# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 07:18:48 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{S},3~{S},4~{S},5~{R})-2-[4-(2-hydroxyethyl)-2-oxidanyl-phenoxy]-2,5-bis(hydroxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCc1ccc(O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)c(O)c1
#
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
 9WZ  9WZ  (2~{S},3~{S},4~{S},5~{R})-2-[4-(2-hydroxyethyl)-2-oxidanyl-phenoxy]-2,5-bis(hydroxymethyl)oxolane-3,4-diol  D-saccharide  42  22  .  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_9WZ
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
 9WZ  C4   C  CH1   0  -0.041  -3.4310  -1.5123   0.1437
 9WZ  C5   C  CH1   0  -0.012  -3.4648   0.0209   0.2475
 9WZ  C6   C  CH2   0  -0.145  -3.2983   0.5116   1.6654
 9WZ  C3   C  CH1   0   0.004  -2.6585  -1.7155  -1.1528
 9WZ  O6   O  OH1   0  -0.673  -3.4627   1.9087   1.6985
 9WZ  O4   O  OH1   0  -0.665  -4.6952  -2.1170   0.0637
 9WZ  O3   O  OH1   0  -0.656  -2.0096  -2.9408  -1.3026
 9WZ  O5   O  O2    0  -0.487  -2.4228   0.5063  -0.6035
 9WZ  C2   C  CT    0   0.445  -1.6684  -0.5516  -1.0974
 9WZ  O2   O  O2    0  -0.516  -0.6850  -0.9430  -0.1493
 9WZ  C1   C  CH2   0  -0.216  -1.1187  -0.1787  -2.4717
 9WZ  O1   O  OH1   0  -0.657  -0.4197   1.0380  -2.5080
 9WZ  CAF  C  CR16  0  -0.436   2.3424   1.0153   0.4441
 9WZ  CAJ  C  CR6   0   0.309   1.0053   0.6360   0.4784
 9WZ  OAC  O  OH1   0  -0.604   0.0732   1.3146   1.1666
 9WZ  CAI  C  CR6   0   0.235   0.6024  -0.5082  -0.2233
 9WZ  CAD  C  CR16  0  -0.315   1.5469  -1.2401  -0.9264
 9WZ  CAE  C  CR16  0  -0.328   2.8791  -0.8479  -0.9588
 9WZ  CAK  C  CR6   0   0.111   3.2901   0.2876  -0.2718
 9WZ  CAH  C  CH2   0  -0.538   4.7361   0.6960  -0.2430
 9WZ  CAG  C  CH2   0  -0.132   5.4238   0.1645   1.0071
 9WZ  OAA  O  OH1   0  -0.671   6.7745   0.5687   0.9848
 9WZ  H1   H  HCH1  0   0.230  -2.8512  -1.9351   0.9752
 9WZ  H2   H  HCH1  0   0.233  -4.4188   0.3821  -0.1558
 9WZ  H3   H  HCH2  0   0.189  -4.0524   0.0029   2.2845
 9WZ  H4   H  HCH2  0   0.209  -2.3140   0.2069   2.0371
 9WZ  H5   H  HCH1  0   0.231  -3.3512  -1.5225  -1.9865
 9WZ  H6   H  HOH1  0   0.454  -3.1724   2.2237   2.5585
 9WZ  H7   H  HOH1  0   0.458  -5.0548  -2.2037   0.9513
 9WZ  H8   H  HOH1  0   0.459  -2.6676  -3.6031  -1.5347
 9WZ  H9   H  HCH2  0   0.233  -0.5289  -1.0139  -2.8644
 9WZ  H10  H  HCH2  0   0.243  -1.9810  -0.0720  -3.1343
 9WZ  H11  H  HOH1  0   0.455   0.5022   0.8776  -2.2879
 9WZ  H13  H  HOH1  0   0.473   0.4766   2.0704   1.6079
 9WZ  H14  H  HCR6  0   0.265   1.2297  -2.1388  -1.4412
 9WZ  H15  H  HCR6  0   0.249   3.5956  -1.4338  -1.5209
 9WZ  H16  H  HCH2  0   0.247   5.2487   0.3094  -1.1270
 9WZ  H17  H  HCH2  0   0.246   4.8230   1.7853  -0.2672
 9WZ  H18  H  HCH2  0   0.196   4.9028   0.5467   1.8949
 9WZ  H19  H  HCH2  0   0.198   5.3280  -0.9288   1.0301
 9WZ  H20  H  HOH1  0   0.454   7.2123   0.1921   1.7534
 9WZ  H12  H  HCR6  0   0.266   2.6501   1.9064   0.9834

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
