# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 24 17:44:43 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O)[C@H](N)[C@@H](O)[C@@H]1F
#
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
 S81  S81  '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-glucopyranoside'  D-saccharide  47  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S81
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
 S81  C1   C  CH1   0   0.271  -0.8586   0.3834  -0.8993
 S81  C10  C  CH1   0   0.040   1.3379  -0.2014  -0.1054
 S81  C11  C  CH1   0   0.003   2.1479   1.0729   0.1301
 S81  C12  C  CH1   0   0.073   3.6453   0.8344  -0.0444
 S81  C2   C  CH1   0  -0.147  -1.7117   1.6033  -0.5337
 S81  C3   C  CH1   0  -0.023  -2.8309   1.2374   0.4429
 S81  C4   C  CH1   0   0.197  -3.5723   0.0117  -0.0633
 S81  C5   C  CH1   0  -0.049  -2.5954  -1.1300  -0.2935
 S81  C6   C  CH2   0  -0.303  -3.2294  -2.4032  -0.8157
 S81  C7   C  CH1   0  -0.118   4.1257  -0.2755   0.8803
 S81  C8   C  CH2   0  -0.464   3.3027  -1.5362   0.6112
 S81  C9   C  CH1   0  -0.100   1.8015  -1.3401   0.7901
 S81  F99  F  F     0  -0.378  -4.5107  -0.3749   0.8961
 S81  N2   N  NH2   0  -0.815  -0.8455   2.6730  -0.0570
 S81  N6   N  NH2   0  -0.796  -2.2399  -3.4658  -0.8529
 S81  N7   N  NH2   0  -0.786   5.5589  -0.4733   0.7274
 S81  N9   N  NH2   0  -0.811   1.1117  -2.5685   0.4277
 S81  O1   O  O2    0  -0.522  -0.0298   0.0680   0.1733
 S81  O11  O  OH1   0  -0.718   1.7859   2.0967  -0.7632
 S81  O12  O  OH1   0  -0.675   4.3647   2.0150   0.2157
 S81  O23  O  OH1   0  -0.667  -3.6713   2.3570   0.5682
 S81  O5   O  O2    0  -0.501  -1.6534  -0.7056  -1.2657
 S81  H1   H  HCH1  0   0.247  -0.2706   0.6184  -1.7919
 S81  H2   H  HCH1  0   0.218   1.4549  -0.5198  -1.1516
 S81  H3   H  HCH1  0   0.194   1.9795   1.3863   1.1748
 S81  H4   H  HCH1  0   0.186   3.8166   0.5004  -1.0840
 S81  H5   H  HCH1  0   0.267  -2.1772   1.9424  -1.4646
 S81  H6   H  HCH1  0   0.226  -2.3800   0.9755   1.4133
 S81  H7   H  HCH1  0   0.217  -4.1189   0.2457  -0.9837
 S81  H8   H  HCH1  0   0.229  -2.0955  -1.3698   0.6554
 S81  H9   H  HCH2  0   0.235  -4.0247  -2.6999  -0.1301
 S81  H10  H  HCH2  0   0.202  -3.7085  -2.1931  -1.7831
 S81  H11  H  HCH1  0   0.222   3.9504   0.0441   1.9154
 S81  H12  H  HCH2  0   0.218   3.4938  -1.8794  -0.4129
 S81  H13  H  HCH2  0   0.243   3.6451  -2.3363   1.2746
 S81  H14  H  HCH1  0   0.203   1.6186  -1.0378   1.8349
 S81  H15  H  HNH2  0   0.378  -1.2713   3.5744  -0.2262
 S81  H16  H  HNH2  0   0.368  -0.7162   2.6043   0.9463
 S81  H18  H  HNH2  0   0.353  -2.6815  -4.3310  -1.1348
 S81  H19  H  HNH2  0   0.344  -1.5425  -3.2647  -1.5572
 S81  H21  H  HNH2  0   0.344   5.8544  -1.2200   1.3451
 S81  H22  H  HNH2  0   0.333   5.7494  -0.8102  -0.2105
 S81  H24  H  HNH2  0   0.344   1.3667  -3.2990   1.0812
 S81  H25  H  HNH2  0   0.349   0.1089  -2.4592   0.5149
 S81  H27  H  HOH1  0   0.468   0.8745   2.4103  -0.5446
