# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:02:57 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 4-amino-4,6-dideoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1N
#
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
 DAG  DAG  4-amino-4,6-dideoxy-beta-D-glucopyranose  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 PERFECT
;

data_comp_DAG
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
 DAG  C1    C  CH1   0   0.279   2.0987   8.3414  -3.7232
 DAG  C2    C  CH1   0   0.007   1.5607   9.4208  -2.7955
 DAG  C3    C  CH1   0  -0.006   0.3110   8.8922  -2.1053
 DAG  C4    C  CH1   0  -0.128  -0.7193   8.3836  -3.1186
 DAG  C5    C  CH1   0   0.046  -0.0433   7.3810  -4.0599
 DAG  C6    C  CH3   0  -0.672  -0.9431   6.9198  -5.1865
 DAG  O1    O  OH1   0  -0.655   3.1780   8.8421  -4.4205
 DAG  O2    O  OH1   0  -0.668   2.5634   9.7575  -1.8716
 DAG  O3    O  OH1   0  -0.671  -0.1946   9.9422  -1.3062
 DAG  N4    N  NH2   0  -0.792  -1.8938   7.7864  -2.5089
 DAG  O5    O  O2    0  -0.497   1.1025   7.9758  -4.6451
 DAG  H1    H  HCH1  0   0.179   2.3817   7.4575  -3.1221
 DAG  H2    H  HCH1  0   0.206   1.2765  10.2889  -3.4140
 DAG  H3    H  HCH1  0   0.205   0.6082   8.0385  -1.4738
 DAG  H4    H  HCH1  0   0.228  -1.0583   9.2333  -3.7237
 DAG  H5    H  HCH1  0   0.201   0.2632   6.5028  -3.4651
 DAG  H61   H  HCH3  0   0.222  -1.2726   7.7642  -5.7945
 DAG  H62   H  HCH3  0   0.233  -0.4238   6.2119  -5.8333
 DAG  H63   H  HCH3  0   0.234  -1.8264   6.4255  -4.7883
 DAG  HO1   H  HOH1  0   0.459   3.6701   8.1116  -4.8103
 DAG  HO2   H  HOH1  0   0.446   2.1663  10.3363  -1.2119
 DAG  HO3   H  HOH1  0   0.453  -0.7184   9.5666  -0.5929
 DAG  HN41  H  HNH2  0   0.349  -2.4147   8.4844  -1.9938
 DAG  HN42  H  HNH2  0   0.340  -1.6191   7.0786  -1.8363

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
 DAG  C1  C2    single  1.522  0.020  1.522
 DAG  C1  O1    single  1.379  0.020  1.379
 DAG  C1  O5    single  1.406  0.020  1.406
 DAG  C1  H1    single  0.970  0.020  1.090
 DAG  C2  C3    single  1.522  0.020  1.522
 DAG  C2  O2    single  1.404  0.020  1.404
 DAG  C2  H2    single  0.970  0.020  1.090
 DAG  C3  C4    single  1.532  0.020  1.532
 DAG  C3  O3    single  1.413  0.020  1.413
 DAG  C3  H3    single  0.970  0.020  1.090
 DAG  C4  C5    single  1.532  0.020  1.532
 DAG  C4  N4    single  1.452  0.020  1.452
 DAG  C4  H4    single  0.970  0.020  1.090
 DAG  C5  C6    single  1.514  0.020  1.514
 DAG  C5  O5    single  1.417  0.020  1.417
 DAG  C5  H5    single  0.970  0.020  1.090
 DAG  C6  H61   single  0.970  0.020  1.090
 DAG  C6  H62   single  0.970  0.020  1.090
 DAG  C6  H63   single  0.970  0.020  1.090
 DAG  O1  HO1   single  0.850  0.020  0.980
 DAG  O2  HO2   single  0.850  0.020  0.980
 DAG  O3  HO3   single  0.850  0.020  0.980
 DAG  N4  HN41  single  0.890  0.020  1.040
 DAG  N4  HN42  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
 DAG  H1    C1  O5    109.27  3.000
 DAG  H1    C1  O1    111.40  3.000
 DAG  O5    C1  O1    108.51  3.000
 DAG  H1    C1  C2    109.04  3.000
 DAG  O5    C1  C2    109.50  3.000
 DAG  O1    C1  C2    109.11  3.000
 DAG  H2    C2  O2    111.35  3.000
 DAG  H2    C2  C3    108.42  3.000
 DAG  O2    C2  C3    111.78  3.000
 DAG  H2    C2  C1    107.91  3.000
 DAG  O2    C2  C1    108.59  3.000
 DAG  C3    C2  C1    108.68  3.000
 DAG  H3    C3  O3    110.35  3.000
 DAG  H3    C3  C4    107.64  3.000
 DAG  O3    C3  C4    112.34  3.000
 DAG  H3    C3  C2    107.89  3.000
 DAG  O3    C3  C2    106.98  3.000
 DAG  C4    C3  C2    111.56  3.000
 DAG  H4    C4  N4    107.48  3.000
 DAG  H4    C4  C5    107.72  3.000
 DAG  N4    C4  C5    110.22  3.000
 DAG  H4    C4  C3    108.40  3.000
 DAG  N4    C4  C3    113.76  3.000
 DAG  C5    C4  C3    109.07  3.000
 DAG  H5    C5  O5    109.38  3.000
 DAG  H5    C5  C6    108.88  3.000
 DAG  O5    C5  C6    107.53  3.000
 DAG  H5    C5  C4    108.17  3.000
 DAG  O5    C5  C4    109.61  3.000
 DAG  C6    C5  C4    113.22  3.000
 DAG  H63   C6  H62   107.99  3.000
 DAG  H63   C6  H61   108.08  3.000
 DAG  H62   C6  H61   108.39  3.000
 DAG  H63   C6  C5    110.41  3.000
 DAG  H62   C6  C5    110.86  3.000
 DAG  H61   C6  C5    111.00  3.000
 DAG  HO1   O1  C1    109.22  3.000
 DAG  HO2   O2  C2    107.47  3.000
 DAG  HO3   O3  C3    108.92  3.000
 DAG  HN42  N4  HN41  106.45  3.000
 DAG  HN42  N4  C4    110.27  3.000
 DAG  HN41  N4  C4    110.27  3.000
 DAG  C5    O5  C1    114.28  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
 DAG  chir_01  C1  C2  O1  O5  positiv
 DAG  chir_02  C2  O2  C1  C3  negativ
 DAG  chir_03  C3  O3  C2  C4  positiv
 DAG  chir_04  C4  N4  C3  C5  negativ
 DAG  chir_05  C5  O5  C4  C6  negativ

