# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 11:36:33 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  28  16  .  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_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  -0.662   2.1552   1.9481  -1.1994
 3LJ  C1   C  CH1    0   0.248   1.9728   1.6043   0.1350
 3LJ  C2   C  CH1    0  -0.137   3.0859   0.6510   0.5674
 3LJ  C3   C  CH1    0   0.009   2.9199  -0.6866  -0.1468
 3LJ  C4   C  CH1    0   0.029   1.5231  -1.2409   0.1026
 3LJ  C5   C  CH1    0  -0.017   0.4753  -0.2027  -0.2987
 3LJ  C6   C  CH2    0  -0.166  -0.9161  -0.6556   0.0886
 3LJ  O3   O  OH1    0  -0.680   3.8463  -1.6453   0.3287
 3LJ  O4   O  OH1    0  -0.674   1.2887  -2.4099  -0.6430
 3LJ  O5   O  O2     0  -0.502   0.7184   1.0187   0.3732
 3LJ  O6   O  OC2    0  -0.616  -1.8435   0.3037  -0.3987
 3LJ  N    N  NH2    0  -0.809   4.3930   1.2173   0.2875
 3LJ  S    S  S      0   1.577  -3.3967   0.1629   0.1129
 3LJ  O7   O  OS     0  -0.736  -4.0248   1.2639  -0.6134
 3LJ  O8   O  OS     0  -0.747  -3.8295  -1.1740  -0.3032
 3LJ  O9   O  OS    -1  -0.746  -3.3520   0.3394   1.5665
 3LJ  H1   H  HOH1   0   0.460   1.5370   2.6517  -1.4252
 3LJ  H2   H  HCH1   0   0.233   1.9815   2.4949   0.7764
 3LJ  H3   H  HCH1   0   0.222   2.9208   0.4755   1.6428
 3LJ  H4   H  HCH1   0   0.222   3.0482  -0.5360  -1.2266
 3LJ  H5   H  HCH1   0   0.207   1.4176  -1.4345   1.1830
 3LJ  H6   H  HCH1   0   0.228   0.5203  -0.0650  -1.3878
 3LJ  H7   H  HCH2   0   0.234  -1.1149  -1.6383  -0.3448
 3LJ  H8   H  HCH2   0   0.218  -0.9781  -0.7447   1.1790
 3LJ  H9   H  HOH1   0   0.460   4.6294  -1.6270  -0.2280
 3LJ  H10  H  HOH1   0   0.451   1.9729  -3.0472  -0.4113
 3LJ  H11  H  HNH2   0   0.348   4.4742   2.1215   0.7375
 3LJ  H12  H  HNH2   0   0.346   5.1003   0.6419   0.7272

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    deloc   1.465  0.020  1.465
 3LJ  O7  S    deloc   1.461  0.020  1.461
 3LJ  S   O9   deloc   1.465  0.020  1.465
 3LJ  S   O6   single  1.641  0.020  1.641
 3LJ  C6  O6   single  1.420  0.020  1.420
 3LJ  C6  C5   single  1.514  0.020  1.514
 3LJ  C5  O5   single  1.415  0.020  1.415
 3LJ  C5  C4   single  1.529  0.020  1.529
 3LJ  O5  C1   single  1.405  0.020  1.405
 3LJ  O4  C4   single  1.406  0.020  1.406
 3LJ  C4  C3   single  1.523  0.020  1.523
 3LJ  C1  O1   single  1.390  0.020  1.390
 3LJ  C1  C2   single  1.528  0.020  1.528
 3LJ  C3  C2   single  1.525  0.020  1.525
 3LJ  C3  O3   single  1.415  0.020  1.415
 3LJ  C2  N    single  1.452  0.020  1.452
 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

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   108.75  3.000
 3LJ  H2   C1  O5   104.26  3.000
 3LJ  H2   C1  C2   109.58  3.000
 3LJ  O5   C1  C2   110.02  3.000
 3LJ  H2   C1  O1   111.05  3.000
 3LJ  C2   C1  O1   109.29  3.000
 3LJ  O5   C1  O1   112.53  3.000
 3LJ  H3   C2  N    112.65  3.000
 3LJ  H3   C2  C3   107.52  3.000
 3LJ  N    C2  C3   110.47  3.000
 3LJ  H3   C2  C1   105.44  3.000
 3LJ  N    C2  C1   110.97  3.000
 3LJ  C3   C2  C1   109.59  3.000
 3LJ  H4   C3  O3   110.30  3.000
 3LJ  H4   C3  C4   108.55  3.000
 3LJ  O3   C3  C4   107.38  3.000
 3LJ  H4   C3  C2   109.12  3.000
 3LJ  O3   C3  C2   111.43  3.000
 3LJ  C4   C3  C2   110.01  3.000
 3LJ  H5   C4  O4   110.95  3.000
 3LJ  H5   C4  C5   108.11  3.000
 3LJ  O4   C4  C5   108.13  3.000
 3LJ  H5   C4  C3   108.18  3.000
 3LJ  O4   C4  C3   111.62  3.000
 3LJ  C5   C4  C3   109.78  3.000
 3LJ  H6   C5  O5   110.83  3.000
 3LJ  H6   C5  C6   109.19  3.000
 3LJ  O5   C5  C6   107.14  3.000
 3LJ  H6   C5  C4   108.50  3.000
 3LJ  O5   C5  C4   110.11  3.000
 3LJ  C6   C5  C4   111.08  3.000
 3LJ  H8   C6  H7   108.14  3.000
 3LJ  H8   C6  O6   111.06  3.000
 3LJ  H7   C6  O6   110.65  3.000
 3LJ  H8   C6  C5   109.33  3.000
 3LJ  H7   C6  C5   109.57  3.000
 3LJ  O6   C6  C5   108.08  3.000
 3LJ  H9   O3  C3   109.01  3.000
 3LJ  H10  O4  C4   107.71  3.000
 3LJ  C5   O5  C1   115.64  3.000
 3LJ  S    O6  C6   116.93  3.000
 3LJ  H12  N   H11  104.97  3.000
 3LJ  H12  N   C2   108.88  3.000
 3LJ  H11  N   C2   109.55  3.000
 3LJ  O9   S   O8   113.62  3.000
 3LJ  O9   S   O7   114.56  3.000
 3LJ  O8   S   O7   114.80  3.000
 3LJ  O9   S   O6   105.66  3.000
 3LJ  O7   S   O6   100.79  3.000
 3LJ  O8   S   O6   105.62  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  -58.56  30.0  3
 3LJ  Var_02  H7  C6  O6  S    69.99  30.0  2

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

