# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:48:19 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@@H](O)O[C@H](CO[S](O)(=O)=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
 3LJ  3LJ  2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose  D-saccharide  29  16  .  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_3LJ
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
 3LJ  O1   O  OH1   0  -0.659   2.1475   1.8997  -1.1871
 3LJ  C1   C  CH1   0   0.247   1.9370   1.5593   0.1421
 3LJ  C2   C  CH1   0  -0.136   3.0419   0.6095   0.6039
 3LJ  C3   C  CH1   0   0.007   2.9038  -0.7272  -0.1186
 3LJ  C4   C  CH1   0   0.026   1.5038  -1.2904   0.0976
 3LJ  C5   C  CH1   0  -0.015   0.4652  -0.2534  -0.3297
 3LJ  C6   C  CH2   0  -0.197  -0.9279  -0.7192   0.0251
 3LJ  O3   O  OH1   0  -0.679   3.8272  -1.6756   0.3814
 3LJ  O4   O  OH1   0  -0.673   1.2855  -2.4566  -0.6545
 3LJ  O5   O  O2    0  -0.501   0.6773   0.9653   0.3496
 3LJ  O6   O  OC2   0  -0.573  -1.8444   0.2642  -0.5061
 3LJ  N    N  NH2   0  -0.807   4.3519   1.1851   0.3629
 3LJ  S    S  S     0   1.664  -3.3593   0.2310  -0.0606
 3LJ  O7   O  OS    0  -0.621  -3.9869   1.2631  -0.8341
 3LJ  O8   O  OS    0  -0.635  -3.8552  -1.1226  -0.0595
 3LJ  O9   O  OS    0  -0.710  -3.2855   0.7682   1.4308
 3LJ  H1   H  HOH1  0   0.462   1.5442   2.6120  -1.4256
 3LJ  H2   H  HCH1  0   0.237   1.9223   2.4495   0.7830
 3LJ  H3   H  HCH1  0   0.224   2.8474   0.4289   1.6736
 3LJ  H4   H  HCH1  0   0.228   3.0574  -0.5741  -1.1942
 3LJ  H5   H  HCH1  0   0.214   1.3752  -1.4838   1.1754
 3LJ  H6   H  HCH1  0   0.244   0.5326  -0.1181  -1.4179
 3LJ  H7   H  HCH2  0   0.276  -1.1377  -1.6893  -0.4229
 3LJ  H8   H  HCH2  0   0.253  -1.0336  -0.7936   1.1108
 3LJ  H9   H  HOH1  0   0.462   4.5756  -1.7317  -0.2180
 3LJ  H10  H  HOH1  0   0.454   1.9466  -3.1057  -0.3909
 3LJ  H11  H  HNH2  0   0.348   4.4338   2.0584   0.8702
 3LJ  H12  H  HNH2  0   0.346   5.0528   0.5788   0.7704
 3LJ  H13  H  H     0   0.515  -3.4081   0.0671   2.0919

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
 3LJ  O8  S    double  1.442  0.020  1.442
 3LJ  O7  S    double  1.434  0.020  1.434
 3LJ  S   O9   single  1.587  0.020  1.587
 3LJ  S   O6   single  1.579  0.020  1.579
 3LJ  C6  O6   single  1.445  0.020  1.445
 3LJ  C6  C5   single  1.511  0.020  1.511
 3LJ  C5  O5   single  1.411  0.020  1.411
 3LJ  C5  C4   single  1.529  0.020  1.529
 3LJ  O5  C1   single  1.408  0.020  1.408
 3LJ  O4  C4   single  1.405  0.020  1.405
 3LJ  C4  C3   single  1.524  0.020  1.524
 3LJ  C1  O1   single  1.388  0.020  1.388
 3LJ  C1  C2   single  1.528  0.020  1.528
 3LJ  C3  C2   single  1.526  0.020  1.526
 3LJ  C3  O3   single  1.415  0.020  1.415
