# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:51:11 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1NC(C)=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
 6S2  6S2  'methyl 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranoside'  D-saccharide  37  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_6S2
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
 6S2  O1   O  OH1   0  -0.670  -0.1006  -3.1597  -0.3383
 6S2  C11  C  CH1   0   0.343   1.2970   0.7158  -0.3781
 6S2  O11  O  O2    0  -0.480   1.6826   1.9567   0.0576
 6S2  O51  O  O2    0  -0.491  -0.0048   0.4594   0.0914
 6S2  C51  C  CH1   0  -0.029  -0.5255  -0.7605  -0.3732
 6S2  C61  C  CH2   0  -0.195  -1.9587  -0.8565   0.0889
 6S2  O61  O  OC2   0  -0.573  -2.6788   0.2112  -0.5668
 6S2  C41  C  CH1   0  -0.002   0.3150  -1.9187   0.1803
 6S2  C31  C  CH1   0   0.032   1.7759  -1.7228  -0.2225
 6S2  O31  O  OH1   0  -0.660   2.6114  -2.6698   0.3834
 6S2  C21  C  CH1   0  -0.157   2.2640  -0.3335   0.1774
 6S2  N2   N  NH1   0  -0.625   3.6000  -0.1093  -0.3040
 6S2  C7   C  C     0   0.519   4.5822   0.4671   0.4160
 6S2  C8   C  CH3   0  -0.783   5.8638   0.6992  -0.3456
 6S2  O7   O  O     0  -0.499   4.4526   0.7956   1.5858
 6S2  S1   S  S     0   1.662  -4.1451   0.5550  -0.1075
 6S2  O21  O  OS    0  -0.635  -4.9096  -0.6401   0.1502
 6S2  O8   O  OS    0  -0.710  -3.7955   1.2681   1.2694
 6S2  O9   O  OS    0  -0.619  -4.6159   1.5273  -1.0544
 6S2  C10  C  CH3   0  -0.412   1.0768   3.0363  -0.6280
 6S2  H13  H  HCH1  0   0.246  -0.5020  -0.8036  -1.4733
 6S2  H14  H  HCH2  0   0.270  -2.3906  -1.8133  -0.2035
 6S2  H15  H  HCH2  0   0.263  -2.0191  -0.7473   1.1743
 6S2  H16  H  HCH1  0   0.238   0.2541  -1.9044   1.2777
 6S2  H17  H  HCH1  0   0.215   1.8263  -1.8015  -1.3229
 6S2  H18  H  HOH1  0   0.453   2.3343  -3.5439   0.0887
 6S2  H19  H  HCH1  0   0.275   2.2689  -0.2518   1.2674
 6S2  H20  H  HNH1  0   0.400   3.7935  -0.3523  -1.2630
 6S2  H21  H  HCH3  0   0.271   5.8604   1.7127  -0.7511
 6S2  H22  H  HCH3  0   0.262   6.7168   0.6132   0.3240
 6S2  H23  H  HCH3  0   0.251   5.9968   0.0097  -1.1777
 6S2  H24  H  HCH3  0   0.240   1.5492   3.9503  -0.2739
 6S2  H25  H  HCH3  0   0.215   1.2317   2.9584  -1.7088
 6S2  H26  H  HCH3  0   0.221   0.0034   3.1009  -0.4359
 6S2  H2   H  HOH1  0   0.466  -0.7528  -3.5500   0.2501
 6S2  H1   H  H     0   0.514  -4.5328   1.2221   1.9017
 6S2  H12  H  HCH1  0   0.184   1.2979   0.6631  -1.4845

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
 6S2  O21  S1   double  1.442  0.020  1.442
 6S2  O9   S1   double  1.437  0.020  1.437
 6S2  S1   O8   single  1.589  0.020  1.589
 6S2  S1   O61  single  1.575  0.020  1.575
 6S2  O61  C61  single  1.445  0.020  1.445
 6S2  C61  C51  single  1.509  0.020  1.509
 6S2  O51  C51  single  1.405  0.020  1.405
 6S2  O51  C11  single  1.407  0.020  1.407
 6S2  O11  C10  single  1.415  0.020  1.415
 6S2  O11  C11  single  1.371  0.020  1.371
 6S2  C51  C41  single  1.534  0.020  1.534
 6S2  C11  C21  single  1.531  0.020  1.531
 6S2  C41  O1   single  1.408  0.020  1.408
 6S2  C41  C31  single  1.528  0.020  1.528
 6S2  C21  C31  single  1.526  0.020  1.526
 6S2  C21  N2   single  1.438  0.020  1.438
 6S2  O7   C7   double  1.222  0.020  1.222
 6S2  C31  O31  single  1.401  0.020  1.401
 6S2  C7   N2   single  1.347  0.020  1.347
 6S2  C7   C8   single  1.509  0.020  1.509
 6S2  C11  H12  single  0.970  0.020  1.090
 6S2  C51  H13  single  0.970  0.020  1.090
 6S2  C61  H14  single  0.970  0.020  1.090
 6S2  C61  H15  single  0.970  0.020  1.090
 6S2  C41  H16  single  0.970  0.020  1.090
 6S2  C31  H17  single  0.970  0.020  1.090
