# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 18 18:32:32 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R},6~{R})-2-[[(2~{S},3~{S},4~{R},5~{S},6~{R})-3,6-bis(oxidanyl)-4,5-disulfooxy-oxan-2-yl]methoxy]-6-(hydroxymethyl)-3,5-disulfooxy-oxan-4-yl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OC[C@@H]2O[C@@H](O)[C@@H](O[S](O)(=O)=O)[C@H](O[S](O)(=O)=O)[C@H]2O)[C@@H](O[S](O)(=O)=O)[C@H](O[S](O)(=O)=O)[C@@H]1O[S](O)(=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
 9QZ  9QZ  '[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-[[(2~{S},3~{S},4~{R},5~{S},6~{R})-3,6-bis(oxidanyl)-4,5-disulfooxy-oxan-2-yl]methoxy]-6-(hydroxymethyl)-3,5-disulfooxy-oxan-4-yl] hydrogen sulfate'  saccharide  60  43  .  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_9QZ
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
 9QZ  C03  C  CH2    0  -0.157   4.6184  -0.3682  -3.2226
 9QZ  C04  C  CH1    0  -0.009   3.6484   0.1654  -2.1900
 9QZ  C06  C  CH1    0   0.317   1.3202   0.1941  -1.7375
 9QZ  C09  C  CH1    0  -0.036  -1.6997   0.5501  -0.9828
 9QZ  C11  C  CH1    0   0.231  -2.5625  -1.0602   0.5333
 9QZ  C13  C  CH1    0   0.004  -3.9473  -0.4155   0.4962
 9QZ  C19  C  CH1    0   0.007  -3.8445   1.0798   0.2083
 9QZ  C25  C  CH1    0   0.026  -3.0369   1.2977  -1.0687
 9QZ  C31  C  CH1    0  -0.051   1.4999  -0.3919  -0.3351
 9QZ  C37  C  CH1    0  -0.061   2.8751   0.0265   0.2039
 9QZ  C43  C  CH1    0   0.032   3.9666  -0.3633  -0.7867
 9QZ  O02  O  OH1    0  -0.672   4.3364   0.2404  -4.4613
 9QZ  O05  O  O2     0  -0.497   2.3511  -0.2439  -2.5756
 9QZ  O07  O  O2     0  -0.488   0.1657  -0.2485  -2.3601
 9QZ  O10  O  O2     0  -0.501  -1.9152  -0.8139  -0.6909
 9QZ  O12  O  OH1    0  -0.695  -1.8705  -0.5656   1.6191
 9QZ  O14  O  OC2    0  -0.607  -4.6068  -0.6067   1.7304
 9QZ  O16  O  OS    -1  -0.749  -5.2252  -2.9781   1.3973
 9QZ  O17  O  OS     0  -0.738  -6.2140  -1.6117   3.1909
 9QZ  O18  O  OS     0  -0.738  -6.8446  -1.2313   0.8388
 9QZ  O20  O  OC2    0  -0.619  -5.1465   1.5976  -0.0015
 9QZ  O22  O  OS     0  -0.729  -5.9448   2.0835   2.3124
 9QZ  O23  O  OS    -1  -0.743  -4.7866   3.8235   1.0429
 9QZ  O24  O  OS     0  -0.748  -7.0073   3.0465   0.3122
 9QZ  O26  O  OH1    0  -0.659  -2.8390   2.6764  -1.2498
 9QZ  O32  O  OC2    0  -0.620   1.3879  -1.7966  -0.4758
 9QZ  O34  O  OS    -1  -0.743   0.4749  -1.9376   1.8401
 9QZ  O35  O  OS     0  -0.719   0.3883  -3.8482   0.2794
 9QZ  O36  O  OS     0  -0.714   2.5255  -3.1329   1.2611
 9QZ  O38  O  OC2    0  -0.623   2.9166   1.4422   0.3201
 9QZ  O40  O  OS     0  -0.735   2.8688   3.5325   1.4729
 9QZ  O41  O  OS     0  -0.722   0.9151   2.0533   1.6629
 9QZ  O42  O  OS    -1  -0.735   3.0078   1.4625   2.8027
 9QZ  O44  O  OC2    0  -0.623   5.2028   0.1941  -0.3766
 9QZ  O46  O  OS    -1  -0.738   6.7034  -1.7277  -0.8266
 9QZ  O47  O  OS     0  -0.735   7.3726   0.1500   0.6210
 9QZ  O48  O  OS     0  -0.724   5.6918  -1.4799   1.3920
