# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:46:03 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R},6~{R})-2-(hydroxymethyl)-3,6-bis(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)[C@H]2O)[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
 DSQ  DSQ  (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R},6~{R})-2-(hydroxymethyl)-3,6-bis(oxidanyl)oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol  ligand  45  21  .  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_DSQ
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
 DSQ  C8   C  CH1   0   0.302  -2.4569  -1.7618   0.0671
 DSQ  C9   C  CH2   0  -0.500  -1.2119  -1.0891  -0.4710
 DSQ  C10  C  CH1   0  -0.280  -1.1012   0.3493   0.0326
 DSQ  C11  C  CH1   0   0.058  -2.4138   1.0934  -0.2113
 DSQ  C12  C  CH1   0  -0.007  -3.6028   0.2746   0.3148
 DSQ  C13  C  CH2   0  -0.161  -4.9308   0.9252  -0.0100
 DSQ  O8   O  OH1   0  -0.661  -2.5811  -3.0140  -0.5053
 DSQ  O12  O  O2    0  -0.501  -3.6031  -1.0109  -0.2654
 DSQ  O13  O  OH1   0  -0.670  -5.9667   0.1867   0.5921
 DSQ  O11  O  OH1   0  -0.672  -2.3405   2.3433   0.4411
 DSQ  C7   C  CH2   0  -0.436   0.0713   1.0963  -0.6079
 DSQ  C1   C  CH1   0   0.023   1.4116   0.3988  -0.4414
 DSQ  C2   C  CH1   0   0.024   2.5600   1.1234  -1.1320
 DSQ  O2   O  OH1   0  -0.673   2.6294   2.4410  -0.6408
 DSQ  C3   C  CH1   0  -0.037   3.8748   0.3780  -0.8736
 DSQ  O3   O  OH1   0  -0.670   3.8499  -0.8089  -1.6324
 DSQ  C4   C  CH1   0   0.022   4.0446   0.1261   0.6214
 DSQ  O4   O  OH1   0  -0.674   5.2053  -0.6562   0.7856
 DSQ  C5   C  CH1   0  -0.018   2.8040  -0.5093   1.2729
 DSQ  O5   O  O2    0  -0.502   1.6642   0.2654   0.9442
 DSQ  C6   C  CH3   0  -0.695   2.5975  -1.9969   1.0146
 DSQ  H1   H  HCH1  0   0.176  -2.3892  -1.8280   1.1677
 DSQ  H2   H  HCH2  0   0.253  -0.3375  -1.6633  -0.1567
 DSQ  H3   H  HCH2  0   0.230  -1.2410  -1.1075  -1.5667
 DSQ  H4   H  HCH1  0   0.233  -0.9472   0.3153   1.1183
 DSQ  H5   H  HCH1  0   0.207  -2.5437   1.2240  -1.2970
 DSQ  H6   H  HCH1  0   0.207  -3.5013   0.1980   1.4111
 DSQ  H7   H  HCH2  0   0.197  -4.9136   1.9578   0.3574
 DSQ  H8   H  HCH2  0   0.197  -5.0453   0.9743  -1.1022
 DSQ  H9   H  HOH1  0   0.459  -3.2418  -3.5210  -0.0217
 DSQ  H10  H  HOH1  0   0.456  -6.7956   0.6393   0.4138
 DSQ  H11  H  HOH1  0   0.455  -2.9058   2.9711  -0.0159
 DSQ  H12  H  HCH2  0   0.221  -0.1160   1.1970  -1.6829
 DSQ  H13  H  HCH2  0   0.243   0.1288   2.1072  -0.2034
 DSQ  H14  H  HCH1  0   0.226   1.3446  -0.5862  -0.9206
 DSQ  H15  H  HCH1  0   0.225   2.3662   1.1121  -2.2148
 DSQ  H16  H  HOH1  0   0.453   3.3268   2.9055  -1.1140
 DSQ  H17  H  HCH1  0   0.224   4.7095   1.0182  -1.2049
 DSQ  H18  H  HOH1  0   0.453   4.5644  -1.3758  -1.3238
 DSQ  H19  H  HCH1  0   0.224   4.1753   1.1125   1.0866
 DSQ  H20  H  HOH1  0   0.458   5.3848  -0.7593   1.7257