 S81  H28  H  HOH1  0   0.441   3.9340   2.7197  -0.2812
 S81  H29  H  HOH1  0   0.458  -4.2238   2.2454   1.3478

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
 S81  N6   C6   single  1.452  0.020  1.452
 S81  C6   C5   single  1.515  0.020  1.515
 S81  O5   C5   single  1.419  0.020  1.419
 S81  O5   C1   single  1.397  0.020  1.397
 S81  C5   C4   single  1.520  0.020  1.520
 S81  C4   F99  single  1.397  0.020  1.397
 S81  C4   C3   single  1.519  0.020  1.519
 S81  C1   C2   single  1.533  0.020  1.533
 S81  C1   O1   single  1.392  0.020  1.392
 S81  C2   C3   single  1.530  0.020  1.530
 S81  C2   N2   single  1.457  0.020  1.457
 S81  O11  C11  single  1.406  0.020  1.406
 S81  C3   O23  single  1.406  0.020  1.406
 S81  O1   C10  single  1.422  0.020  1.422
 S81  C10  C11  single  1.528  0.020  1.528
 S81  C10  C9   single  1.521  0.020  1.521
 S81  C11  C12  single  1.526  0.020  1.526
 S81  C12  O12  single  1.407  0.020  1.407
 S81  C12  C7   single  1.522  0.020  1.522
 S81  N9   C9   single  1.455  0.020  1.455
 S81  C9   C8   single  1.524  0.020  1.524
 S81  C8   C7   single  1.529  0.020  1.529
 S81  C7   N7   single  1.455  0.020  1.455
 S81  C1   H1   single  0.970  0.020  1.090
 S81  C10  H2   single  0.970  0.020  1.090
 S81  C11  H3   single  0.970  0.020  1.090
 S81  C12  H4   single  0.970  0.020  1.090
 S81  C2   H5   single  0.970  0.020  1.090
 S81  C3   H6   single  0.970  0.020  1.090
 S81  C4   H7   single  0.970  0.020  1.090
 S81  C5   H8   single  0.970  0.020  1.090
 S81  C6   H9   single  0.970  0.020  1.090
 S81  C6   H10  single  0.970  0.020  1.090
 S81  C7   H11  single  0.970  0.020  1.090
 S81  C8   H12  single  0.970  0.020  1.090
 S81  C8   H13  single  0.970  0.020  1.090
 S81  C9   H14  single  0.970  0.020  1.090
 S81  N2   H15  single  0.890  0.020  1.040
 S81  N2   H16  single  0.890  0.020  1.040
 S81  N6   H18  single  0.890  0.020  1.040
 S81  N6   H19  single  0.890  0.020  1.040
 S81  N7   H21  single  0.890  0.020  1.040
 S81  N7   H22  single  0.890  0.020  1.040
 S81  N9   H24  single  0.890  0.020  1.040
 S81  N9   H25  single  0.890  0.020  1.040
 S81  O11  H27  single  0.850  0.020  0.980
 S81  O12  H28  single  0.850  0.020  0.980
 S81  O23  H29  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
 S81  H1   C1   O5   105.02  3.000
 S81  H1   C1   O1   110.93  3.000
 S81  O5   C1   O1   111.36  3.000
 S81  H1   C1   C2   108.82  3.000
 S81  O1   C1   C2   109.15  3.000
 S81  O5   C1   C2   111.49  3.000
 S81  H2   C10  O1   110.09  3.000
 S81  H2   C10  C9   108.12  3.000
 S81  O1   C10  C9   108.65  3.000
 S81  H2   C10  C11  109.36  3.000
 S81  C9   C10  C11  111.84  3.000
 S81  O1   C10  C11  108.77  3.000
 S81  H3   C11  O11  110.81  3.000
 S81  H3   C11  C12  107.60  3.000
 S81  O11  C11  C12  107.08  3.000
 S81  H3   C11  C10  107.57  3.000
 S81  C12  C11  C10  111.85  3.000
 S81  O11  C11  C10  111.89  3.000
 S81  H4   C12  O12  110.39  3.000
 S81  H4   C12  C7   107.58  3.000
