# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 13:12:58 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{S},4~{R},6~{R})-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](C[C@@H]2C[C@H](O)O[C@H](CO)C2)[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
 DS8  DS8  (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{S},4~{R},6~{R})-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol  ligand  44  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DS8
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
 DS8  C1   C  CH1   0   0.030  -1.3033  -0.4530  -0.3871
 DS8  C2   C  CH1   0   0.021  -2.4532  -1.1482  -1.1050
 DS8  C3   C  CH1   0  -0.038  -3.7624  -0.3930  -0.8494
 DS8  C4   C  CH1   0   0.022  -3.9481  -0.1685   0.6477
 DS8  C5   C  CH1   0  -0.019  -2.7086   0.4423   1.3251
 DS8  C6   C  CH3   0  -0.692  -2.4856   1.9322   1.0961
 DS8  C7   C  CH2   0  -0.434   0.0254  -1.1755  -0.5422
 DS8  C8   C  CH1   0   0.298   2.7427   1.5622  -0.1688
 DS8  O2   O  OH1   0  -0.673  -2.5417  -2.4741  -0.6396
 DS8  O3   O  OH1   0  -0.670  -3.7112   0.8080  -1.5839
 DS8  C9   C  CH2   0  -0.483   1.4733   0.9110  -0.6845
 DS8  O4   O  OH1   0  -0.674  -5.1030   0.6223   0.8127
 DS8  C10  C  CH1   0  -0.259   1.2234  -0.4177   0.0274
 DS8  C11  C  CH2   0  -0.434   2.4839  -1.2777  -0.0477
 DS8  C12  C  CH1   0   0.011   3.7111  -0.5017   0.4130
 DS8  C13  C  CH2   0  -0.153   4.9759  -1.3106   0.2346
 DS8  O5   O  O2    0  -0.501  -1.5729  -0.3383   0.9974
 DS8  O8   O  OH1   0  -0.663   2.9920   2.7121  -0.8972
 DS8  O12  O  O2    0  -0.501   3.8472   0.6996  -0.3208
 DS8  O13  O  OH1   0  -0.672   6.0633  -0.6184   0.8012
 DS8  H1   H  HCH1  0   0.224  -1.2102   0.5400  -0.8449
 DS8  H2   H  HCH1  0   0.226  -2.2462  -1.1190  -2.1850
 DS8  H3   H  HCH1  0   0.224  -4.6004  -1.0153  -1.2053
 DS8  H4   H  HCH1  0   0.224  -4.0940  -1.1623   1.0924
 DS8  H5   H  HCH1  0   0.235  -2.8349   0.3029   2.4048
 DS8  H6   H  HCH3  0   0.231  -3.3384   2.5052   1.4594
 DS8  H7   H  HCH3  0   0.232  -1.6127   2.2595   1.6627
 DS8  H8   H  HCH3  0   0.232  -2.3332   2.1989   0.0524
 DS8  H9   H  HCH2  0   0.235  -0.0377  -2.1593  -0.0700
 DS8  H10  H  HCH2  0   0.223   0.1945  -1.3541  -1.6096
 DS8  H11  H  HCH1  0   0.172   2.6218   1.7876   0.9061
 DS8  H12  H  HOH1  0   0.453  -3.2413  -2.9218  -1.1257
 DS8  H13  H  HOH1  0   0.453  -4.4243   1.3774  -1.2769
 DS8  H15  H  HCH2  0   0.225   1.5712   0.7443  -1.7637
 DS8  H16  H  HOH1  0   0.458  -5.2925   0.7097   1.7523
 DS8  H17  H  HCH1  0   0.228   1.0294  -0.2064   1.0855
 DS8  H18  H  HCH2  0   0.237   2.3653  -2.1673   0.5763
 DS8  H19  H  HCH2  0   0.219   2.6371  -1.6244  -1.0767
 DS8  H20  H  HCH1  0   0.204   3.5919  -0.2688   1.4848
 DS8  H21  H  HCH2  0   0.199   4.8204  -2.2855   0.7151
