# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:55:26 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1N[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
 5KV  5KV  2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose  D-saccharide  33  20  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5KV
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
 5KV  O13  O  OH1   0  -0.667   0.7304   2.9057   0.0316
 5KV  C18  C  CH1   0  -0.022  -1.1979   1.5211  -0.1809
 5KV  C19  C  CH1   0   0.037   0.2338   1.6246   0.3442
 5KV  C20  C  CH1   0  -0.054   1.0886   0.5354  -0.3109
 5KV  C21  C  CH1   0  -0.188  -1.7292   0.1021  -0.0085
 5KV  C22  C  CH1   0   0.348  -0.7466  -0.9019  -0.6179
 5KV  O25  O  O2    0  -0.465   0.5256  -0.7251  -0.0374
 5KV  O28  O  OH1   0  -0.631  -1.1781  -2.1737  -0.3382
 5KV  N29  N  NC1   0  -0.752  -3.0248  -0.0499  -0.6440
 5KV  O30  O  OH1   0  -0.673  -2.0619   2.3982   0.4827
 5KV  C31  C  CH2   0  -0.198   2.4987   0.5503   0.2241
 5KV  O32  O  OC2   0  -0.586   3.2409  -0.4343  -0.5280
 5KV  S33  S  S     0   1.591   4.7953  -0.5842  -0.2949
 5KV  S34  S  S     0   1.548  -4.3613  -0.5072   0.1279
 5KV  O35  O  OS    0  -0.683  -4.0066  -1.3939   1.2128
 5KV  O36  O  OS    0  -0.743  -4.8710   0.8769   0.7613
 5KV  O37  O  OS    0  -0.610  -5.3332  -0.9319  -0.8555
 5KV  O38  O  OS    0  -0.725   5.4393   0.7049  -0.2701
 5KV  O39  O  OS    0  -0.714   4.8164  -1.2104   1.1641
 5KV  O40  O  OS    0  -0.472   5.2028  -1.6027  -1.2202
 5KV  H1   H  HOH1  0   0.466   1.0787   3.3126   0.8291
 5KV  H2   H  HCH1  0   0.284  -1.1643   1.7424  -1.2620
 5KV  H3   H  HCH1  0   0.253   0.2220   1.4561   1.4292
 5KV  H4   H  HCH1  0   0.250   1.1201   0.7182  -1.3974
 5KV  H5   H  HCH1  0   0.308  -1.8247  -0.1187   1.0584
 5KV  H6   H  HCH1  0   0.176  -0.6756  -0.7200  -1.7045
 5KV  H7   H  HOH1  0   0.447  -0.8020  -2.7873  -0.9778
 5KV  H8   H  HNC1  0   0.438  -3.1821   0.4291  -1.5227
 5KV  H9   H  HOH1  0   0.427  -1.7870   3.2978   0.2771
 5KV  H10  H  HCH2  0   0.291   2.9352   1.5381   0.0816
 5KV  H11  H  HCH2  0   0.295   2.5150   0.2929   1.2860
 5KV  H12  H  H     0   0.511  -5.7185   0.7571   1.2229
 5KV  H13  H  H     0   0.513   5.3394  -0.6791   1.7873

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
 5KV  O30  C18  single  1.399  0.020  1.399
 5KV  O13  C19  single  1.409  0.020  1.409
 5KV  C18  C19  single  1.528  0.020  1.528
 5KV  C18  C21  single  1.525  0.020  1.525
 5KV  O37  S34  double  1.446  0.020  1.446
 5KV  C19  C20  single  1.532  0.020  1.532
 5KV  O35  S34  double  1.445  0.020  1.445
 5KV  N29  S34  single  1.610  0.020  1.610
 5KV  N29  C21  single  1.451  0.020  1.451
 5KV  S34  O36  single  1.605  0.020  1.605
 5KV  C21  C22  single  1.531  0.020  1.531
 5KV  C20  C31  single  1.508  0.020  1.508
 5KV  C20  O25  single  1.407  0.020  1.407
 5KV  C22  O25  single  1.410  0.020  1.410
 5KV  C22  O28  single  1.372  0.020  1.372
 5KV  C31  O32  single  1.444  0.020  1.444
 5KV  O32  S33  single  1.579  0.020  1.579
 5KV  O38  S33  double  1.441  0.020  1.441
 5KV  S33  O40  double  1.435  0.020  1.435
