# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:57:52 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=N[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
 GNL  GNL  (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol  ligand  27  14  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GNL
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
 GNL  C1   C  CR15  0  -0.089   0.3452  -0.6041  -0.9229
 GNL  S1   S  S2    0  -0.019   1.4270  -1.5944   0.2226
 GNL  C2   C  CR15  0  -0.188   0.8028   0.8434  -0.6524
 GNL  N2   N  N     0  -0.341   2.2160   0.8305  -0.3417
 GNL  C3   C  CH1   0   0.075   0.0386   1.4645   0.5196
 GNL  O3   O  OH1   0  -0.663   0.3387   2.8329   0.5452
 GNL  C4   C  CH1   0  -0.043  -1.4542   1.1780   0.4067
 GNL  O4   O  OH1   0  -0.668  -1.9521   1.8199  -0.7395
 GNL  C5   C  CH1   0  -0.008  -1.6344  -0.3392   0.3558
 GNL  O5   O  O2    0  -0.455  -0.9971  -0.8647  -0.7958
 GNL  C6   C  CH2   0  -0.166  -3.0866  -0.7562   0.3090
 GNL  O6   O  OH1   0  -0.667  -3.1628  -2.1565   0.4161
 GNL  C7   C  CR5   0   0.097   2.6006  -0.2716   0.1486
 GNL  C8   C  CH3   0  -0.715   3.9841  -0.5093   0.6592
 GNL  H1   H  HCR5  0   0.308   0.6246  -0.9018  -1.9348
 GNL  H2   H  HCR5  0   0.276   0.6255   1.4405  -1.5507
 GNL  H3   H  HCH1  0   0.220   0.3772   0.9675   1.4407
 GNL  HO3  H  HOH1  0   0.453  -0.0219   3.2084   1.3551
 GNL  H4   H  HCH1  0   0.243  -1.9451   1.5458   1.3200
 GNL  HO4  H  HOH1  0   0.458  -2.9107   1.8670  -0.6828
 GNL  H5   H  HCH1  0   0.230  -1.1814  -0.7630   1.2658
 GNL  H6   H  HCH2  0   0.208  -3.6022  -0.2550   1.1388
 GNL  H6A  H  HCH2  0   0.203  -3.5463  -0.3994  -0.6218
 GNL  HO6  H  HOH1  0   0.458  -4.0879  -2.4100   0.3514
 GNL  H8   H  HCH3  0   0.253   4.1151  -1.5192   1.0403
 GNL  H8A  H  HCH3  0   0.271   4.7061  -0.3496  -0.1414
 GNL  H8B  H  HCH3  0   0.269   4.2136   0.1952   1.4577

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
 GNL  C1  S1   single  1.861  0.020  1.861
 GNL  C1  C2   single  1.542  0.020  1.542
 GNL  C1  O5   single  1.373  0.020  1.373
 GNL  S1  C7   single  1.770  0.020  1.770
 GNL  C2  N2   single  1.447  0.020  1.447
 GNL  C2  C3   single  1.531  0.020  1.531
 GNL  N2  C7   double  1.266  0.020  1.266
 GNL  C3  O3   single  1.401  0.020  1.401
 GNL  C3  C4   single  1.524  0.020  1.524
 GNL  C4  O4   single  1.405  0.020  1.405
 GNL  C4  C5   single  1.529  0.020  1.529
 GNL  C5  O5   single  1.417  0.020  1.417
 GNL  C5  C6   single  1.512  0.020  1.512
 GNL  C6  O6   single  1.406  0.020  1.406
 GNL  C7  C8   single  1.494  0.020  1.494
 GNL  C1  H1   single  0.970  0.020  1.090