 9WZ  O3   C3   single    1.395  0.020  1.395
 9WZ  C3   C4   single    1.523  0.020  1.523
 9WZ  C3   C2   single    1.529  0.020  1.529
 9WZ  O4   C4   single    1.404  0.020  1.404
 9WZ  O2   C2   single    1.421  0.020  1.421
 9WZ  O2   CAI  single    1.361  0.020  1.361
 9WZ  C1   C2   single    1.526  0.020  1.526
 9WZ  C1   O1   single    1.404  0.020  1.404
 9WZ  C4   C5   single    1.537  0.020  1.537
 9WZ  C2   O5   single    1.390  0.020  1.390
 9WZ  OAC  CAJ  single    1.343  0.020  1.343
 9WZ  CAI  CAJ  aromatic  1.401  0.020  1.401
 9WZ  CAI  CAD  aromatic  1.386  0.020  1.386
 9WZ  CAJ  CAF  aromatic  1.390  0.020  1.390
 9WZ  CAG  OAA  single    1.410  0.020  1.410
 9WZ  CAG  CAH  single    1.523  0.020  1.523
 9WZ  CAD  CAE  aromatic  1.389  0.020  1.389
 9WZ  CAF  CAK  aromatic  1.393  0.020  1.393
 9WZ  CAE  CAK  aromatic  1.389  0.020  1.389
 9WZ  CAK  CAH  single    1.503  0.020  1.503
 9WZ  C5   O5   single    1.430  0.020  1.430
 9WZ  C5   C6   single    1.510  0.020  1.510
 9WZ  C6   O6   single    1.407  0.020  1.407
 9WZ  C4   H1   single    0.970  0.020  1.090
 9WZ  C5   H2   single    0.970  0.020  1.090
 9WZ  C6   H3   single    0.970  0.020  1.090
 9WZ  C6   H4   single    0.970  0.020  1.090
 9WZ  C3   H5   single    0.970  0.020  1.090
 9WZ  O6   H6   single    0.850  0.020  0.980
 9WZ  O4   H7   single    0.850  0.020  0.980
 9WZ  O3   H8   single    0.850  0.020  0.980
 9WZ  C1   H9   single    0.970  0.020  1.090
 9WZ  C1   H10  single    0.970  0.020  1.090
 9WZ  O1   H11  single    0.850  0.020  0.980
 9WZ  CAF  H12  single    0.930  0.020  1.080
 9WZ  OAC  H13  single    0.850  0.020  0.980
 9WZ  CAD  H14  single    0.930  0.020  1.080
 9WZ  CAE  H15  single    0.930  0.020  1.080
 9WZ  CAH  H16  single    0.970  0.020  1.090
 9WZ  CAH  H17  single    0.970  0.020  1.090
 9WZ  CAG  H18  single    0.970  0.020  1.090
 9WZ  CAG  H19  single    0.970  0.020  1.090
 9WZ  OAA  H20  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
 9WZ  H1   C4   O4   110.66  3.000
 9WZ  H1   C4   C3   108.99  3.000
 9WZ  O4   C4   C3   110.54  3.000
 9WZ  H1   C4   C5   110.15  3.000
 9WZ  O4   C4   C5   114.44  3.000
 9WZ  C3   C4   C5   101.64  3.000
 9WZ  H2   C5   O5   107.65  3.000
 9WZ  H2   C5   C6   109.53  3.000
 9WZ  O5   C5   C6   111.60  3.000
 9WZ  H2   C5   C4   108.83  3.000
 9WZ  C6   C5   C4   112.66  3.000
 9WZ  O5   C5   C4   106.40  3.000
 9WZ  H4   C6   H3   107.24  3.000
 9WZ  H4   C6   O6   111.91  3.000
 9WZ  H3   C6   O6   111.45  3.000
 9WZ  H4   C6   C5   109.11  3.000
 9WZ  H3   C6   C5   107.61  3.000
 9WZ  O6   C6   C5   109.39  3.000
 9WZ  H5   C3   C2   107.55  3.000
 9WZ  H5   C3   O3   111.43  3.000
 9WZ  C2   C3   O3   111.80  3.000
 9WZ  H5   C3   C4   107.59  3.000
 9WZ  C2   C3   C4   101.31  3.000
 9WZ  O3   C3   C4   116.40  3.000
 9WZ  H6   O6   C6   108.13  3.000
 9WZ  H7   O4   C4   108.85  3.000
 9WZ  H8   O3   C3   108.21  3.000
 9WZ  C2   O5   C5   110.40  3.000
 9WZ  C1   C2   O2   114.76  3.000
 9WZ  C1   C2   O5   109.24  3.000