 DS8  H22  H  HCH2  0   0.195   5.1291  -1.5045  -0.8358
 DS8  H23  H  HOH1  0   0.458   3.6562   3.2395  -0.4408
 DS8  H24  H  HOH1  0   0.455   6.8543  -1.1480   0.6687
 DS8  H14  H  HCH2  0   0.242   0.6394   1.6007  -0.5347

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
 DS8  C6   C5   single  1.524  0.020  1.524
 DS8  C5   C4   single  1.539  0.020  1.539
 DS8  C5   O5   single  1.417  0.020  1.417
 DS8  C4   O4   single  1.409  0.020  1.409
 DS8  C4   C3   single  1.525  0.020  1.525
 DS8  O5   C1   single  1.415  0.020  1.415
 DS8  O8   C8   single  1.384  0.020  1.384
 DS8  C9   C8   single  1.517  0.020  1.517
 DS8  C9   C10  single  1.528  0.020  1.528
 DS8  C7   C10  single  1.528  0.020  1.528
 DS8  C7   C1   single  1.520  0.020  1.520
 DS8  C3   O3   single  1.409  0.020  1.409
 DS8  C3   C2   single  1.533  0.020  1.533
 DS8  O12  C8   single  1.410  0.020  1.410
 DS8  O12  C12  single  1.414  0.020  1.414
 DS8  C11  C10  single  1.528  0.020  1.528
 DS8  C11  C12  single  1.523  0.020  1.523
 DS8  C1   C2   single  1.523  0.020  1.523
 DS8  C13  C12  single  1.512  0.020  1.512
 DS8  C13  O13  single  1.408  0.020  1.408
 DS8  C2   O2   single  1.408  0.020  1.408
 DS8  C1   H1   single  0.970  0.020  1.090
 DS8  C2   H2   single  0.970  0.020  1.090
 DS8  C3   H3   single  0.970  0.020  1.090
 DS8  C4   H4   single  0.970  0.020  1.090
 DS8  C5   H5   single  0.970  0.020  1.090
 DS8  C6   H6   single  0.970  0.020  1.090
 DS8  C6   H7   single  0.970  0.020  1.090
 DS8  C6   H8   single  0.970  0.020  1.090
 DS8  C7   H9   single  0.970  0.020  1.090
 DS8  C7   H10  single  0.970  0.020  1.090
 DS8  C8   H11  single  0.970  0.020  1.090
 DS8  O2   H12  single  0.850  0.020  0.980
 DS8  O3   H13  single  0.850  0.020  0.980
 DS8  C9   H14  single  0.970  0.020  1.090
 DS8  C9   H15  single  0.970  0.020  1.090
 DS8  O4   H16  single  0.850  0.020  0.980
 DS8  C10  H17  single  0.970  0.020  1.090
 DS8  C11  H18  single  0.970  0.020  1.090
 DS8  C11  H19  single  0.970  0.020  1.090
 DS8  C12  H20  single  0.970  0.020  1.090
 DS8  C13  H21  single  0.970  0.020  1.090
 DS8  C13  H22  single  0.970  0.020  1.090
 DS8  O8   H23  single  0.850  0.020  0.980
 DS8  O13  H24  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
 DS8  H1   C1   O5   110.54  3.000
 DS8  H1   C1   C7   108.26  3.000
 DS8  O5   C1   C7   107.75  3.000
 DS8  H1   C1   C2   106.28  3.000
 DS8  C7   C1   C2   113.25  3.000
 DS8  O5   C1   C2   110.75  3.000
 DS8  H2   C2   O2   111.18  3.000
 DS8  H2   C2   C3   108.14  3.000
 DS8  O2   C2   C3   110.80  3.000
 DS8  H2   C2   C1   107.97  3.000
 DS8  O2   C2   C1   108.75  3.000
 DS8  C3   C2   C1   109.95  3.000
 DS8  H3   C3   O3   109.90  3.000
 DS8  H3   C3   C4   107.90  3.000
 DS8  O3   C3   C4   113.00  3.000
 DS8  H3   C3   C2   108.49  3.000