 9QZ  S15  S  S      0   1.572  -5.8294  -1.6969   1.7845
 9QZ  S21  S  S      0   1.565  -5.7632   2.7319   1.0153
 9QZ  S33  S  S      0   1.605   1.1800  -2.7571   0.8349
 9QZ  S39  S  S      0   1.575   2.3746   2.1753   1.6925
 9QZ  S45  S  S      0   1.564   6.3367  -0.8150   0.2603
 9QZ  H1   H  HCH2   0   0.211   5.6368  -0.1503  -2.8886
 9QZ  H2   H  HCH2   0   0.195   4.5222  -1.4617  -3.2720
 9QZ  H3   H  HCH1   0   0.226   3.7099   1.2646  -2.1818
 9QZ  H4   H  HCH1   0   0.202   1.3261   1.2946  -1.6548
 9QZ  H5   H  HCH2   0   0.238  -1.6229   0.2490  -3.1100
 9QZ  H6   H  HCH2   0   0.222  -0.6802   1.6323  -2.5405
 9QZ  H7   H  HCH1   0   0.236  -1.0886   1.0301  -0.2053
 9QZ  H8   H  HCH1   0   0.221  -2.6668  -2.1513   0.5738
 9QZ  H9   H  HCH1   0   0.241  -4.5025  -0.8776  -0.3290
 9QZ  H10  H  HCH1   0   0.240  -3.3392   1.5854   1.0394
 9QZ  H11  H  HCH1   0   0.217  -3.6113   0.8664  -1.9029
 9QZ  H12  H  HCH1   0   0.283   0.7257  -0.0043   0.3277
 9QZ  H13  H  HCH1   0   0.276   3.0831  -0.4441   1.1689
 9QZ  H14  H  HCH1   0   0.253   4.0080  -1.4578  -0.8225
 9QZ  H15  H  HOH1   0   0.456   4.9855  -0.0710  -5.0979
 9QZ  H16  H  HOH1   0   0.469  -1.0278  -1.0558   1.7042
 9QZ  H17  H  HOH1   0   0.456  -2.7598   2.8571  -2.1902
 9QZ  C08  C  CH2    0  -0.211  -0.9593   0.5963  -2.3130

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
 9QZ  O02  C03  single  1.409  0.020  1.409
 9QZ  C03  C04  single  1.514  0.020  1.514
 9QZ  C04  O05  single  1.414  0.020  1.414
 9QZ  C04  C43  single  1.533  0.020  1.533
 9QZ  O05  C06  single  1.399  0.020  1.399
 9QZ  O07  C06  single  1.384  0.020  1.384
 9QZ  O07  C08  single  1.408  0.020  1.408
 9QZ  C06  C31  single  1.531  0.020  1.531
 9QZ  O44  C43  single  1.417  0.020  1.417
 9QZ  O44  S45  single  1.646  0.020  1.646
 9QZ  O10  C09  single  1.411  0.020  1.411
 9QZ  O10  C11  single  1.407  0.020  1.407
 9QZ  C43  C37  single  1.525  0.020  1.525
 9QZ  O12  C11  single  1.379  0.020  1.379
 9QZ  O48  S45  deloc   1.462  0.020  1.462
 9QZ  C09  C08  single  1.523  0.020  1.523
 9QZ  C09  C25  single  1.534  0.020  1.534
 9QZ  O26  C25  single  1.405  0.020  1.405
 9QZ  O38  C37  single  1.421  0.020  1.421
 9QZ  O38  S39  single  1.648  0.020  1.648
 9QZ  C11  C13  single  1.528  0.020  1.528
 9QZ  S45  O47  deloc   1.461  0.020  1.461
 9QZ  S45  O46  deloc   1.466  0.020  1.466
 9QZ  C37  C31  single  1.535  0.020  1.535
 9QZ  C31  O32  single  1.416  0.020  1.416
 9QZ  C25  C19  single  1.527  0.020  1.527
 9QZ  O32  S33  single  1.638  0.020  1.638
 9QZ  O40  S39  deloc   1.461  0.020  1.461
 9QZ  C19  C13  single  1.526  0.020  1.526
 9QZ  C19  O20  single  1.417  0.020  1.417
 9QZ  O41  S39  deloc   1.465  0.020  1.465
 9QZ  S39  O42  deloc   1.463  0.020  1.463
 9QZ  C13  O14  single  1.412  0.020  1.412
 9QZ  O18  S15  deloc   1.463  0.020  1.463
 9QZ  O14  S15  single  1.639  0.020  1.639
