# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 17:42:05 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{R})-3-azanyl-6-(hydroxymethyl)oxane-2,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@@H](O)O[C@H](CO)[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
 95Z  95Z  (2~{S},3~{S},4~{R},5~{S},6~{R})-3-azanyl-6-(hydroxymethyl)oxane-2,4,5-triol  D-saccharide  25  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 PERFECT
;

data_comp_95Z
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
 95Z  C1   C  CH1   0   0.250   0.3962   1.6824  -0.0675
 95Z  O1   O  OH1   0  -0.667   0.3039   1.9890  -1.4227
 95Z  C2   C  CH1   0  -0.232   1.6080   0.7707   0.1495
 95Z  N2   N  NH2   0  -0.788   1.9817   0.6377   1.5460
 95Z  C3   C  CH1   0   0.081   1.3352  -0.6015  -0.4785
 95Z  O3   O  OH1   0  -0.672   2.3682  -1.5230  -0.2310
 95Z  C4   C  CH1   0   0.001   0.0306  -1.1835   0.0486
 95Z  O4   O  OH1   0  -0.670  -0.2211  -2.3798  -0.6526
 95Z  C5   C  CH1   0  -0.017  -1.1019  -0.1666  -0.1599
 95Z  O5   O  O2    0  -0.501  -0.7687   1.0775   0.4322
 95Z  C6   C  CH2   0  -0.159  -2.4012  -0.6303   0.4638
 95Z  O6   O  OH1   0  -0.669  -3.4191   0.2833   0.1329
 95Z  H1   H  HCH1  0   0.229   0.5149   2.5908   0.5363
 95Z  H2   H  HOH1  0   0.461  -0.3417   2.6936  -1.5446
 95Z  H3   H  HCH1  0   0.261   2.4606   1.2209  -0.3686
 95Z  H4   H  HNH2  0   0.355   2.2873   1.5343   1.9023
 95Z  H5   H  HNH2  0   0.342   1.1834   0.3710   2.1092
 95Z  H7   H  HCH1  0   0.209   1.2148  -0.4501  -1.5620
 95Z  H8   H  HOH1  0   0.449   3.1840  -1.0368  -0.0779
 95Z  H9   H  HCH1  0   0.214   0.1380  -1.3805   1.1259
 95Z  H10  H  HOH1  0   0.455  -0.7697  -2.9536  -0.1111
 95Z  H11  H  HCH1  0   0.219  -1.2591  -0.0504  -1.2413
 95Z  H12  H  HCH2  0   0.197  -2.6292  -1.6323   0.0815
 95Z  H13  H  HCH2  0   0.197  -2.2696  -0.7205   1.5511
 95Z  H14  H  HOH1  0   0.456  -4.2396  -0.0310   0.5230

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
 95Z  O6  C6   single  1.407  0.020  1.407
 95Z  O4  C4   single  1.409  0.020  1.409
 95Z  C6  C5   single  1.514  0.020  1.514
 95Z  C4  C5   single  1.536  0.020  1.536
 95Z  C4  C3   single  1.523  0.020  1.523
 95Z  C5  O5   single  1.417  0.020  1.417
 95Z  C3  O3   single  1.406  0.020  1.406
 95Z  C3  C2   single  1.533  0.020  1.533
 95Z  C2  N2   single  1.452  0.020  1.452
 95Z  C2  C1   single  1.532  0.020  1.532
 95Z  O5  C1   single  1.405  0.020  1.405
 95Z  C1  O1   single  1.392  0.020  1.392
 95Z  C1  H1   single  0.970  0.020  1.090
 95Z  O1  H2   single  0.850  0.020  0.980
 95Z  C2  H3   single  0.970  0.020  1.090
 95Z  N2  H4   single  0.890  0.020  1.040
 95Z  N2  H5   single  0.890  0.020  1.040
 95Z  C3  H7   single  0.970  0.020  1.090
 95Z  O3  H8   single  0.850  0.020  0.980
 95Z  C4  H9   single  0.970  0.020  1.090
 95Z  O4  H10  single  0.850  0.020  0.980
 95Z  C5  H11  single  0.970  0.020  1.090
 95Z  C6  H12  single  0.970  0.020  1.090
 95Z  C6  H13  single  0.970  0.020  1.090
 95Z  O6  H14  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
 95Z  H1   C1  O5   104.50  3.000
 95Z  H1   C1  C2   109.22  3.000
 95Z  O5   C1  C2   110.45  3.000
 95Z  H1   C1  O1   111.13  3.000
 95Z  O5   C1  O1   112.71  3.000
 95Z  C2   C1  O1   108.75  3.000
 95Z  H2   O1  C1   109.19  3.000
 95Z  H3   C2  C3   108.23  3.000
 95Z  H3   C2  N2   107.01  3.000
 95Z  C3   C2  N2   110.96  3.000
 95Z  H3   C2  C1   107.72  3.000
 95Z  N2   C2  C1   113.23  3.000
 95Z  C3   C2  C1   109.50  3.000
 95Z  H5   N2  H4   106.00  3.000
 95Z  H5   N2  C2   110.87  3.000
 95Z  H4   N2  C2   109.59  3.000
 95Z  H7   C3  C4   107.44  3.000
 95Z  H7   C3  O3   110.11  3.000
 95Z  C4   C3  O3   108.54  3.000
 95Z  H7   C3  C2   107.43  3.000
 95Z  O3   C3  C2   112.56  3.000
 95Z  C4   C3  C2   110.65  3.000
 95Z  H8   O3  C3   108.65  3.000
 95Z  H9   C4  C5   108.87  3.000
 95Z  H9   C4  O4   110.64  3.000
 95Z  C5   C4  O4   111.26  3.000
 95Z  H9   C4  C3   108.89  3.000
 95Z  C5   C4  C3   109.37  3.000
 95Z  O4   C4  C3   107.77  3.000
 95Z  H10  O4  C4   109.18  3.000
 95Z  H11  C5  C6   108.36  3.000
 95Z  H11  C5  O5   110.60  3.000
 95Z  C6   C5  O5   107.37  3.000
 95Z  H11  C5  C4   108.00  3.000
 95Z  O5   C5  C4   110.55  3.000
 95Z  C6   C5  C4   111.96  3.000
 95Z  C5   O5  C1   115.11  3.000
 95Z  H13  C6  H12  107.15  3.000
 95Z  H13  C6  O6   111.88  3.000
 95Z  H12  C6  O6   111.16  3.000
 95Z  H13  C6  C5   109.26  3.000
 95Z  H12  C6  C5   108.34  3.000
 95Z  O6   C6  C5   108.97  3.000
 95Z  H14  O6  C6   108.04  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
 95Z  chir_01  C1  C2  O5  O1  positiv
 95Z  chir_02  C2  N2  C3  C1  negativ
 95Z  chir_03  C3  O3  C2  C4  positiv
 95Z  chir_04  C4  O4  C5  C3  positiv
 95Z  chir_05  C5  O5  C4  C6  negativ