 S81  O12  C12  C7   109.76  3.000
 S81  H4   C12  C11  107.87  3.000
 S81  C7   C12  C11  110.73  3.000
 S81  O12  C12  C11  110.46  3.000
 S81  H5   C2   N2   107.69  3.000
 S81  H5   C2   C3   107.81  3.000
 S81  N2   C2   C3   113.69  3.000
 S81  H5   C2   C1   106.28  3.000
 S81  N2   C2   C1   109.37  3.000
 S81  C3   C2   C1   111.65  3.000
 S81  H6   C3   O23  110.83  3.000
 S81  H6   C3   C4   107.55  3.000
 S81  O23  C3   C4   112.37  3.000
 S81  H6   C3   C2   108.65  3.000
 S81  O23  C3   C2   107.68  3.000
 S81  C4   C3   C2   109.71  3.000
 S81  H7   C4   F99  107.51  3.000
 S81  H7   C4   C5   110.72  3.000
 S81  F99  C4   C5   109.14  3.000
 S81  H7   C4   C3   110.55  3.000
 S81  F99  C4   C3   108.81  3.000
 S81  C5   C4   C3   110.04  3.000
 S81  H8   C5   O5   110.79  3.000
 S81  H8   C5   C6   107.73  3.000
 S81  O5   C5   C6   107.04  3.000
 S81  H8   C5   C4   108.99  3.000
 S81  O5   C5   C4   107.81  3.000
 S81  C6   C5   C4   114.48  3.000
 S81  H10  C6   H9   106.68  3.000
 S81  H10  C6   N6   114.46  3.000
 S81  H9   C6   N6   108.29  3.000
 S81  H10  C6   C5   108.96  3.000
 S81  H9   C6   C5   108.47  3.000
 S81  N6   C6   C5   109.79  3.000
 S81  H11  C7   N7   107.22  3.000
 S81  H11  C7   C8   108.67  3.000
 S81  N7   C7   C8   113.55  3.000
 S81  H11  C7   C12  108.07  3.000
 S81  N7   C7   C12  110.25  3.000
 S81  C8   C7   C12  108.92  3.000
 S81  H13  C8   H12  106.42  3.000
 S81  H13  C8   C9   109.33  3.000
 S81  H12  C8   C9   108.74  3.000
 S81  H13  C8   C7   109.13  3.000
 S81  H12  C8   C7   109.18  3.000
 S81  C9   C8   C7   113.78  3.000
 S81  H14  C9   N9   112.87  3.000
 S81  H14  C9   C8   108.04  3.000
 S81  N9   C9   C8   109.22  3.000
 S81  H14  C9   C10  107.58  3.000
 S81  C8   C9   C10  109.11  3.000
 S81  N9   C9   C10  109.94  3.000
 S81  H16  N2   H15  106.24  3.000
 S81  H16  N2   C2   110.49  3.000
 S81  H15  N2   C2   110.45  3.000
 S81  H19  N6   H18  106.09  3.000
 S81  H19  N6   C6   110.00  3.000
 S81  H18  N6   C6   109.60  3.000
 S81  H22  N7   H21  105.31  3.000
 S81  H22  N7   C7   109.10  3.000
 S81  H21  N7   C7   108.88  3.000
 S81  H25  N9   H24  105.77  3.000
 S81  H25  N9   C9   110.92  3.000
 S81  H24  N9   C9   109.21  3.000
 S81  C10  O1   C1   117.70  3.000
 S81  H27  O11  C11  109.15  3.000
 S81  H28  O12  C12  106.84  3.000
 S81  H29  O23  C3   108.86  3.000
 S81  C5   O5   C1   115.54  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
 S81  Var_01  H18  N6  C6  C5  175.74  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
 S81  chir_01  C1   O5   C2   O1   negativ
 S81  chir_02  C10  O1   C11  C9   negativ
 S81  chir_03  C11  O11  C10  C12  negativ
 S81  chir_04  C12  O12  C11  C7   positiv
 S81  chir_05  C2   N2   C1   C3   negativ
 S81  chir_06  C3   O23  C2   C4   positiv
 S81  chir_07  C4   F99  C5   C3   positiv
 S81  chir_08  C5   O5   C4   C6   negativ
 S81  chir_09  C7   N7   C8   C12  positiv
 S81  chir_10  C9   N9   C10  C8   positiv