 DSQ  H21  H  HCH1  0   0.235   2.9157  -0.3879   2.3564
 DSQ  H22  H  HCH3  0   0.233   3.4515  -2.5695   1.3758
 DSQ  H23  H  HCH3  0   0.233   1.7210  -2.3421   1.5652
 DSQ  H24  H  HCH3  0   0.233   2.4579  -2.2453  -0.0356

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
 DSQ  C6   C5   single  1.524  0.020  1.524
 DSQ  C5   C4   single  1.539  0.020  1.539
 DSQ  C5   O5   single  1.417  0.020  1.417
 DSQ  C4   O4   single  1.409  0.020  1.409
 DSQ  C4   C3   single  1.526  0.020  1.526
 DSQ  O5   C1   single  1.415  0.020  1.415
 DSQ  C7   C1   single  1.520  0.020  1.520
 DSQ  C7   C10  single  1.531  0.020  1.531
 DSQ  C3   O3   single  1.409  0.020  1.409
 DSQ  C3   C2   single  1.533  0.020  1.533
 DSQ  C9   C10  single  1.528  0.020  1.528
 DSQ  C9   C8   single  1.514  0.020  1.514
 DSQ  C1   C2   single  1.523  0.020  1.523
 DSQ  C11  C10  single  1.528  0.020  1.528
 DSQ  C11  O11  single  1.412  0.020  1.412
 DSQ  C11  C12  single  1.537  0.020  1.537
 DSQ  O12  C8   single  1.410  0.020  1.410
 DSQ  O12  C12  single  1.410  0.020  1.410
 DSQ  O8   C8   single  1.382  0.020  1.382
 DSQ  C13  C12  single  1.514  0.020  1.514
 DSQ  C13  O13  single  1.408  0.020  1.408
 DSQ  C2   O2   single  1.408  0.020  1.408
 DSQ  C8   H1   single  0.970  0.020  1.090
 DSQ  C9   H2   single  0.970  0.020  1.090
 DSQ  C9   H3   single  0.970  0.020  1.090
 DSQ  C10  H4   single  0.970  0.020  1.090
 DSQ  C11  H5   single  0.970  0.020  1.090
 DSQ  C12  H6   single  0.970  0.020  1.090
 DSQ  C13  H7   single  0.970  0.020  1.090
 DSQ  C13  H8   single  0.970  0.020  1.090
 DSQ  O8   H9   single  0.850  0.020  0.980
 DSQ  O13  H10  single  0.850  0.020  0.980
 DSQ  O11  H11  single  0.850  0.020  0.980
 DSQ  C7   H12  single  0.970  0.020  1.090
 DSQ  C7   H13  single  0.970  0.020  1.090
 DSQ  C1   H14  single  0.970  0.020  1.090
 DSQ  C2   H15  single  0.970  0.020  1.090
 DSQ  O2   H16  single  0.850  0.020  0.980
 DSQ  C3   H17  single  0.970  0.020  1.090
 DSQ  O3   H18  single  0.850  0.020  0.980
 DSQ  C4   H19  single  0.970  0.020  1.090
 DSQ  O4   H20  single  0.850  0.020  0.980
 DSQ  C5   H21  single  0.970  0.020  1.090
 DSQ  C6   H22  single  0.970  0.020  1.090
 DSQ  C6   H23  single  0.970  0.020  1.090
 DSQ  C6   H24  single  0.970  0.020  1.090

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
 DSQ  H1   C8   O12  108.46  3.000
 DSQ  H1   C8   O8   111.33  3.000
 DSQ  O12  C8   O8   108.17  3.000
 DSQ  H1   C8   C9   109.29  3.000
 DSQ  O8   C8   C9   109.22  3.000
 DSQ  O12  C8   C9   110.37  3.000
 DSQ  H3   C9   H2   107.46  3.000
 DSQ  H3   C9   C10  110.31  3.000
 DSQ  H2   C9   C10  110.00  3.000
 DSQ  H3   C9   C8   109.03  3.000
 DSQ  H2   C9   C8   108.81  3.000
 DSQ  C10  C9   C8   111.15  3.000
 DSQ  H4   C10  C7   108.77  3.000
 DSQ  H4   C10  C11  107.07  3.000
 DSQ  C7   C10  C11  110.70  3.000