 9QZ  O24  S21  deloc   1.463  0.020  1.463
 9QZ  S33  O35  deloc   1.458  0.020  1.458
 9QZ  S33  O36  deloc   1.461  0.020  1.461
 9QZ  S33  O34  deloc   1.476  0.020  1.476
 9QZ  O20  S21  single  1.643  0.020  1.643
 9QZ  S15  O17  deloc   1.461  0.020  1.461
 9QZ  S15  O16  deloc   1.468  0.020  1.468
 9QZ  S21  O22  deloc   1.461  0.020  1.461
 9QZ  S21  O23  deloc   1.465  0.020  1.465
 9QZ  C03  H1   single  0.970  0.020  1.090
 9QZ  C03  H2   single  0.970  0.020  1.090
 9QZ  C04  H3   single  0.970  0.020  1.090
 9QZ  C06  H4   single  0.970  0.020  1.090
 9QZ  C08  H5   single  0.970  0.020  1.090
 9QZ  C08  H6   single  0.970  0.020  1.090
 9QZ  C09  H7   single  0.970  0.020  1.090
 9QZ  C11  H8   single  0.970  0.020  1.090
 9QZ  C13  H9   single  0.970  0.020  1.090
 9QZ  C19  H10  single  0.970  0.020  1.090
 9QZ  C25  H11  single  0.970  0.020  1.090
 9QZ  C31  H12  single  0.970  0.020  1.090
 9QZ  C37  H13  single  0.970  0.020  1.090
 9QZ  C43  H14  single  0.970  0.020  1.090
 9QZ  O02  H15  single  0.850  0.020  0.980
 9QZ  O12  H16  single  0.850  0.020  0.980
 9QZ  O26  H17  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
 9QZ  H2   C03  H1   107.06  3.000
 9QZ  H2   C03  O02  111.89  3.000
 9QZ  H1   C03  O02  111.64  3.000
 9QZ  H2   C03  C04  108.99  3.000
 9QZ  H1   C03  C04  108.55  3.000
 9QZ  O02  C03  C04  108.62  3.000
 9QZ  H3   C04  O05  110.02  3.000
 9QZ  H3   C04  C43  109.02  3.000
 9QZ  O05  C04  C43  109.89  3.000
 9QZ  H3   C04  C03  108.73  3.000
 9QZ  C43  C04  C03  111.71  3.000
 9QZ  O05  C04  C03  107.45  3.000
 9QZ  H4   C06  O07  110.92  3.000
 9QZ  H4   C06  O05  110.68  3.000
 9QZ  O07  C06  O05  104.19  3.000
 9QZ  H4   C06  C31  108.21  3.000
 9QZ  O07  C06  C31  112.80  3.000
 9QZ  O05  C06  C31  110.03  3.000
 9QZ  H7   C09  O10  111.14  3.000
 9QZ  H7   C09  C25  108.14  3.000
 9QZ  O10  C09  C25  110.44  3.000
 9QZ  H7   C09  C08  109.53  3.000
 9QZ  C25  C09  C08  111.10  3.000
 9QZ  O10  C09  C08  106.51  3.000
 9QZ  H8   C11  O12  112.05  3.000
 9QZ  H8   C11  O10  104.48  3.000
 9QZ  O12  C11  O10  113.05  3.000
 9QZ  H8   C11  C13  109.54  3.000
 9QZ  O12  C11  C13  108.82  3.000
 9QZ  O10  C11  C13  108.79  3.000
 9QZ  H9   C13  O14  111.35  3.000
 9QZ  H9   C13  C19  107.76  3.000
 9QZ  O14  C13  C19  109.20  3.000
 9QZ  H9   C13  C11  107.42  3.000
 9QZ  O14  C13  C11  110.18  3.000
 9QZ  C19  C13  C11  110.91  3.000
 9QZ  H10  C19  O20  111.55  3.000
 9QZ  H10  C19  C25  108.93  3.000
 9QZ  O20  C19  C25  108.07  3.000
 9QZ  H10  C19  C13  109.87  3.000
 9QZ  O20  C19  C13  108.92  3.000
 9QZ  C25  C19  C13  109.47  3.000
 9QZ  H11  C25  O26  111.13  3.000
 9QZ  H11  C25  C19  107.57  3.000
 9QZ  O26  C25  C19  108.81  3.000
 9QZ  H11  C25  C09  107.84  3.000
 9QZ  C19  C25  C09  110.16  3.000
 9QZ  O26  C25  C09  111.26  3.000
 9QZ  H12  C31  O32  110.91  3.000
 9QZ  H12  C31  C37  109.01  3.000
 9QZ  O32  C31  C37  112.09  3.000
 9QZ  H12  C31  C06  109.72  3.000