 9WZ  O2   C2   O5   110.37  3.000
 9WZ  O5   C2   C3   103.93  3.000
 9WZ  C1   C2   C3   112.74  3.000
 9WZ  O2   C2   C3   105.23  3.000
 9WZ  CAI  O2   C2   122.03  3.000
 9WZ  H10  C1   H9   106.38  3.000
 9WZ  H10  C1   O1   107.01  3.000
 9WZ  H9   C1   O1   112.56  3.000
 9WZ  H10  C1   C2   106.60  3.000
 9WZ  H9   C1   C2   109.30  3.000
 9WZ  O1   C1   C2   114.48  3.000
 9WZ  H11  O1   C1   109.09  3.000
 9WZ  H12  CAF  CAK  119.41  3.000
 9WZ  H12  CAF  CAJ  118.96  3.000
 9WZ  CAK  CAF  CAJ  121.63  3.000
 9WZ  CAI  CAJ  OAC  118.02  3.000
 9WZ  CAI  CAJ  CAF  119.14  3.000
 9WZ  OAC  CAJ  CAF  122.84  3.000
 9WZ  H13  OAC  CAJ  109.91  3.000
 9WZ  CAD  CAI  CAJ  119.28  3.000
 9WZ  CAD  CAI  O2   120.23  3.000
 9WZ  CAJ  CAI  O2   120.37  3.000
 9WZ  H14  CAD  CAE  120.27  3.000
 9WZ  H14  CAD  CAI  118.65  3.000
 9WZ  CAE  CAD  CAI  121.07  3.000
 9WZ  H15  CAE  CAK  120.21  3.000
 9WZ  H15  CAE  CAD  119.60  3.000
 9WZ  CAK  CAE  CAD  120.20  3.000
 9WZ  CAH  CAK  CAE  121.08  3.000
 9WZ  CAH  CAK  CAF  120.19  3.000
 9WZ  CAE  CAK  CAF  118.68  3.000
 9WZ  H17  CAH  H16  107.30  3.000
 9WZ  H17  CAH  CAG  109.28  3.000
 9WZ  H16  CAH  CAG  109.20  3.000
 9WZ  H17  CAH  CAK  110.29  3.000
 9WZ  H16  CAH  CAK  109.86  3.000
 9WZ  CAG  CAH  CAK  110.82  3.000
 9WZ  H19  CAG  H18  106.75  3.000
 9WZ  H19  CAG  OAA  111.68  3.000
 9WZ  H18  CAG  OAA  111.56  3.000
 9WZ  H19  CAG  CAH  108.99  3.000
 9WZ  H18  CAG  CAH  109.15  3.000
 9WZ  OAA  CAG  CAH  108.64  3.000
 9WZ  H20  OAA  CAG  108.14  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
 9WZ  CONST_01  CAD  CAI  CAJ  CAF    0.00   0.0  0
 9WZ  CONST_02  CAD  CAE  CAK  CAF    0.00   0.0  0
 9WZ  CONST_03  CAE  CAD  CAI  CAJ    0.00   0.0  0
 9WZ  CONST_04  CAE  CAK  CAF  CAJ    0.00   0.0  0
 9WZ  CONST_05  CAK  CAF  CAJ  CAI    0.00   0.0  0
 9WZ  CONST_06  CAK  CAE  CAD  CAI    0.00   0.0  0
 9WZ  CONST_07  CAF  CAJ  CAI  O2   180.00   0.0  0
 9WZ  CONST_08  CAE  CAD  CAI  O2   180.00   0.0  0
 9WZ  CONST_09  CAH  CAK  CAF  CAJ  180.00   0.0  0
 9WZ  CONST_10  CAD  CAI  CAJ  OAC  180.00   0.0  0
 9WZ  CONST_11  CAK  CAF  CAJ  OAC  180.00   0.0  0
 9WZ  CONST_12  CAH  CAK  CAE  CAD  180.00   0.0  0
 9WZ  CONST_13  H15  CAE  CAK  CAF  180.00   0.0  0
 9WZ  CONST_14  H14  CAD  CAI  CAJ  180.00   0.0  0
 9WZ  CONST_15  H12  CAF  CAJ  CAI  180.00   0.0  0
 9WZ  Var_01    CAJ  CAI  O2   C2    93.13  30.0  2
 9WZ  Var_02    CAG  CAH  CAK  CAF   82.10  30.0  2
 9WZ  Var_03    OAA  CAG  CAH  CAK  179.78  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
 9WZ  chir_01  C4  C3  O4  C5  positiv
 9WZ  chir_02  C5  O5  C4  C6  negativ
 9WZ  chir_03  C3  O3  C4  C2  negativ
 9WZ  chir_04  C2  O5  C1  C3  positiv

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
 9WZ  plan-1  O2   0.020
 9WZ  plan-1  CAF  0.020
 9WZ  plan-1  CAJ  0.020
 9WZ  plan-1  OAC  0.020
 9WZ  plan-1  CAI  0.020
 9WZ  plan-1  CAD  0.020
 9WZ  plan-1  CAE  0.020
 9WZ  plan-1  CAK  0.020
 9WZ  plan-1  CAH  0.020
 9WZ  plan-1  H14  0.020
 9WZ  plan-1  H15  0.020
 9WZ  plan-1  H12  0.020

