# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:40:22 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3aR,5R,6S,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
 NGT  NGT  (3aR,5R,6S,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  .  2022-07-22  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_NGT
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
 NGT  C1    C  CH1   0  -0.088   0.6850   0.9623   0.4733
 NGT  C2    C  CH1   0  -0.193  -0.8005   0.8019   0.8400
 NGT  C3    C  CH1   0   0.064  -1.4997  -0.2380  -0.0368
 NGT  C4    C  CH1   0  -0.007  -1.1034  -0.0785  -1.4991
 NGT  C5    C  CH1   0  -0.021   0.4213  -0.1528  -1.6084
 NGT  C6    C  CH2   0  -0.161   0.9136  -0.0145  -3.0314
 NGT  C7    C  C     0   0.113   0.1360  -0.2185   2.6251
 NGT  C8    C  CH3   0  -0.723   0.2750  -0.8371   3.9702
 NGT  N2    N  N     0  -0.337  -0.8959   0.3973   2.2263
 NGT  S1    S  S2    0  -0.021   1.5073  -0.3453   1.5077
 NGT  O3    O  OH1   0  -0.665  -2.8819  -0.0936   0.1557
 NGT  O4    O  OH1   0  -0.671  -1.7279  -1.1239  -2.2098
 NGT  O5    O  O2    0  -0.457   0.9900   0.9142  -0.8648
 NGT  O6    O  OH1   0  -0.668   2.3134  -0.1568  -3.0437
 NGT  HC1   H  HCH1  0   0.311   1.0593   1.9196   0.8394
 NGT  HC2   H  HCH1  0   0.277  -1.2975   1.7658   0.6945
 NGT  HC3   H  HCH1  0   0.212  -1.1617  -1.2379   0.2810
 NGT  HC4   H  HCH1  0   0.231  -1.4377   0.9043  -1.8618
 NGT  HC5   H  HCH1  0   0.231   0.7613  -1.1180  -1.2010
 NGT  HC61  H  HCH2  0   0.210   0.4269  -0.7854  -3.6388
 NGT  HC62  H  HCH2  0   0.201   0.5976   0.9602  -3.4293
 NGT  HC81  H  HCH3  0   0.264   0.5108  -1.8980   3.8782
 NGT  HC82  H  HCH3  0   0.265   1.0907  -0.3710   4.5237
 NGT  HC83  H  HCH3  0   0.262  -0.6482  -0.7277   4.5348
 NGT  HO3   H  HOH1  0   0.451  -3.3238  -0.7777  -0.3586
 NGT  HO4   H  HOH1  0   0.465  -1.9495  -0.8183  -3.0939
 NGT  HO6   H  HOH1  0   0.457   2.6033  -0.1482  -3.9602

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
 NGT  C1  C2    single  1.538  0.020  1.538
 NGT  C1  S1    single  1.859  0.020  1.859
 NGT  C1  O5    single  1.373  0.020  1.373
 NGT  C1  HC1   single  0.970  0.020  1.090
 NGT  C2  C3    single  1.529  0.020  1.529
 NGT  C2  N2    single  1.447  0.020  1.447
 NGT  C2  HC2   single  0.970  0.020  1.090
 NGT  C3  C4    single  1.523  0.020  1.523
 NGT  C3  O3    single  1.403  0.020  1.403
 NGT  C3  HC3   single  0.970  0.020  1.090
 NGT  C4  C5    single  1.530  0.020  1.530
 NGT  C4  O4    single  1.410  0.020  1.410
 NGT  C4  HC4   single  0.970  0.020  1.090
 NGT  C5  C6    single  1.512  0.020  1.512
 NGT  C5  O5    single  1.419  0.020  1.419
 NGT  C5  HC5   single  0.970  0.020  1.090
 NGT  C6  O6    single  1.407  0.020  1.407
