# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 19:14:39 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 2,6-diammonio-2,3,6-trideoxy-alpha-D-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]C[C@H]1O[C@H](O)[C@H]([NH3+])C[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
 TOC  TOC  2,6-diammonio-2,3,6-trideoxy-alpha-D-ribo-hexopyranose  D-saccharide  27  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_TOC
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
 TOC  C1    C  CH1   0   0.268  -10.8187  -4.7655  -6.8319
 TOC  C2    C  CH1   0  -0.173   -9.5564  -5.6030  -7.0461
 TOC  C3    C  CH2   0  -0.498   -9.8880  -6.9846  -7.5871
 TOC  C4    C  CH1   0   0.047  -10.8991  -7.6485  -6.6587
 TOC  C5    C  CH1   0   0.027  -12.1139  -6.7393  -6.4899
 TOC  C6    C  CH2   0  -0.357  -13.1011  -7.2467  -5.4472
 TOC  N2    N  NT3   1  -0.788   -8.6345  -4.8902  -7.9708
 TOC  N6    N  NT3   1  -0.787  -13.8493  -8.4292  -5.9437
 TOC  O1    O  OH1   0  -0.656  -11.3433  -4.4777  -8.0802
 TOC  O4    O  OH1   0  -0.670  -11.3607  -8.8761  -7.1731
 TOC  O5    O  O2    0  -0.492  -11.6997  -5.4757  -6.0080
 TOC  H1    H  HCH1  0   0.274  -10.5797  -3.8572  -6.2685
 TOC  H2    H  HCH1  0   0.330   -9.0276  -5.6835  -6.0955
 TOC  H3    H  HCH2  0   0.287   -8.9792  -7.5890  -7.6427
 TOC  H32   H  HCH2  0   0.269  -10.3055  -6.9153  -8.5953
 TOC  H4    H  HCH1  0   0.242  -10.4392  -7.7851  -5.6699
 TOC  H5    H  HCH1  0   0.258  -12.6296  -6.6422  -7.4563
 TOC  H61   H  HCH2  0   0.317  -13.8335  -6.4772  -5.2122
 TOC  H62   H  HCH2  0   0.303  -12.5953  -7.5451  -4.5301
 TOC  HN21  H  HNT3  0   0.480   -7.7839  -5.4306  -8.1403
 TOC  HN22  H  HNT3  0   0.470   -9.0690  -4.7098  -8.8787
 TOC  HN23  H  HNT3  0   0.478   -8.3364  -3.9883  -7.5940
 TOC  HN61  H  HNT3  0   0.479  -14.4360  -8.8287  -5.2109
 TOC  HN62  H  HNT3  0   0.470  -14.4649  -8.1941  -6.7234
 TOC  HN63  H  HNT3  0   0.470  -13.2052  -9.1543  -6.2747
 TOC  HO1   H  HOH1  0   0.478  -11.9560  -3.7360  -8.0167
 TOC  HO4   H  HOH1  0   0.472  -10.6810  -9.5481  -7.0524

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
 TOC  C1  C2    single  1.530  0.020  1.530
 TOC  C1  O1    single  1.384  0.020  1.384
 TOC  C1  O5    single  1.400  0.020  1.400
 TOC  C1  H1    single  0.970  0.020  1.090
 TOC  C2  C3    single  1.520  0.020  1.520
 TOC  C2  N2    single  1.488  0.020  1.488
 TOC  C2  H2    single  0.970  0.020  1.090
 TOC  C3  C4    single  1.525  0.020  1.525
 TOC  C3  H3    single  0.970  0.020  1.090
 TOC  C3  H32   single  0.970  0.020  1.090
 TOC  C4  C5    single  1.527  0.020  1.527
 TOC  C4  O4    single  1.409  0.020  1.409
 TOC  C4  H4    single  0.970  0.020  1.090
 TOC  C5  C6    single  1.523  0.020  1.523
