# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 15:26:28 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2R,3R,4R,5S)-2-azido-5-(hydroxymethyl)tetrahydrofuran-3,4-diol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@@H](N=[N+]=[N-])[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
 AH8  AH8  '(2R,3R,4R,5S)-2-azido-5-(hydroxymethyl)tetrahydrofuran-3,4-diol (non-preferred name)'  L-saccharide  21  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AH8
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
 AH8  C1   C  CH1    0   0.110   0.9375   0.1950   0.5504
 AH8  N1   N  N      0  -0.401   1.9340   0.0918  -0.5268
 AH8  C2   C  CH1    0  -0.011   0.2144   1.5271   0.3827
 AH8  N2   N  N      1   0.378   2.4120  -1.0153  -0.6898
 AH8  O2   O  OH1    0  -0.666  -0.4312   1.8972   1.5717
 AH8  C3   C  CH1    0  -0.027  -0.8730   1.1621  -0.6365
 AH8  N3   N  N     -1  -0.214   2.8951  -2.0035  -0.9163
 AH8  O3   O  OH1    0  -0.661  -0.4552   1.3131  -1.9667
 AH8  C4   C  CH1    0   0.007  -1.1218  -0.3286  -0.3630
 AH8  O4   O  O2     0  -0.485  -0.0476  -0.7817   0.4659
 AH8  C5   C  CH2    0  -0.161  -2.4381  -0.5749   0.3400
 AH8  O5   O  OH1    0  -0.670  -2.5964  -1.9584   0.5389
 AH8  H1   H  HCH1   0   0.279   1.4427   0.0937   1.5170
 AH8  H2   H  HCH1   0   0.251   0.8840   2.3108   0.0097
 AH8  HO2  H  HOH1   0   0.460   0.2333   2.1119   2.2344
 AH8  H3   H  HCH1   0   0.246  -1.7729   1.7583  -0.4344
 AH8  HO3  H  HOH1   0   0.455  -0.3250   2.2512  -2.1387
 AH8  H4   H  HCH1   0   0.248  -1.1101  -0.8825  -1.3089
 AH8  H5   H  HCH2   0   0.202  -2.4525  -0.0174   1.2850
 AH8  H5A  H  HCH2   0   0.204  -3.2347  -0.1600  -0.2917
 AH8  HO5  H  HOH1   0   0.457  -3.4223  -2.0980   1.0105

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
 AH8  C1  N1   single  1.471  0.020  1.471
 AH8  C1  C2   single  1.525  0.020  1.525
 AH8  C1  O4   single  1.390  0.020  1.390
 AH8  N1  N2   double  1.217  0.020  1.217
 AH8  C2  O2   single  1.403  0.020  1.403
 AH8  C2  C3   single  1.534  0.020  1.534
 AH8  N2  N3   double  1.123  0.020  1.123
 AH8  C3  O3   single  1.402  0.020  1.402
 AH8  C3  C4   single  1.536  0.020  1.536
 AH8  C4  O4   single  1.431  0.020  1.431
 AH8  C4  C5   single  1.512  0.020  1.512
 AH8  C5  O5   single  1.407  0.020  1.407
 AH8  C1  H1   single  0.970  0.020  1.090
 AH8  C2  H2   single  0.970  0.020  1.090
 AH8  O2  HO2  single  0.850  0.020  0.980
 AH8  C3  H3   single  0.970  0.020  1.090
 AH8  O3  HO3  single  0.850  0.020  0.980
 AH8  C4  H4   single  0.970  0.020  1.090
 AH8  C5  H5   single  0.970  0.020  1.090
 AH8  C5  H5A  single  0.970  0.020  1.090
 AH8  O5  HO5  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
 AH8  H1   C1  O4  108.39  3.000
 AH8  H1   C1  C2  113.36  3.000
 AH8  O4   C1  C2  105.73  3.000
 AH8  H1   C1  N1  109.11  3.000
 AH8  O4   C1  N1  112.73  3.000
 AH8  C2   C1  N1  107.58  3.000
 AH8  N2   N1  C1  115.34  3.000
 AH8  H2   C2  C3  112.14  3.000
 AH8  H2   C2  O2  112.39  3.000
 AH8  C3   C2  O2  107.44  3.000
 AH8  H2   C2  C1  111.86  3.000
 AH8  C3   C2  C1  101.61  3.000
 AH8  O2   C2  C1  110.83  3.000
 AH8  N3   N2  N1  175.24  3.000
 AH8  HO2  O2  C2  108.94  3.000
 AH8  H3   C3  C4  111.18  3.000
 AH8  H3   C3  O3  111.12  3.000
 AH8  C4   C3  O3  108.77  3.000
 AH8  H3   C3  C2  109.22  3.000
 AH8  C4   C3  C2  103.14  3.000
 AH8  O3   C3  C2  113.16  3.000
 AH8  HO3  O3  C3  108.34  3.000
 AH8  H4   C4  C5  109.15  3.000
 AH8  H4   C4  O4  109.38  3.000
 AH8  C5   C4  O4  109.43  3.000
 AH8  H4   C4  C3  109.57  3.000
 AH8  C5   C4  C3  112.45  3.000
 AH8  O4   C4  C3  106.80  3.000
 AH8  C4   O4  C1  110.18  3.000
 AH8  H5A  C5  H5  107.09  3.000
 AH8  H5A  C5  O5  111.80  3.000
 AH8  H5   C5  O5  112.11  3.000
 AH8  H5A  C5  C4  107.61  3.000
 AH8  H5   C5  C4  109.21  3.000
 AH8  O5   C5  C4  108.90  3.000
 AH8  HO5  O5  C5  107.99  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
 AH8  chir_01  C1  N1  C2  O4  negativ
 AH8  chir_02  C2  O2  C3  C1  positiv
 AH8  chir_03  C3  O3  C4  C2  negativ
 AH8  chir_04  C4  O4  C3  C5  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 AH8  plan-1  C1  0.020
 AH8  plan-1  N1  0.020
 AH8  plan-1  C2  0.020
 AH8  plan-1  N2  0.020
 AH8  plan-1  N3  0.020
 AH8  plan-1  O4  0.020
 AH8  plan-1  H1  0.020

