# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  8 17:09:08 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@H]2[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H]2O
#
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
 MYG  MYG  '(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside'  D-saccharide  46  23  .  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_MYG
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
 MYG  C1    C  CH1   0   0.051   1.5455  -0.1357   1.9515
 MYG  C2    C  CH1   0  -0.027   1.3211  -0.4485   3.4302
 MYG  C3    C  CH1   0  -0.036   0.2323   0.4518   4.0144
 MYG  C4    C  CH1   0  -0.016  -1.0556   0.3193   3.2047
 MYG  C5    C  CH1   0   0.040  -0.8388   0.6160   1.7237
 MYG  C6    C  CH1   0   0.021   0.2568  -0.2664   1.1365
 MYG  C7    C  CH1   0   0.265   0.7087  -0.8005  -1.1552
 MYG  C8    C  CH1   0  -0.140   1.5502  -0.1930  -2.2788
 MYG  C9    C  CH1   0   0.050   0.7289   0.8408  -3.0347
 MYG  C10   C  CH1   0  -0.011  -0.5820   0.2289  -3.5077
 MYG  C11   C  CH1   0  -0.006  -1.3306  -0.4054  -2.3296
 MYG  C12   C  CH2   0  -0.167  -2.5409  -1.1751  -2.8134
 MYG  N8    N  NH2   0  -0.803   2.7624   0.4054  -1.7494
 MYG  O1    O  OH1   0  -0.669   2.5110  -0.9932   1.3892
 MYG  O2    O  OH1   0  -0.669   0.9551  -1.8038   3.5410
 MYG  O3    O  OH1   0  -0.672   0.7164   1.7742   4.0161
 MYG  O4    O  OH1   0  -0.678  -2.0312   1.2377   3.6623
 MYG  O5    O  OH1   0  -0.655  -2.0185   0.3950   0.9920
 MYG  O6    O  O2    0  -0.505   0.4990   0.1726  -0.1839
 MYG  O9    O  OH1   0  -0.676   1.5006   1.3034  -4.1195
 MYG  O10   O  OH1   0  -0.677  -1.3393   1.2622  -4.1067
 MYG  O11   O  O2    0  -0.501  -0.4875  -1.3248  -1.6564
 MYG  O12   O  OH1   0  -0.663  -3.2626  -1.6712  -1.7133
 MYG  H1    H  HCH1  0   0.224   1.8727   0.9095   1.8834
 MYG  H2    H  HCH1  0   0.234   2.2596  -0.2497   3.9700
 MYG  H3    H  HCH1  0   0.228   0.0249   0.1196   5.0456
 MYG  H4    H  HCH1  0   0.225  -1.4162  -0.7118   3.3029
 MYG  H5    H  HCH1  0   0.204  -0.5131   1.6639   1.6262
 MYG  H6    H  HCH1  0   0.230  -0.0863  -1.3093   1.1427
 MYG  H7    H  HCH1  0   0.236   1.2353  -1.6651  -0.7372
 MYG  H8    H  HCH1  0   0.220   1.7540  -1.0257  -2.9709
 MYG  H9    H  HCH1  0   0.201   0.4959   1.6684  -2.3477
 MYG  H10   H  HCH1  0   0.215  -0.3516  -0.5573  -4.2421
 MYG  H11   H  HCH1  0   0.229  -1.6586   0.3857  -1.6450
 MYG  H121  H  HCH2  0   0.194  -3.1567  -0.5000  -3.4199
 MYG  H122  H  HCH2  0   0.191  -2.2037  -1.9838  -3.4783
 MYG  HN81  H  HNH2  0   0.344   3.1716  -0.2026  -1.0515
 MYG  HN82  H  HNH2  0   0.345   3.4465   0.4894  -2.4891
 MYG  HO1   H  HOH1  0   0.455   3.3813  -0.7057   1.6812
 MYG  HO2   H  HOH1  0   0.455   0.8971  -2.0288   4.4750
 MYG  HO3   H  HOH1  0   0.450  -0.0193   2.3553   4.2407
 MYG  HO4   H  HOH1  0   0.461  -2.4412   0.8859   4.4589
 MYG  HO5   H  HOH1  0   0.445  -2.7059   0.9489   1.3769
 MYG  HO9   H  HOH1  0   0.447   0.9807   1.9640  -4.5891