 5KV  S33  O39  single  1.588  0.020  1.588
 5KV  O13  H1   single  0.850  0.020  0.980
 5KV  C18  H2   single  0.970  0.020  1.090
 5KV  C19  H3   single  0.970  0.020  1.090
 5KV  C20  H4   single  0.970  0.020  1.090
 5KV  C21  H5   single  0.970  0.020  1.090
 5KV  C22  H6   single  0.970  0.020  1.090
 5KV  O28  H7   single  0.850  0.020  0.980
 5KV  N29  H8   single  0.890  0.020  1.040
 5KV  O30  H9   single  0.850  0.020  0.980
 5KV  C31  H10  single  0.970  0.020  1.090
 5KV  C31  H11  single  0.970  0.020  1.090
 5KV  O36  H12  single  0.850  0.020  0.980
 5KV  O39  H13  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
 5KV  H1   O13  C19  109.19  3.000
 5KV  H2   C18  O30  110.96  3.000
 5KV  H2   C18  C21  107.93  3.000
 5KV  O30  C18  C21  108.34  3.000
 5KV  H2   C18  C19  107.12  3.000
 5KV  C21  C18  C19  110.52  3.000
 5KV  O30  C18  C19  111.91  3.000
 5KV  H3   C19  C20  108.63  3.000
 5KV  H3   C19  C18  108.61  3.000
 5KV  C20  C19  C18  109.13  3.000
 5KV  H3   C19  O13  111.25  3.000
 5KV  C20  C19  O13  110.79  3.000
 5KV  C18  C19  O13  108.39  3.000
 5KV  H4   C20  C31  108.74  3.000
 5KV  H4   C20  O25  110.58  3.000
 5KV  C31  C20  O25  108.29  3.000
 5KV  H4   C20  C19  108.64  3.000
 5KV  O25  C20  C19  109.30  3.000
 5KV  C31  C20  C19  111.29  3.000
 5KV  H5   C21  N29  109.15  3.000
 5KV  H5   C21  C22  108.17  3.000
 5KV  N29  C21  C22  109.26  3.000
 5KV  H5   C21  C18  109.19  3.000
 5KV  C22  C21  C18  109.97  3.000
 5KV  N29  C21  C18  111.04  3.000
 5KV  H6   C22  O28  111.94  3.000
 5KV  H6   C22  O25  109.06  3.000
 5KV  O28  C22  O25  108.44  3.000
 5KV  H6   C22  C21  108.96  3.000
 5KV  O28  C22  C21  108.96  3.000
 5KV  O25  C22  C21  109.45  3.000
 5KV  C22  O25  C20  113.16  3.000
 5KV  H7   O28  C22  109.42  3.000
 5KV  H8   N29  S34  114.92  3.000
 5KV  H8   N29  C21  117.97  3.000
 5KV  S34  N29  C21  124.13  3.000
 5KV  H9   O30  C18  107.95  3.000
 5KV  H11  C31  H10  109.56  3.000
 5KV  H11  C31  O32  109.74  3.000
 5KV  H10  C31  O32  110.13  3.000
 5KV  H11  C31  C20  110.87  3.000
 5KV  H10  C31  C20  109.70  3.000
 5KV  O32  C31  C20  106.80  3.000
 5KV  S33  O32  C31  119.59  3.000
 5KV  O40  S33  O39  107.99  3.000
 5KV  O39  S33  O38  109.33  3.000
 5KV  O40  S33  O38  121.26  3.000
 5KV  O39  S33  O32  100.73  3.000
 5KV  O40  S33  O32  104.58  3.000
 5KV  O38  S33  O32  110.95  3.000
 5KV  O37  S34  O36  107.94  3.000
 5KV  O36  S34  O35  108.10  3.000
 5KV  O37  S34  O35  119.68  3.000
 5KV  O36  S34  N29  102.00  3.000
 5KV  O35  S34  N29  109.29  3.000
 5KV  O37  S34  N29  108.38  3.000
 5KV  H12  O36  S34  110.96  3.000
 5KV  H13  O39  S33  112.38  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
 5KV  Var_01  O37  S34  N29  C21  -163.09  30.0  3
 5KV  Var_02  O38  S33  O32  C31   -45.86  30.0  3
 5KV  Var_03  H10  C31  O32  S33    55.80  30.0  1

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
 5KV  chir_01  C18  O30  C19  C21  negativ
 5KV  chir_02  C19  O13  C18  C20  negativ
 5KV  chir_03  C20  O25  C19  C31  negativ
 5KV  chir_04  C21  N29  C22  C18  negativ
 5KV  chir_05  C22  O25  O28  C21  negativ