 3LJ  C2  N    single  1.451  0.020  1.451
 3LJ  O1  H1   single  0.850  0.020  0.980
 3LJ  C1  H2   single  0.970  0.020  1.090
 3LJ  C2  H3   single  0.970  0.020  1.090
 3LJ  C3  H4   single  0.970  0.020  1.090
 3LJ  C4  H5   single  0.970  0.020  1.090
 3LJ  C5  H6   single  0.970  0.020  1.090
 3LJ  C6  H7   single  0.970  0.020  1.090
 3LJ  C6  H8   single  0.970  0.020  1.090
 3LJ  O3  H9   single  0.850  0.020  0.980
 3LJ  O4  H10  single  0.850  0.020  0.980
 3LJ  N   H11  single  0.890  0.020  1.040
 3LJ  N   H12  single  0.890  0.020  1.040
 3LJ  O9  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
 3LJ  H1   O1  C1   108.87  3.000
 3LJ  H2   C1  O5   104.13  3.000
 3LJ  H2   C1  C2   109.72  3.000
 3LJ  O5   C1  C2   109.88  3.000
 3LJ  H2   C1  O1   111.25  3.000
 3LJ  C2   C1  O1   109.40  3.000
 3LJ  O5   C1  O1   112.34  3.000
 3LJ  H3   C2  N    112.68  3.000
 3LJ  H3   C2  C3   107.46  3.000
 3LJ  N    C2  C3   110.52  3.000
 3LJ  H3   C2  C1   105.52  3.000
 3LJ  N    C2  C1   110.85  3.000
 3LJ  C3   C2  C1   109.63  3.000
 3LJ  H4   C3  O3   110.40  3.000
 3LJ  H4   C3  C4   108.61  3.000
 3LJ  O3   C3  C4   107.55  3.000
 3LJ  H4   C3  C2   109.23  3.000
 3LJ  O3   C3  C2   111.15  3.000
 3LJ  C4   C3  C2   109.85  3.000
 3LJ  H5   C4  O4   111.08  3.000
 3LJ  H5   C4  C5   108.24  3.000
 3LJ  O4   C4  C5   107.93  3.000
 3LJ  H5   C4  C3   108.10  3.000
 3LJ  O4   C4  C3   111.93  3.000
 3LJ  C5   C4  C3   109.49  3.000
 3LJ  H6   C5  O5   111.17  3.000
 3LJ  H6   C5  C6   109.09  3.000
 3LJ  O5   C5  C6   106.96  3.000
 3LJ  H6   C5  C4   108.59  3.000
 3LJ  O5   C5  C4   110.44  3.000
 3LJ  C6   C5  C4   110.59  3.000
 3LJ  H8   C6  H7   109.22  3.000
 3LJ  H8   C6  O6   110.48  3.000
 3LJ  H7   C6  O6   109.43  3.000
 3LJ  H8   C6  C5   110.07  3.000
 3LJ  H7   C6  C5   110.83  3.000
 3LJ  O6   C6  C5   106.77  3.000
 3LJ  H9   O3  C3   109.09  3.000
 3LJ  H10  O4  C4   107.83  3.000
 3LJ  C5   O5  C1   115.33  3.000
 3LJ  S    O6  C6   119.36  3.000
 3LJ  H12  N   H11  104.99  3.000
 3LJ  H12  N   C2   108.70  3.000
 3LJ  H11  N   C2   109.37  3.000
 3LJ  O9   S   O8   109.46  3.000
 3LJ  O9   S   O7   106.47  3.000
 3LJ  O8   S   O7   121.70  3.000
 3LJ  O9   S   O6   102.32  3.000
 3LJ  O7   S   O6   104.63  3.000
 3LJ  O8   S   O6   110.48  3.000
 3LJ  H13  O9  S    112.92  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
 3LJ  Var_01  O8  S   O6  C6  -43.47  30.0  2
 3LJ  Var_02  H7  C6  O6  S    72.25  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
 3LJ  chir_01  C1  O5  O1  C2  positiv
 3LJ  chir_02  C2  N   C3  C1  positiv
 3LJ  chir_03  C3  O3  C2  C4  positiv
 3LJ  chir_04  C4  O4  C3  C5  negativ
 3LJ  chir_05  C5  O5  C4  C6  negativ