 MYG  HO10  H  HOH1  0   0.459  -1.8733   0.8903  -4.8133
 MYG  HO12  H  HOH1  0   0.452  -4.0396  -2.1230  -2.0541

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
 MYG  C1   C2    single  1.528  0.020  1.528
 MYG  C1   C6    single  1.530  0.020  1.530
 MYG  C1   O1    single  1.408  0.020  1.408
 MYG  C1   H1    single  0.970  0.020  1.090
 MYG  C2   C3    single  1.529  0.020  1.529
 MYG  C2   O2    single  1.408  0.020  1.408
 MYG  C2   H2    single  0.970  0.020  1.090
 MYG  C3   C4    single  1.527  0.020  1.527
 MYG  C3   O3    single  1.408  0.020  1.408
 MYG  C3   H3    single  0.970  0.020  1.090
 MYG  C4   C5    single  1.526  0.020  1.526
 MYG  C4   O4    single  1.416  0.020  1.416
 MYG  C4   H4    single  0.970  0.020  1.090
 MYG  C5   C6    single  1.524  0.020  1.524
 MYG  C5   O5    single  1.406  0.020  1.406
 MYG  C5   H5    single  0.970  0.020  1.090
 MYG  C6   O6    single  1.412  0.020  1.412
 MYG  C6   H6    single  0.970  0.020  1.090
 MYG  C7   C8    single  1.530  0.020  1.530
 MYG  C7   O6    single  1.391  0.020  1.391
 MYG  C7   O11   single  1.399  0.020  1.399
 MYG  C7   H7    single  0.970  0.020  1.090
 MYG  C8   C9    single  1.521  0.020  1.521
 MYG  C8   N8    single  1.452  0.020  1.452
 MYG  C8   H8    single  0.970  0.020  1.090
 MYG  C9   C10   single  1.522  0.020  1.522
 MYG  C9   O9    single  1.409  0.020  1.409
 MYG  C9   H9    single  0.970  0.020  1.090
 MYG  C10  C11   single  1.533  0.020  1.533
 MYG  C10  O10   single  1.414  0.020  1.414
 MYG  C10  H10   single  0.970  0.020  1.090
 MYG  C11  C12   single  1.514  0.020  1.514
 MYG  C11  O11   single  1.418  0.020  1.418
 MYG  C11  H11   single  0.970  0.020  1.090
 MYG  C12  O12   single  1.406  0.020  1.406
 MYG  C12  H121  single  0.970  0.020  1.090
 MYG  C12  H122  single  0.970  0.020  1.090
 MYG  N8   HN81  single  0.890  0.020  1.040
 MYG  N8   HN82  single  0.890  0.020  1.040
 MYG  O1   HO1   single  0.850  0.020  0.980
 MYG  O2   HO2   single  0.850  0.020  0.980
 MYG  O3   HO3   single  0.850  0.020  0.980
 MYG  O4   HO4   single  0.850  0.020  0.980
 MYG  O5   HO5   single  0.850  0.020  0.980
 MYG  O9   HO9   single  0.850  0.020  0.980
 MYG  O10  HO10  single  0.850  0.020  0.980
 MYG  O12  HO12  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
 MYG  H1    C1   O1    110.53  3.000
 MYG  H1    C1   C6    107.41  3.000
 MYG  O1    C1   C6    108.22  3.000
 MYG  H1    C1   C2    107.39  3.000
 MYG  O1    C1   C2    111.25  3.000
 MYG  C6    C1   C2    111.98  3.000
 MYG  H2    C2   O2    110.90  3.000
 MYG  H2    C2   C3    108.26  3.000
 MYG  O2    C2   C3    110.58  3.000
 MYG  H2    C2   C1    108.21  3.000
 MYG  O2    C2   C1    108.14  3.000
 MYG  C3    C2   C1    110.72  3.000
 MYG  H3    C3   O3    110.27  3.000
 MYG  H3    C3   C4    108.12  3.000
 MYG  O3    C3   C4    111.84  3.000
 MYG  H3    C3   C2    108.29  3.000
 MYG  O3    C3   C2    107.98  3.000
 MYG  C4    C3   C2    110.30  3.000
