# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 05:10:54 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)C[C@@H](N)[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
 RST  RST  3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose  L-saccharide  23  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RST
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
 RST  C1    C  CH1   0   0.265  20.7806  22.1952  16.5822
 RST  O1    O  OH1   0  -0.660  21.1433  20.9294  17.0437
 RST  C2    C  CH2   0  -0.491  20.0254  22.9436  17.6706
 RST  C3    C  CH1   0  -0.138  20.9111  23.5351  18.7644
 RST  N3    N  NH2   0  -0.789  21.4351  22.5022  19.6451
 RST  C4    C  CH1   0   0.063  22.0552  24.2939  18.0971
 RST  O4    O  OH1   0  -0.672  22.9041  24.7851  19.1091
 RST  C5    C  CH1   0   0.029  22.7959  23.3877  17.1095
 RST  O5    O  O2    0  -0.507  21.8813  22.9321  16.1183
 RST  C6    C  CH3   0  -0.702  23.9150  24.1037  16.3788
 RST  H1    H  HCH1  0   0.211  20.1332  22.1066  15.7008
 RST  HO1   H  HOH1  0   0.448  21.4855  20.4209  16.3004
 RST  H2    H  HCH2  0   0.242  19.4913  23.7665  17.1890
 RST  H22   H  HCH2  0   0.247  19.2577  22.2965  18.1026
 RST  H3    H  HCH1  0   0.219  20.2996  24.2717  19.3078
 RST  HN31  H  HNH2  0   0.341  21.8475  22.9324  20.4624
 RST  HN32  H  HNH2  0   0.342  20.6709  21.9332  19.9863
 RST  H4    H  HCH1  0   0.200  21.6133  25.1221  17.5206
 RST  HO4   H  HOH1  0   0.452  23.4906  25.4466  18.7313
 RST  H5    H  HCH1  0   0.206  23.2137  22.5381  17.6623
 RST  H61   H  HCH3  0   0.241  24.3779  23.4470  15.6417
 RST  H62   H  HCH3  0   0.224  23.5514  24.9941  15.8613
 RST  H63   H  HCH3  0   0.229  24.7007  24.4084  17.0700

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
 RST  C1  O1    single  1.395  0.020  1.395
 RST  C1  C2    single  1.522  0.020  1.522
 RST  C1  O5    single  1.403  0.020  1.403
 RST  C1  H1    single  0.970  0.020  1.090
 RST  O1  HO1   single  0.850  0.020  0.980
 RST  C2  C3    single  1.527  0.020  1.527
 RST  C2  H2    single  0.970  0.020  1.090
 RST  C2  H22   single  0.970  0.020  1.090
 RST  C3  N3    single  1.455  0.020  1.455
 RST  C3  C4    single  1.526  0.020  1.526
 RST  C3  H3    single  0.970  0.020  1.090
 RST  N3  HN31  single  0.890  0.020  1.040
 RST  N3  HN32  single  0.890  0.020  1.040
 RST  C4  O4    single  1.409  0.020  1.409
 RST  C4  C5    single  1.531  0.020  1.531
 RST  C4  H4    single  0.970  0.020  1.090
 RST  O4  HO4   single  0.850  0.020  0.980
 RST  C5  O5    single  1.424  0.020  1.424
 RST  C5  C6    single  1.516  0.020  1.516
 RST  C5  H5    single  0.970  0.020  1.090
 RST  C6  H61   single  0.970  0.020  1.090
 RST  C6  H62   single  0.970  0.020  1.090
 RST  C6  H63   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
 RST  H1    C1  O5    103.86  3.000
 RST  H1    C1  C2    108.75  3.000
 RST  O5    C1  C2    111.56  3.000
 RST  H1    C1  O1    110.23  3.000
 RST  O5    C1  O1    112.45  3.000
 RST  C2    C1  O1    109.80  3.000
 RST  HO1   O1  C1    108.42  3.000
 RST  H22   C2  H2    106.07  3.000
 RST  H22   C2  C3    110.72  3.000
 RST  H2    C2  C3    107.91  3.000
 RST  H22   C2  C1    109.89  3.000
 RST  H2    C2  C1    107.32  3.000
 RST  C3    C2  C1    114.52  3.000
 RST  H3    C3  C4    107.43  3.000
 RST  H3    C3  N3    112.10  3.000
 RST  C4    C3  N3    110.34  3.000
 RST  H3    C3  C2    106.89  3.000
 RST  C4    C3  C2    108.32  3.000
 RST  N3    C3  C2    111.57  3.000
 RST  HN32  N3  HN31  105.94  3.000
 RST  HN32  N3  C3    109.34  3.000
 RST  HN31  N3  C3    109.51  3.000
 RST  H4    C4  C5    107.54  3.000
 RST  H4    C4  O4    110.82  3.000
 RST  C5    C4  O4    112.21  3.000
 RST  H4    C4  C3    107.57  3.000
 RST  C5    C4  C3    110.50  3.000
 RST  O4    C4  C3    108.11  3.000
 RST  HO4   O4  C4    108.97  3.000
 RST  H5    C5  C6    109.12  3.000
 RST  H5    C5  O5    110.36  3.000
 RST  C6    C5  O5    106.85  3.000
 RST  H5    C5  C4    108.53  3.000
 RST  C6    C5  C4    112.85  3.000
 RST  O5    C5  C4    109.13  3.000
 RST  C5    O5  C1    116.21  3.000
 RST  H63   C6  H62   108.21  3.000
 RST  H63   C6  H61   106.92  3.000
 RST  H62   C6  H61   108.19  3.000
 RST  H63   C6  C5    111.01  3.000
 RST  H62   C6  C5    111.56  3.000
 RST  H61   C6  C5    110.78  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
 RST  chir_01  C1  O1  C2  O5  negativ
 RST  chir_02  C3  N3  C2  C4  positiv
 RST  chir_03  C4  O4  C5  C3  negativ
 RST  chir_04  C5  O5  C4  C6  positiv