 DS8  O3   C3   C2   107.58  3.000
 DS8  C4   C3   C2   109.89  3.000
 DS8  H4   C4   O4   110.58  3.000
 DS8  H4   C4   C5   106.73  3.000
 DS8  O4   C4   C5   112.69  3.000
 DS8  H4   C4   C3   106.28  3.000
 DS8  O4   C4   C3   107.29  3.000
 DS8  C5   C4   C3   113.10  3.000
 DS8  H5   C5   O5   104.49  3.000
 DS8  H5   C5   C6   106.82  3.000
 DS8  O5   C5   C6   112.75  3.000
 DS8  H5   C5   C4   106.88  3.000
 DS8  O5   C5   C4   108.98  3.000
 DS8  C6   C5   C4   116.10  3.000
 DS8  H8   C6   H7   108.22  3.000
 DS8  H8   C6   H6   107.48  3.000
 DS8  H7   C6   H6   107.18  3.000
 DS8  H8   C6   C5   113.85  3.000
 DS8  H7   C6   C5   109.42  3.000
 DS8  H6   C6   C5   110.45  3.000
 DS8  H10  C7   H9   106.44  3.000
 DS8  H10  C7   C10  108.85  3.000
 DS8  H9   C7   C10  109.31  3.000
 DS8  H10  C7   C1   108.17  3.000
 DS8  H9   C7   C1   109.46  3.000
 DS8  C10  C7   C1   114.31  3.000
 DS8  H11  C8   O12  108.39  3.000
 DS8  H11  C8   O8   111.24  3.000
 DS8  O12  C8   O8   108.10  3.000
 DS8  H11  C8   C9   109.07  3.000
 DS8  O12  C8   C9   110.87  3.000
 DS8  O8   C8   C9   109.18  3.000
 DS8  H12  O2   C2   108.47  3.000
 DS8  H13  O3   C3   108.12  3.000
 DS8  H15  C9   H14  107.41  3.000
 DS8  H15  C9   C10  109.94  3.000
 DS8  H14  C9   C10  111.11  3.000
 DS8  H15  C9   C8   108.98  3.000
 DS8  H14  C9   C8   108.73  3.000
 DS8  C10  C9   C8   110.59  3.000
 DS8  H16  O4   C4   109.06  3.000
 DS8  H17  C10  C11  107.58  3.000
 DS8  H17  C10  C9   108.12  3.000
 DS8  C11  C10  C9   109.37  3.000
 DS8  H17  C10  C7   108.46  3.000
 DS8  C11  C10  C7   110.46  3.000
 DS8  C9   C10  C7   112.70  3.000
 DS8  H19  C11  H18  107.07  3.000
 DS8  H19  C11  C12  109.41  3.000
 DS8  H18  C11  C12  109.23  3.000
 DS8  H19  C11  C10  109.84  3.000
 DS8  H18  C11  C10  109.91  3.000
 DS8  C12  C11  C10  111.28  3.000
 DS8  H20  C12  O12  109.58  3.000
 DS8  H20  C12  C13  108.54  3.000
 DS8  O12  C12  C13  108.22  3.000
 DS8  H20  C12  C11  108.32  3.000
 DS8  C13  C12  C11  111.45  3.000
 DS8  O12  C12  C11  110.69  3.000
 DS8  H22  C13  H21  106.83  3.000
 DS8  H22  C13  O13  111.79  3.000
 DS8  H21  C13  O13  111.70  3.000
 DS8  H22  C13  C12  109.03  3.000
 DS8  H21  C13  C12  107.76  3.000
 DS8  O13  C13  C12  109.60  3.000
 DS8  C5   O5   C1   115.07  3.000
 DS8  H23  O8   C8   109.26  3.000
 DS8  C12  O12  C8   112.86  3.000
 DS8  H24  O13  C13  108.01  3.000

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
 DS8  chir_01  C1   O5   C7   C2   negativ
 DS8  chir_02  C2   O2   C1   C3   positiv
 DS8  chir_03  C3   O3   C2   C4   negativ
 DS8  chir_04  C4   O4   C5   C3   positiv
 DS8  chir_05  C5   O5   C4   C6   positiv
 DS8  chir_06  C8   O8   O12  C9   positiv
 DS8  chir_07  C10  C9   C7   C11  negativ
 DS8  chir_08  C12  O12  C13  C11  positiv