 MYG  H4    C4   O4    110.75  3.000
 MYG  H4    C4   C5    108.45  3.000
 MYG  O4    C4   C5    106.59  3.000
 MYG  H4    C4   C3    108.15  3.000
 MYG  O4    C4   C3    110.70  3.000
 MYG  C5    C4   C3    112.21  3.000
 MYG  H5    C5   O5    110.59  3.000
 MYG  H5    C5   C6    107.69  3.000
 MYG  O5    C5   C6    108.16  3.000
 MYG  H5    C5   C4    108.23  3.000
 MYG  O5    C5   C4    110.82  3.000
 MYG  C6    C5   C4    111.31  3.000
 MYG  H6    C6   O6    110.74  3.000
 MYG  H6    C6   C5    108.84  3.000
 MYG  O6    C6   C5    107.67  3.000
 MYG  H6    C6   C1    109.95  3.000
 MYG  O6    C6   C1    109.09  3.000
 MYG  C5    C6   C1    110.53  3.000
 MYG  H7    C7   O11   104.60  3.000
 MYG  H7    C7   O6    111.00  3.000
 MYG  O11   C7   O6    112.55  3.000
 MYG  H7    C7   C8    109.23  3.000
 MYG  O11   C7   C8    110.86  3.000
 MYG  O6    C7   C8    108.55  3.000
 MYG  H8    C8   N8    112.71  3.000
 MYG  H8    C8   C9    107.54  3.000
 MYG  N8    C8   C9    110.60  3.000
 MYG  H8    C8   C7    105.25  3.000
 MYG  N8    C8   C7    110.80  3.000
 MYG  C9    C8   C7    109.75  3.000
 MYG  H9    C9   O9    110.46  3.000
 MYG  H9    C9   C10   108.30  3.000
 MYG  O9    C9   C10   111.37  3.000
 MYG  H9    C9   C8    108.37  3.000
 MYG  O9    C9   C8    108.06  3.000
 MYG  C10   C9   C8    110.25  3.000
 MYG  H10   C10  O10   110.58  3.000
 MYG  H10   C10  C11   108.64  3.000
 MYG  O10   C10  C11   111.49  3.000
 MYG  H10   C10  C9    108.31  3.000
 MYG  O10   C10  C9    107.40  3.000
 MYG  C11   C10  C9    110.37  3.000
 MYG  H11   C11  O11   110.45  3.000
 MYG  H11   C11  C12   109.10  3.000
 MYG  O11   C11  C12   107.31  3.000
 MYG  H11   C11  C10   109.11  3.000
 MYG  O11   C11  C10   110.05  3.000
 MYG  C12   C11  C10   110.80  3.000
 MYG  H122  C12  H121  106.88  3.000
 MYG  H122  C12  O12   111.78  3.000
 MYG  H121  C12  O12   111.20  3.000
 MYG  H122  C12  C11   108.78  3.000
 MYG  H121  C12  C11   108.22  3.000
 MYG  O12   C12  C11   109.86  3.000
 MYG  HN82  N8   HN81  106.31  3.000
 MYG  HN82  N8   C8    109.42  3.000
 MYG  HN81  N8   C8    109.96  3.000
 MYG  HO1   O1   C1    108.49  3.000
 MYG  HO2   O2   C2    108.48  3.000
 MYG  HO3   O3   C3    107.70  3.000
 MYG  HO4   O4   C4    108.90  3.000
 MYG  HO5   O5   C5    107.49  3.000
 MYG  C7    O6   C6    117.47  3.000
 MYG  HO9   O9   C9    107.76  3.000
 MYG  HO10  O10  C10   109.05  3.000
 MYG  C11   O11  C7    115.83  3.000
 MYG  HO12  O12  C12   107.65  3.000

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
 MYG  chir_01  C1   C2   C6   O1   positiv
 MYG  chir_02  C2   O2   C1   C3   negativ
 MYG  chir_03  C3   O3   C2   C4   positiv
 MYG  chir_04  C4   O4   C3   C5   positiv
 MYG  chir_05  C5   O5   C4   C6   negativ
 MYG  chir_06  C6   O6   C1   C5   negativ
 MYG  chir_07  C7   O11  O6   C8   positiv
 MYG  chir_08  C8   N8   C9   C7   positiv
 MYG  chir_09  C9   O9   C8   C10  positiv
 MYG  chir_10  C10  O10  C11  C9   positiv
 MYG  chir_11  C11  O11  C10  C12  negativ

