# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:03:41 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 2-amino-2,3-dideoxy-alpha-D-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C[C@H](O)[C@@H](CO)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
 GCN  GCN  2-amino-2,3-dideoxy-alpha-D-ribo-hexopyranose  D-saccharide  24  11  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GCN
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
 GCN  C1    C  CH1   0   0.260  54.9125  73.7213  59.6566
 GCN  C2    C  CH1   0  -0.111  53.9802  74.7952  59.0999
 GCN  C3    C  CH2   0  -0.483  52.8354  74.1336  58.3456
 GCN  C4    C  CH1   0   0.053  53.3750  73.2169  57.2598
 GCN  C5    C  CH1   0  -0.007  54.3779  72.2249  57.8633
 GCN  C6    C  CH2   0  -0.183  55.1520  71.4466  56.8086
 GCN  N2    N  NH2   0  -0.800  53.4717  75.6467  60.1614
 GCN  O1    O  OH1   0  -0.658  54.2511  72.9991  60.6417
 GCN  O4    O  OH1   0  -0.681  52.2894  72.5628  56.6473
 GCN  O5    O  O2    0  -0.509  55.3743  72.9033  58.6098
 GCN  O6    O  OH1   0  -0.672  54.2367  70.6884  56.0410
 GCN  H1    H  HCH1  0   0.226  55.8235  74.1881  60.0537
 GCN  H2    H  HCH1  0   0.213  54.5861  75.3528  58.3687
 GCN  H3    H  HCH2  0   0.228  52.2128  73.5619  59.0397
 GCN  H32   H  HCH2  0   0.243  52.1973  74.9008  57.8967
 GCN  H4    H  HCH1  0   0.186  53.9233  73.8353  56.5283
 GCN  H5    H  HCH1  0   0.215  53.8264  71.5191  58.5014
 GCN  H61   H  HCH2  0   0.209  55.7070  72.1559  56.1822
 GCN  H62   H  HCH2  0   0.218  55.8853  70.7978  57.3026
 GCN  HN21  H  HNH2  0   0.345  52.9045  76.3766  59.7473
 GCN  HN22  H  HNH2  0   0.342  54.2430  76.1278  60.6097
 GCN  HO1   H  HOH1  0   0.456  54.8863  72.4369  61.0980
 GCN  HO4   H  HOH1  0   0.443  52.6581  71.8713  56.0810
 GCN  HO6   H  HOH1  0   0.467  54.6841  70.3661  55.2531

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
 GCN  C1  C2    single  1.527  0.020  1.527
 GCN  C1  O1    single  1.389  0.020  1.389
 GCN  C1  O5    single  1.406  0.020  1.406
 GCN  C1  H1    single  0.970  0.020  1.090
 GCN  C2  C3    single  1.522  0.020  1.522
 GCN  C2  N2    single  1.453  0.020  1.453
 GCN  C2  H2    single  0.970  0.020  1.090
 GCN  C3  C4    single  1.520  0.020  1.520
 GCN  C3  H3    single  0.970  0.020  1.090
 GCN  C3  H32   single  0.970  0.020  1.090
 GCN  C4  C5    single  1.534  0.020  1.534
 GCN  C4  O4    single  1.408  0.020  1.408
 GCN  C4  H4    single  0.970  0.020  1.090
 GCN  C5  C6    single  1.522  0.020  1.522
 GCN  C5  O5    single  1.418  0.020  1.418
 GCN  C5  H5    single  0.970  0.020  1.090
 GCN  C6  O6    single  1.415  0.020  1.415
 GCN  C6  H61   single  0.970  0.020  1.090
 GCN  C6  H62   single  0.970  0.020  1.090
 GCN  N2  HN21  single  0.890  0.020  1.040
 GCN  N2  HN22  single  0.890  0.020  1.040
 GCN  O1  HO1   single  0.850  0.020  0.980
 GCN  O4  HO4   single  0.850  0.020  0.980
 GCN  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
 GCN  H1    C1  O5    104.13  3.000
 GCN  H1    C1  O1    111.08  3.000
 GCN  O5    C1  O1    112.44  3.000
 GCN  H1    C1  C2    109.84  3.000
 GCN  O5    C1  C2    109.76  3.000
 GCN  O1    C1  C2    109.48  3.000
 GCN  H2    C2  N2    112.39  3.000
 GCN  H2    C2  C3    107.75  3.000
 GCN  N2    C2  C3    110.71  3.000
 GCN  H2    C2  C1    105.20  3.000
 GCN  N2    C2  C1    111.07  3.000
 GCN  C3    C2  C1    109.52  3.000
 GCN  H32   C3  H3    107.15  3.000
 GCN  H32   C3  C4    109.68  3.000
 GCN  H3    C3  C4    109.89  3.000
 GCN  H32   C3  C2    109.70  3.000
 GCN  H3    C3  C2    109.93  3.000
 GCN  C4    C3  C2    110.43  3.000
 GCN  H4    C4  O4    110.80  3.000
 GCN  H4    C4  C5    107.35  3.000
 GCN  O4    C4  C5    112.01  3.000
 GCN  H4    C4  C3    108.18  3.000
 GCN  O4    C4  C3    108.50  3.000
 GCN  C5    C4  C3    109.94  3.000
 GCN  H5    C5  O5    110.73  3.000
 GCN  H5    C5  C6    109.20  3.000
 GCN  O5    C5  C6    104.60  3.000
 GCN  H5    C5  C4    108.39  3.000
 GCN  O5    C5  C4    110.92  3.000
 GCN  C6    C5  C4    112.98  3.000
 GCN  H62   C6  H61   107.55  3.000
 GCN  H62   C6  O6    111.09  3.000
 GCN  H61   C6  O6    111.35  3.000
 GCN  H62   C6  C5    109.29  3.000
 GCN  H61   C6  C5    108.80  3.000
 GCN  O6    C6  C5    108.72  3.000
 GCN  HN22  N2  HN21  105.36  3.000
 GCN  HN22  N2  C2    109.58  3.000
 GCN  HN21  N2  C2    108.65  3.000
 GCN  HO1   O1  C1    109.00  3.000
 GCN  HO4   O4  C4    107.04  3.000
 GCN  C5    O5  C1    116.07  3.000
 GCN  HO6   O6  C6    108.85  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
 GCN  chir_01  C1  C2  O1  O5  negativ
 GCN  chir_02  C2  N2  C3  C1  positiv
 GCN  chir_03  C4  O4  C5  C3  positiv
 GCN  chir_04  C5  O5  C4  C6  negativ

