 FDK  CAI  CAK  OAD  112.21  3.000
 FDK  H5   CAK  CAL  108.74  3.000
 FDK  OAD  CAK  CAL  108.87  3.000
 FDK  CAI  CAK  CAL  109.41  3.000
 FDK  H6   OAD  CAK  108.14  3.000
 FDK  H7   CAI  CAF  108.33  3.000
 FDK  H7   CAI  OAB  109.59  3.000
 FDK  CAF  CAI  OAB  110.80  3.000
 FDK  H7   CAI  CAK  108.13  3.000
 FDK  OAB  CAI  CAK  108.39  3.000
 FDK  CAF  CAI  CAK  111.57  3.000
 FDK  H8   OAB  CAI  107.94  3.000
 FDK  H9   CAF  CAH  119.91  3.000
 FDK  H9   CAF  CAI  115.93  3.000
 FDK  CAH  CAF  CAI  124.11  3.000
 FDK  CAG  CAH  CAF  123.40  3.000
 FDK  CAF  CAH  CAJ  122.02  3.000
 FDK  CAG  CAH  CAJ  114.57  3.000
 FDK  H11  CAG  H10  105.63  3.000
 FDK  H11  CAG  OAA  111.32  3.000
 FDK  H10  CAG  OAA  111.79  3.000
 FDK  H11  CAG  CAH  108.82  3.000
 FDK  H10  CAG  CAH  107.72  3.000
 FDK  OAA  CAG  CAH  111.32  3.000
 FDK  H12  OAA  CAG  108.13  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
 FDK  Var_01  CAI  CAF  CAH  CAJ    4.00  30.0  1
 FDK  Var_02  OAA  CAG  CAH  CAJ  176.68  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
 FDK  chir_01  CAJ  OAC  CAH  CAL  negativ
 FDK  chir_02  CAL  OAE  CAJ  CAK  negativ
 FDK  chir_03  CAK  OAD  CAL  CAI  positiv
 FDK  chir_04  CAI  OAB  CAK  CAF  positiv