 GNL  C2  H2   single  0.970  0.020  1.090
 GNL  C3  H3   single  0.970  0.020  1.090
 GNL  O3  HO3  single  0.850  0.020  0.980
 GNL  C4  H4   single  0.970  0.020  1.090
 GNL  O4  HO4  single  0.850  0.020  0.980
 GNL  C5  H5   single  0.970  0.020  1.090
 GNL  C6  H6   single  0.970  0.020  1.090
 GNL  C6  H6A  single  0.970  0.020  1.090
 GNL  O6  HO6  single  0.850  0.020  0.980
 GNL  C8  H8   single  0.970  0.020  1.090
 GNL  C8  H8A  single  0.970  0.020  1.090
 GNL  C8  H8B  single  0.970  0.020  1.090

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
 GNL  H1   C1  O5   106.52  3.000
 GNL  H1   C1  C2   110.05  3.000
 GNL  O5   C1  C2   116.87  3.000
 GNL  H1   C1  S1   106.07  3.000
 GNL  O5   C1  S1   114.22  3.000
 GNL  C2   C1  S1   102.65  3.000
 GNL  C7   S1  C1    87.82  3.000
 GNL  H2   C2  C3   109.05  3.000
 GNL  H2   C2  N2   109.86  3.000
 GNL  C3   C2  N2   109.07  3.000
 GNL  H2   C2  C1   108.69  3.000
 GNL  C3   C2  C1   111.53  3.000
 GNL  N2   C2  C1   108.61  3.000
 GNL  C7   N2  C2   112.81  3.000
 GNL  H3   C3  C4   106.17  3.000
 GNL  H3   C3  O3   111.10  3.000
 GNL  C4   C3  O3   113.25  3.000
 GNL  H3   C3  C2   107.70  3.000
 GNL  C4   C3  C2   110.85  3.000
 GNL  O3   C3  C2   107.66  3.000
 GNL  HO3  O3  C3   108.43  3.000
 GNL  H4   C4  C5   107.87  3.000
 GNL  H4   C4  O4   111.49  3.000
 GNL  C5   C4  O4   112.61  3.000
 GNL  H4   C4  C3   108.22  3.000
 GNL  C5   C4  C3   107.73  3.000
 GNL  O4   C4  C3   108.76  3.000
 GNL  HO4  O4  C4   109.13  3.000
 GNL  H5   C5  C6   108.34  3.000
 GNL  H5   C5  O5   110.11  3.000
 GNL  C6   C5  O5   107.73  3.000
 GNL  H5   C5  C4   107.81  3.000
 GNL  C6   C5  C4   112.84  3.000
 GNL  O5   C5  C4   110.00  3.000
 GNL  C5   O5  C1   116.39  3.000
 GNL  H6A  C6  H6   107.20  3.000
 GNL  H6A  C6  O6   111.44  3.000
 GNL  H6   C6  O6   111.81  3.000
 GNL  H6A  C6  C5   109.81  3.000
 GNL  H6   C6  C5   107.56  3.000
 GNL  O6   C6  C5   108.93  3.000
 GNL  HO6  O6  C6   108.03  3.000
 GNL  C8   C7  N2   123.53  3.000
 GNL  C8   C7  S1   118.74  3.000
 GNL  N2   C7  S1   117.73  3.000
 GNL  H8B  C8  H8A  107.71  3.000
 GNL  H8B  C8  H8   108.56  3.000
 GNL  H8A  C8  H8   108.29  3.000
 GNL  H8B  C8  C7   110.05  3.000
 GNL  H8A  C8  C7   109.82  3.000
 GNL  H8   C8  C7   112.29  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
 GNL  Var_01  N2  C7  S1  C1  13.37  30.0  1
 GNL  Var_02  H8  C8  C7  S1  -0.22  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
 GNL  chir_01  C1  S1  C2  O5  positiv
 GNL  chir_02  C2  N2  C3  C1  positiv
 GNL  chir_03  C3  O3  C2  C4  positiv
 GNL  chir_04  C4  O4  C5  C3  negativ
 GNL  chir_05  C5  O5  C6  C4  positiv