 DSQ  H4   C10  C9   107.88  3.000
 DSQ  C11  C10  C9   110.09  3.000
 DSQ  C7   C10  C9   112.15  3.000
 DSQ  H5   C11  O11  110.89  3.000
 DSQ  H5   C11  C12  108.03  3.000
 DSQ  O11  C11  C12  110.72  3.000
 DSQ  H5   C11  C10  108.44  3.000
 DSQ  C12  C11  C10  110.52  3.000
 DSQ  O11  C11  C10  108.22  3.000
 DSQ  H6   C12  O12  110.20  3.000
 DSQ  H6   C12  C13  108.88  3.000
 DSQ  O12  C12  C13  107.65  3.000
 DSQ  H6   C12  C11  107.81  3.000
 DSQ  C13  C12  C11  112.10  3.000
 DSQ  O12  C12  C11  110.18  3.000
 DSQ  H8   C13  H7   107.01  3.000
 DSQ  H8   C13  O13  111.83  3.000
 DSQ  H7   C13  O13  111.25  3.000
 DSQ  H8   C13  C12  108.89  3.000
 DSQ  H7   C13  C12  108.61  3.000
 DSQ  O13  C13  C12  109.16  3.000
 DSQ  H9   O8   C8   109.30  3.000
 DSQ  C12  O12  C8   112.85  3.000
 DSQ  H10  O13  C13  107.95  3.000
 DSQ  H11  O11  C11  109.16  3.000
 DSQ  H13  C7   H12  106.72  3.000
 DSQ  H13  C7   C1   109.77  3.000
 DSQ  H12  C7   C1   107.47  3.000
 DSQ  H13  C7   C10  109.73  3.000
 DSQ  H12  C7   C10  108.93  3.000
 DSQ  C1   C7   C10  113.93  3.000
 DSQ  H14  C1   O5   110.72  3.000
 DSQ  H14  C1   C2   105.96  3.000
 DSQ  O5   C1   C2   110.75  3.000
 DSQ  H14  C1   C7   108.07  3.000
 DSQ  C2   C1   C7   113.38  3.000
 DSQ  O5   C1   C7   107.94  3.000
 DSQ  H15  C2   C3   108.18  3.000
 DSQ  H15  C2   O2   111.20  3.000
 DSQ  C3   C2   O2   110.73  3.000
 DSQ  H15  C2   C1   107.97  3.000
 DSQ  O2   C2   C1   108.91  3.000
 DSQ  C3   C2   C1   109.80  3.000
 DSQ  H16  O2   C2   108.41  3.000
 DSQ  H17  C3   C4   107.82  3.000
 DSQ  H17  C3   O3   109.91  3.000
 DSQ  C4   C3   O3   113.00  3.000
 DSQ  H17  C3   C2   108.43  3.000
 DSQ  O3   C3   C2   107.68  3.000
 DSQ  C4   C3   C2   109.93  3.000
 DSQ  H18  O3   C3   108.07  3.000
 DSQ  H19  C4   C5   106.70  3.000
 DSQ  H19  C4   O4   110.56  3.000
 DSQ  C5   C4   O4   112.68  3.000
 DSQ  H19  C4   C3   106.26  3.000
 DSQ  O4   C4   C3   107.31  3.000
 DSQ  C5   C4   C3   113.16  3.000
 DSQ  H20  O4   C4   109.07  3.000
 DSQ  H21  C5   C6   106.83  3.000
 DSQ  H21  C5   O5   104.53  3.000
 DSQ  C6   C5   O5   112.67  3.000
 DSQ  H21  C5   C4   106.89  3.000
 DSQ  O5   C5   C4   108.94  3.000
 DSQ  C6   C5   C4   116.14  3.000
 DSQ  C5   O5   C1   114.99  3.000
 DSQ  H24  C6   H23  108.17  3.000
 DSQ  H24  C6   H22  107.49  3.000
 DSQ  H23  C6   H22  107.22  3.000
 DSQ  H24  C6   C5   113.81  3.000
 DSQ  H23  C6   C5   109.39  3.000
 DSQ  H22  C6   C5   110.52  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
 DSQ  chir_01  C8   C9   O12  O8   negativ
 DSQ  chir_02  C10  C7   C9   C11  positiv
 DSQ  chir_03  C11  O11  C12  C10  positiv
 DSQ  chir_04  C12  O12  C11  C13  negativ
 DSQ  chir_05  C1   O5   C7   C2   negativ
 DSQ  chir_06  C2   O2   C1   C3   positiv
 DSQ  chir_07  C3   O3   C2   C4   negativ
 DSQ  chir_08  C4   O4   C5   C3   positiv
 DSQ  chir_09  C5   O5   C4   C6   positiv

