# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 01:13:42 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2R,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methylhexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@@H]2[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]2S1
#
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
 58Y  58Y  (2R,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methylhexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol  ligand  29  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_58Y
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
 58Y  C1   C  CH1   0  -0.069  -0.1996   0.6872  -1.0900
 58Y  C2   C  CH1   0  -0.141  -0.8561  -0.6699  -0.8412
 58Y  C3   C  CH1   0   0.047  -0.3252  -1.3170   0.4399
 58Y  C4   C  CH1   0  -0.026   1.1979  -1.2690   0.4743
 58Y  C5   C  CH1   0  -0.004   1.6069   0.2013   0.3838
 58Y  C6   C  CH2   0  -0.166   3.1053   0.3947   0.4552
 58Y  C7   C  CH1   0  -0.193  -2.6780   0.7749  -0.1014
 58Y  C8   C  CH3   0  -0.661  -3.2303   0.4993   1.2879
 58Y  N2   N  NH1   0  -0.597  -2.2751  -0.3974  -0.8722
 58Y  S1   S  S2    0  -0.072  -1.1914   1.8459  -0.0380
 58Y  O3   O  OH1   0  -0.668  -0.8492  -2.6195   0.4930
 58Y  O4   O  OH1   0  -0.670   1.7018  -2.0411  -0.5870
 58Y  O5   O  O2    0  -0.463   1.1551   0.7650  -0.8352
 58Y  O6   O  OH1   0  -0.668   3.3867   1.7702   0.5391
 58Y  H1   H  HCH1  0   0.290  -0.3299   0.9800  -2.1321
 58Y  H2   H  HCH1  0   0.268  -0.6133  -1.3298  -1.6811
 58Y  H3   H  HCH1  0   0.216  -0.6620  -0.7278   1.3025
 58Y  H4   H  HCH1  0   0.236   1.5380  -1.6557   1.4469
 58Y  H5   H  HCH1  0   0.226   1.1519   0.7290   1.2353
 58Y  H6   H  HCH2  0   0.205   3.4661  -0.1494   1.3385
 58Y  H7   H  HCH2  0   0.201   3.5821  -0.0608  -0.4224
 58Y  H8   H  HCH1  0   0.265  -3.4415   1.3162  -0.6653
 58Y  H9   H  HCH3  0   0.240  -3.5471   1.4256   1.7680
 58Y  H10  H  HCH3  0   0.238  -4.1093  -0.1451   1.2145
 58Y  H11  H  HCH3  0   0.236  -2.5015   0.0133   1.9343
 58Y  H12  H  HNH1  0   0.364  -2.8203  -1.2095  -0.6120
 58Y  H14  H  HOH1  0   0.453  -0.6770  -2.9829   1.3672
 58Y  H15  H  HOH1  0   0.457   2.6333  -2.2222  -0.4324
 58Y  H16  H  HOH1  0   0.457   4.3420   1.8785   0.5410

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
 58Y  C8  C7   single  1.520  0.020  1.520
 58Y  C7  S1   single  1.833  0.020  1.833
 58Y  C7  N2   single  1.460  0.020  1.460
 58Y  S1  C1   single  1.853  0.020  1.853
 58Y  N2  C2   single  1.445  0.020  1.445
 58Y  C1  C2   single  1.528  0.020  1.528
 58Y  C1  O5   single  1.381  0.020  1.381
 58Y  C2  C3   single  1.530  0.020  1.530
 58Y  O5  C5   single  1.417  0.020  1.417
 58Y  C5  C4   single  1.529  0.020  1.529
 58Y  C5  C6   single  1.513  0.020  1.513
 58Y  C3  C4   single  1.524  0.020  1.524
 58Y  C3  O3   single  1.405  0.020  1.405
 58Y  C4  O4   single  1.406  0.020  1.406
