# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 11:23:07 2019
#
#   Ligand name: 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H](O)[C@H](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
BDG        BDG '2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose' d-saccharide 26 12 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_BDG
#
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
BDG         C5     C   CH1    0    .      -0.4060   -0.5048   -0.9405
BDG         O5     O   O2     0    .       1.0718   -0.5048   -0.9405
BDG         C1     C   CH1    0    .       1.6294   -0.5048    0.4287
BDG         O1     O   OH1    0    .       1.3383   -1.7012    1.0257
BDG         C2     C   CH1    0    .       1.0569    0.6286    1.2842
BDG         N2     N   NH2    0    .       1.5396    0.4649    2.6853
BDG         C3     C   CH1    0    .      -0.4252    0.6303    1.2859
BDG         O3     O   OH1    0    .      -0.8950    1.8278    1.9845
BDG         C4     C   CH1    0    .      -0.9825    0.6288   -0.0873
BDG         O4     O   OH1    0    .      -2.4092    0.4712   -0.0090
BDG         C6     C   CH2    0    .      -0.8898   -0.3475   -2.3446
BDG         N6     N   NH2    0    .      -0.3998   -1.4502   -3.1515
BDG         H5     H   HCH1   0    .      -0.7558   -1.4515   -0.5468
BDG         H1     H   HCH1   0    .       2.7048   -0.3887    0.3684
BDG         HO1    H   HOH1   0    .       2.0518   -2.3024    0.8896
BDG         H2     H   HCH1   0    .       1.4086    1.5757    0.8930
BDG        HN21    H   HNH2   0    .       1.3257    1.2897    3.2104
BDG        HN22    H   HNH2   0    .       2.5297    0.3187    2.6822
BDG         H3     H   HCH1   0    .      -0.7771   -0.2507    1.8089
BDG         HO3    H   HOH1   0    .      -1.5103    1.5798    2.6545
BDG         H4     H   HCH1   0    .      -0.7527    1.5758   -0.5604
BDG         HO4    H   HOH1   0    .      -2.8251    1.3086   -0.1304
BDG         H61    H   HCH2   0    .      -0.5231    0.5876   -2.7504
BDG         H62    H   HCH2   0    .      -1.9730   -0.3457   -2.3554
BDG        HN61    H   HNH2   0    .       0.0325   -1.0913   -3.9797
BDG        HN62    H   HNH2   0    .      -1.1647   -2.0439   -3.4049
#
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
BDG   C5      O5    single        1.478 0.020     1.478
BDG   C5      C4    single        1.531 0.020     1.531
BDG   C5      C6    single        1.493 0.020     1.493
BDG   C5      H5    single        0.970 0.020     1.090
BDG   O5      C1    single        1.478 0.020     1.478
BDG   C1      O1    single        1.368 0.020     1.368
BDG   C1      C2    single        1.531 0.020     1.531
BDG   C1      H1    single        0.970 0.020     1.090
BDG   O1      HO1   single        0.850 0.020     0.980
BDG   C2      N2    single        1.491 0.020     1.491
BDG   C2      C3    single        1.482 0.020     1.482
BDG   C2      H2    single        0.970 0.020     1.090
BDG   N2     HN21   single        0.890 0.020     1.040
BDG   N2     HN22   single        0.890 0.020     1.040
BDG   C3      O3    single        1.464 0.020     1.464
BDG   C3      C4    single        1.482 0.020     1.482
BDG   C3      H3    single        0.970 0.020     1.090
BDG   O3      HO3   single        0.850 0.020     0.980
BDG   C4      O4    single        1.437 0.020     1.437
BDG   C4      H4    single        0.970 0.020     1.090
BDG   O4      HO4   single        0.850 0.020     0.980
BDG   C6      N6    single        1.452 0.020     1.452
BDG   C6      H61   single        0.970 0.020     1.090
BDG   C6      H62   single        0.970 0.020     1.090
BDG   N6     HN61   single        0.890 0.020     1.040
BDG   N6     HN62   single        0.890 0.020     1.040
#
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
BDG   H5      C5      C6          109.21 3.000
BDG   H5      C5      C4          108.84 3.000
BDG   C6      C5      C4          108.90 3.000
BDG   H5      C5      O5          108.84 3.000
BDG   C6      C5      O5          108.90 3.000
BDG   C4      C5      O5          112.11 3.000
BDG   C1      O5      C5          112.16 3.000
BDG   H1      C1      C2          108.84 3.000
BDG   H1      C1      O1          109.22 3.000
BDG   C2      C1      O1          108.90 3.000
BDG   H1      C1      O5          108.84 3.000
BDG   C2      C1      O5          112.11 3.000
BDG   O1      C1      O5          108.90 3.000
BDG   HO1     O1      C1          109.48 3.000
BDG   H2      C2      C3          108.91 3.000
BDG   H2      C2      N2          109.28 3.000
BDG   C3      C2      N2          108.83 3.000
BDG   H2      C2      C1          108.91 3.000
BDG   C3      C2      C1          112.05 3.000
BDG   N2      C2      C1          108.83 3.000
BDG  HN22     N2     HN21         109.47 3.000
BDG  HN22     N2      C2          109.48 3.000
BDG  HN21     N2      C2          109.48 3.000
BDG   H3      C3      C4          108.93 3.000
BDG   H3      C3      O3          109.30 3.000
BDG   C4      C3      O3          108.81 3.000
BDG   H3      C3      C2          108.93 3.000
BDG   C4      C3      C2          112.02 3.000
BDG   O3      C3      C2          108.81 3.000
BDG   HO3     O3      C3          109.48 3.000
BDG   H4      C4      O4          109.28 3.000
BDG   H4      C4      C3          108.90 3.000
BDG   O4      C4      C3          108.83 3.000
BDG   H4      C4      C5          108.90 3.000
BDG   O4      C4      C5          108.83 3.000
BDG   C3      C4      C5          112.05 3.000
BDG   HO4     O4      C4          109.48 3.000
BDG   H62     C6      H61         109.47 3.000
BDG   H62     C6      N6          109.47 3.000
BDG   H61     C6      N6          109.47 3.000
BDG   H62     C6      C5          109.47 3.000
BDG   H61     C6      C5          109.47 3.000
BDG   N6      C6      C5          109.47 3.000
BDG  HN62     N6     HN61         109.47 3.000
BDG  HN62     N6      C6          109.48 3.000
BDG  HN61     N6      C6          109.48 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
BDG Var_01        HN61     N6      C6      C5         -129.44  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
BDG chir_01   C5      O5      C4      C6    negativ
BDG chir_02   C1      O5      O1      C2    positiv
BDG chir_03   C2      N2      C3      C1    positiv
BDG chir_04   C3      O3      C2      C4    positiv
BDG chir_05   C4      O4      C3      C5    negativ