 NGT  C6  HC61  single  0.970  0.020  1.090
 NGT  C6  HC62  single  0.970  0.020  1.090
 NGT  C7  C8    single  1.487  0.020  1.487
 NGT  C7  N2    double  1.266  0.020  1.266
 NGT  C7  S1    single  1.773  0.020  1.773
 NGT  C8  HC81  single  0.970  0.020  1.090
 NGT  C8  HC82  single  0.970  0.020  1.090
 NGT  C8  HC83  single  0.970  0.020  1.090
 NGT  O3  HO3   single  0.850  0.020  0.980
 NGT  O4  HO4   single  0.850  0.020  0.980
 NGT  O6  HO6   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
 NGT  HC1   C1  O5    106.35  3.000
 NGT  HC1   C1  S1    106.18  3.000
 NGT  O5    C1  S1    114.79  3.000
 NGT  HC1   C1  C2    110.05  3.000
 NGT  O5    C1  C2    116.30  3.000
 NGT  S1    C1  C2    102.77  3.000
 NGT  HC2   C2  N2    110.10  3.000
 NGT  HC2   C2  C3    108.37  3.000
 NGT  N2    C2  C3    109.20  3.000
 NGT  HC2   C2  C1    108.36  3.000
 NGT  N2    C2  C1    108.73  3.000
 NGT  C3    C2  C1    112.06  3.000
 NGT  HC3   C3  O3    110.84  3.000
 NGT  HC3   C3  C4    106.98  3.000
 NGT  O3    C3  C4    112.16  3.000
 NGT  HC3   C3  C2    108.14  3.000
 NGT  O3    C3  C2    107.56  3.000
 NGT  C4    C3  C2    111.11  3.000
 NGT  HC4   C4  O4    111.21  3.000
 NGT  HC4   C4  C5    108.82  3.000
 NGT  O4    C4  C5    111.67  3.000
 NGT  HC4   C4  C3    109.34  3.000
 NGT  O4    C4  C3    106.92  3.000
 NGT  C5    C4  C3    108.82  3.000
 NGT  HC5   C5  O5    109.95  3.000
 NGT  HC5   C5  C6    109.13  3.000
 NGT  O5    C5  C6    107.09  3.000
 NGT  HC5   C5  C4    108.88  3.000
 NGT  O5    C5  C4    108.98  3.000
 NGT  C6    C5  C4    112.78  3.000
 NGT  HC62  C6  HC61  107.19  3.000
 NGT  HC62  C6  O6    111.87  3.000
 NGT  HC61  C6  O6    111.47  3.000
 NGT  HC62  C6  C5    109.16  3.000
 NGT  HC61  C6  C5    108.23  3.000
 NGT  O6    C6  C5    108.83  3.000
 NGT  S1    C7  N2    117.81  3.000
 NGT  S1    C7  C8    117.90  3.000
 NGT  N2    C7  C8    124.29  3.000
 NGT  HC83  C8  HC82  109.18  3.000
 NGT  HC83  C8  HC81  108.98  3.000
 NGT  HC82  C8  HC81  107.26  3.000
 NGT  HC83  C8  C7    110.39  3.000
 NGT  HC82  C8  C7    110.56  3.000
 NGT  HC81  C8  C7    110.40  3.000
 NGT  C7    N2  C2    112.58  3.000
 NGT  C7    S1  C1     87.61  3.000
 NGT  HO3   O3  C3    107.80  3.000
 NGT  HO4   O4  C4    109.27  3.000
 NGT  C5    O5  C1    116.60  3.000
 NGT  HO6   O6  C6    107.90  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
 NGT  Var_01  N2    C7  S1  C1   13.76  30.0  1
 NGT  Var_02  S1    C7  N2  C2    4.99  30.0  1
 NGT  Var_03  HC81  C8  C7  N2  123.40  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
 NGT  chir_01  C1  C2  S1  O5  negativ
 NGT  chir_02  C2  N2  C3  C1  positiv
 NGT  chir_03  C3  O3  C2  C4  positiv
 NGT  chir_04  C4  O4  C5  C3  positiv
 NGT  chir_05  C5  O5  C6  C4  positiv