 9QZ  O32  C31  C06  106.23  3.000
 9QZ  C37  C31  C06  108.82  3.000
 9QZ  H13  C37  O38  110.55  3.000
 9QZ  H13  C37  C43  109.09  3.000
 9QZ  O38  C37  C43  106.67  3.000
 9QZ  H13  C37  C31  111.28  3.000
 9QZ  O38  C37  C31  109.05  3.000
 9QZ  C43  C37  C31  110.09  3.000
 9QZ  H14  C43  O44  111.68  3.000
 9QZ  H14  C43  C37  107.67  3.000
 9QZ  O44  C43  C37  109.64  3.000
 9QZ  H14  C43  C04  108.80  3.000
 9QZ  C37  C43  C04  110.98  3.000
 9QZ  O44  C43  C04  108.08  3.000
 9QZ  H15  O02  C03  107.90  3.000
 9QZ  C06  O05  C04  114.97  3.000
 9QZ  C08  O07  C06  117.36  3.000
 9QZ  C11  O10  C09  114.80  3.000
 9QZ  H16  O12  C11  108.72  3.000
 9QZ  S15  O14  C13  117.85  3.000
 9QZ  S21  O20  C19  120.36  3.000
 9QZ  H17  O26  C25  108.80  3.000
 9QZ  S33  O32  C31  120.80  3.000
 9QZ  S39  O38  C37  120.12  3.000
 9QZ  S45  O44  C43  118.16  3.000
 9QZ  O18  S15  O17  114.90  3.000
 9QZ  O17  S15  O16  114.40  3.000
 9QZ  O18  S15  O16  113.12  3.000
 9QZ  O16  S15  O14  105.35  3.000
 9QZ  O17  S15  O14  100.92  3.000
 9QZ  O18  S15  O14  106.53  3.000
 9QZ  O24  S21  O23  114.56  3.000
 9QZ  O23  S21  O22  113.37  3.000
 9QZ  O24  S21  O22  114.59  3.000
 9QZ  O23  S21  O20  106.01  3.000
 9QZ  O22  S21  O20  106.83  3.000
 9QZ  O24  S21  O20   99.80  3.000
 9QZ  O36  S33  O35  114.76  3.000
 9QZ  O36  S33  O34  112.59  3.000
 9QZ  O35  S33  O34  114.55  3.000
 9QZ  O34  S33  O32  106.26  3.000
 9QZ  O36  S33  O32  105.51  3.000
 9QZ  O35  S33  O32  101.70  3.000
 9QZ  O42  S39  O41  113.94  3.000
 9QZ  O42  S39  O40  114.84  3.000
 9QZ  O41  S39  O40  114.29  3.000
 9QZ  O42  S39  O38  105.83  3.000
 9QZ  O41  S39  O38  105.89  3.000
 9QZ  O40  S39  O38  100.19  3.000
 9QZ  O48  S45  O47  114.96  3.000
 9QZ  O47  S45  O46  114.64  3.000
 9QZ  O48  S45  O46  113.64  3.000
 9QZ  O46  S45  O44  105.49  3.000
 9QZ  O47  S45  O44  100.31  3.000
 9QZ  O48  S45  O44  105.93  3.000
 9QZ  H6   C08  H5   107.65  3.000
 9QZ  H6   C08  O07  110.89  3.000
 9QZ  H5   C08  O07  105.66  3.000
 9QZ  H6   C08  C09  109.48  3.000
 9QZ  H5   C08  C09  109.39  3.000
 9QZ  O07  C08  C09  113.55  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
 9QZ  Var_01  C09  C08  O07  C06  -78.57  30.0  3
 9QZ  Var_02  O18  S15  O14  C13  -60.55  30.0  3
 9QZ  Var_03  O24  S21  O20  C19  173.66  30.0  3
 9QZ  Var_04  O35  S33  O32  C31  148.77  30.0  3
 9QZ  Var_05  O40  S39  O38  C37  168.51  30.0  3
 9QZ  Var_06  O48  S45  O44  C43  -56.40  30.0  3

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
 9QZ  chir_01  C04  C03  O05  C43  negativ
 9QZ  chir_02  C06  O07  O05  C31  positiv
 9QZ  chir_03  C09  O10  C25  C08  positiv
 9QZ  chir_04  C11  O12  O10  C13  positiv
 9QZ  chir_05  C13  O14  C19  C11  negativ
 9QZ  chir_06  C19  O20  C25  C13  positiv
 9QZ  chir_07  C25  O26  C19  C09  positiv
 9QZ  chir_08  C31  O32  C06  C37  positiv
 9QZ  chir_09  C37  O38  C43  C31  positiv
 9QZ  chir_10  C43  O44  C37  C04  negativ