 TOC  C5  O5    single  1.414  0.020  1.414
 TOC  C5  H5    single  0.970  0.020  1.090
 TOC  C6  N6    single  1.485  0.020  1.485
 TOC  C6  H61   single  0.970  0.020  1.090
 TOC  C6  H62   single  0.970  0.020  1.090
 TOC  N2  HN21  single  0.890  0.020  1.040
 TOC  N2  HN22  single  0.890  0.020  1.040
 TOC  N2  HN23  single  0.890  0.020  1.040
 TOC  N6  HN61  single  0.890  0.020  1.040
 TOC  N6  HN62  single  0.890  0.020  1.040
 TOC  N6  HN63  single  0.890  0.020  1.040
 TOC  O1  HO1   single  0.850  0.020  0.980
 TOC  O4  HO4   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
 TOC  H1    C1  O5    104.80  3.000
 TOC  H1    C1  O1    111.97  3.000
 TOC  O5    C1  O1    113.43  3.000
 TOC  H1    C1  C2    110.24  3.000
 TOC  O5    C1  C2    108.90  3.000
 TOC  O1    C1  C2    107.47  3.000
 TOC  H2    C2  N2    106.06  3.000
 TOC  H2    C2  C3    110.41  3.000
 TOC  N2    C2  C3    110.45  3.000
 TOC  H2    C2  C1    108.56  3.000
 TOC  N2    C2  C1    109.64  3.000
 TOC  C3    C2  C1    111.55  3.000
 TOC  H32   C3  H3    107.79  3.000
 TOC  H32   C3  C4    109.63  3.000
 TOC  H3    C3  C4    109.98  3.000
 TOC  H32   C3  C2    110.71  3.000
 TOC  H3    C3  C2    109.83  3.000
 TOC  C4    C3  C2    108.88  3.000
 TOC  H4    C4  O4    110.93  3.000
 TOC  H4    C4  C5    107.91  3.000
 TOC  O4    C4  C5    107.37  3.000
 TOC  H4    C4  C3    108.93  3.000
 TOC  O4    C4  C3    111.98  3.000
 TOC  C5    C4  C3    109.61  3.000
 TOC  H5    C5  O5    110.97  3.000
 TOC  H5    C5  C6    109.10  3.000
 TOC  O5    C5  C6    104.73  3.000
 TOC  H5    C5  C4    109.18  3.000
 TOC  O5    C5  C4    109.67  3.000
 TOC  C6    C5  C4    113.14  3.000
 TOC  H62   C6  H61   108.94  3.000
 TOC  H62   C6  N6    107.31  3.000
 TOC  H61   C6  N6    107.23  3.000
 TOC  H62   C6  C5    111.52  3.000
 TOC  H61   C6  C5    110.39  3.000
 TOC  N6    C6  C5    111.29  3.000
 TOC  HN23  N2  HN22  107.19  3.000
 TOC  HN23  N2  HN21  106.57  3.000
 TOC  HN22  N2  HN21  107.44  3.000
 TOC  HN23  N2  C2    112.00  3.000
 TOC  HN22  N2  C2    111.91  3.000
 TOC  HN21  N2  C2    111.44  3.000
 TOC  HN63  N6  HN62  107.17  3.000
 TOC  HN63  N6  HN61  108.44  3.000
 TOC  HN62  N6  HN61  106.97  3.000
 TOC  HN63  N6  C6    110.78  3.000
 TOC  HN62  N6  C6    112.08  3.000
 TOC  HN61  N6  C6    111.19  3.000
 TOC  HO1   O1  C1    109.96  3.000
 TOC  HO4   O4  C4    109.33  3.000
 TOC  C5    O5  C1    115.92  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
 TOC  Var_01  HN61  N6  C6  C5  173.89  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
 TOC  chir_01  C1  C2  O1  O5  negativ
 TOC  chir_02  C2  N2  C1  C3  negativ
 TOC  chir_03  C4  O4  C3  C5  negativ
 TOC  chir_04  C5  O5  C4  C6  negativ