 6S2  O31  H18  single  0.850  0.020  0.980
 6S2  C21  H19  single  0.970  0.020  1.090
 6S2  N2   H20  single  0.860  0.020  1.020
 6S2  C8   H21  single  0.970  0.020  1.090
 6S2  C8   H22  single  0.970  0.020  1.090
 6S2  C8   H23  single  0.970  0.020  1.090
 6S2  C10  H24  single  0.970  0.020  1.090
 6S2  C10  H25  single  0.970  0.020  1.090
 6S2  C10  H26  single  0.970  0.020  1.090
 6S2  O1   H2   single  0.850  0.020  0.980
 6S2  O8   H1   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
 6S2  H2   O1   C41  109.43  3.000
 6S2  H12  C11  C21  109.23  3.000
 6S2  H12  C11  O51  108.98  3.000
 6S2  C21  C11  O51  109.77  3.000
 6S2  H12  C11  O11  111.12  3.000
 6S2  C21  C11  O11  109.12  3.000
 6S2  O51  C11  O11  108.61  3.000
 6S2  C10  O11  C11  114.60  3.000
 6S2  C51  O51  C11  112.99  3.000
 6S2  H13  C51  C41  108.62  3.000
 6S2  H13  C51  C61  108.89  3.000
 6S2  C41  C51  C61  111.21  3.000
 6S2  H13  C51  O51  110.87  3.000
 6S2  C41  C51  O51  109.45  3.000
 6S2  C61  C51  O51  107.81  3.000
 6S2  H15  C61  H14  109.42  3.000
 6S2  H15  C61  O61  110.45  3.000
 6S2  H14  C61  O61  109.23  3.000
 6S2  H15  C61  C51  110.51  3.000
 6S2  H14  C61  C51  110.49  3.000
 6S2  O61  C61  C51  106.70  3.000
 6S2  S1   O61  C61  119.54  3.000
 6S2  H16  C41  C31  108.33  3.000
 6S2  H16  C41  C51  108.66  3.000
 6S2  C31  C41  C51  109.38  3.000
 6S2  H16  C41  O1   111.28  3.000
 6S2  C31  C41  O1   107.34  3.000
 6S2  C51  C41  O1   111.77  3.000
 6S2  H17  C31  C21  108.15  3.000
 6S2  H17  C31  O31  110.83  3.000
 6S2  C21  C31  O31  108.15  3.000
 6S2  H17  C31  C41  107.29  3.000
 6S2  O31  C31  C41  111.69  3.000
 6S2  C21  C31  C41  110.70  3.000
 6S2  H18  O31  C31  108.03  3.000
 6S2  H19  C21  N2   108.55  3.000
 6S2  H19  C21  C31  109.32  3.000
 6S2  N2   C21  C31  110.57  3.000
 6S2  H19  C21  C11  108.27  3.000
 6S2  N2   C21  C11  111.01  3.000
 6S2  C31  C21  C11  109.08  3.000
 6S2  H20  N2   C7   118.13  3.000
 6S2  H20  N2   C21  117.35  3.000
 6S2  C7   N2   C21  124.41  3.000
 6S2  O7   C7   C8   122.14  3.000
 6S2  C8   C7   N2   114.53  3.000
 6S2  O7   C7   N2   123.32  3.000
 6S2  H23  C8   H22  108.93  3.000
 6S2  H23  C8   H21  107.73  3.000
 6S2  H22  C8   H21  107.73  3.000
 6S2  H23  C8   C7   113.09  3.000
 6S2  H22  C8   C7   110.07  3.000
 6S2  H21  C8   C7   109.13  3.000
 6S2  O9   S1   O8   109.85  3.000
 6S2  O8   S1   O21  109.49  3.000
 6S2  O9   S1   O21  120.33  3.000
 6S2  O8   S1   O61   98.39  3.000
 6S2  O9   S1   O61  105.11  3.000
 6S2  O21  S1   O61  111.40  3.000
 6S2  H1   O8   S1   112.04  3.000
 6S2  H26  C10  H25  108.48  3.000
 6S2  H26  C10  H24  108.65  3.000
 6S2  H25  C10  H24  108.64  3.000
 6S2  H26  C10  O11  112.37  3.000
 6S2  H25  C10  O11  111.31  3.000
 6S2  H24  C10  O11  107.30  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
 6S2  CONST_01  O7   C7   N2   C21     0.00   0.0  0
 6S2  CONST_02  C8   C7   N2   C21   180.00   0.0  0
 6S2  CONST_03  H20  N2   C7   C8      0.00   0.0  0
 6S2  Var_01    H24  C10  O11  C11  -173.41  30.0  3
 6S2  Var_02    O21  S1   O61  C61   -41.24  30.0  2
 6S2  Var_03    H21  C8   C7   N2     94.02  30.0  3
 6S2  Var_04    H14  C61  O61  S1     71.44  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
 6S2  chir_01  C11  O51  O11  C21  negativ
 6S2  chir_02  C51  O51  C41  C61  negativ
 6S2  chir_03  C41  O1   C51  C31  positiv
 6S2  chir_04  C31  O31  C41  C21  negativ
 6S2  chir_05  C21  N2   C31  C11  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
 6S2  plan-1  C21  0.020
 6S2  plan-1  N2   0.020
 6S2  plan-1  C7   0.020
 6S2  plan-1  C8   0.020
 6S2  plan-1  O7   0.020
 6S2  plan-1  H20  0.020