 58Y  C6  O6   single  1.407  0.020  1.407
 58Y  C1  H1   single  0.970  0.020  1.090
 58Y  C2  H2   single  0.970  0.020  1.090
 58Y  C3  H3   single  0.970  0.020  1.090
 58Y  C4  H4   single  0.970  0.020  1.090
 58Y  C5  H5   single  0.970  0.020  1.090
 58Y  C6  H6   single  0.970  0.020  1.090
 58Y  C6  H7   single  0.970  0.020  1.090
 58Y  C7  H8   single  0.970  0.020  1.090
 58Y  C8  H9   single  0.970  0.020  1.090
 58Y  C8  H10  single  0.970  0.020  1.090
 58Y  C8  H11  single  0.970  0.020  1.090
 58Y  N2  H12  single  0.890  0.020  1.040
 58Y  O3  H14  single  0.850  0.020  0.980
 58Y  O4  H15  single  0.850  0.020  0.980
 58Y  O6  H16  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
 58Y  H1   C1  O5   106.17  3.000
 58Y  H1   C1  S1   108.11  3.000
 58Y  O5   C1  S1   112.66  3.000
 58Y  H1   C1  C2   110.05  3.000
 58Y  O5   C1  C2   116.20  3.000
 58Y  S1   C1  C2   103.48  3.000
 58Y  H2   C2  N2   108.35  3.000
 58Y  H2   C2  C3   108.08  3.000
 58Y  N2   C2  C3   115.99  3.000
 58Y  H2   C2  C1   108.36  3.000
 58Y  C3   C2  C1   111.27  3.000
 58Y  N2   C2  C1   104.53  3.000
 58Y  H3   C3  O3   110.71  3.000
 58Y  H3   C3  C4   105.78  3.000
 58Y  O3   C3  C4   113.64  3.000
 58Y  H3   C3  C2   108.94  3.000
 58Y  O3   C3  C2   107.11  3.000
 58Y  C4   C3  C2   110.62  3.000
 58Y  H4   C4  O4   111.31  3.000
 58Y  H4   C4  C5   107.92  3.000
 58Y  O4   C4  C5   112.80  3.000
 58Y  H4   C4  C3   108.52  3.000
 58Y  O4   C4  C3   108.89  3.000
 58Y  C5   C4  C3   107.23  3.000
 58Y  H5   C5  O5   110.07  3.000
 58Y  H5   C5  C6   108.17  3.000
 58Y  O5   C5  C6   107.80  3.000
 58Y  H5   C5  C4   107.74  3.000
 58Y  C6   C5  C4   112.66  3.000
 58Y  O5   C5  C4   110.38  3.000
 58Y  H7   C6  H6   107.14  3.000
 58Y  H7   C6  O6   111.50  3.000
 58Y  H6   C6  O6   111.76  3.000
 58Y  H7   C6  C5   109.85  3.000
 58Y  H6   C6  C5   107.46  3.000
 58Y  O6   C6  C5   109.03  3.000
 58Y  H8   C7  S1   107.16  3.000
 58Y  H8   C7  N2   108.56  3.000
 58Y  S1   C7  N2   105.28  3.000
 58Y  H8   C7  C8   107.91  3.000
 58Y  N2   C7  C8   115.93  3.000
 58Y  S1   C7  C8   111.65  3.000
 58Y  H11  C8  H10  108.38  3.000
 58Y  H11  C8  H9   108.20  3.000
 58Y  H10  C8  H9   107.27  3.000
 58Y  H11  C8  C7   112.36  3.000
 58Y  H10  C8  C7   109.75  3.000
 58Y  H9   C8  C7   110.73  3.000
 58Y  H12  N2  C7   111.10  3.000
 58Y  H12  N2  C2   111.84  3.000
 58Y  C7   N2  C2   114.28  3.000
 58Y  C7   S1  C1    92.82  3.000
 58Y  H14  O3  C3   108.52  3.000
 58Y  H15  O4  C4   109.23  3.000
 58Y  C5   O5  C1   116.69  3.000
 58Y  H16  O6  C6   108.00  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
 58Y  chir_01  C1  S1  C2  O5  positiv
 58Y  chir_02  C2  N2  C3  C1  positiv
 58Y  chir_03  C3  O3  C2  C4  positiv
 58Y  chir_04  C4  O4  C5  C3  negativ
 58Y  chir_05  C5  O5  C4  C6  negativ
 58Y  chir_06  C7  S1  N2  C8  negativ

