# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:04:13 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 4-amino-4,6-dideoxy-alpha-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
 AGL  AGL  4-amino-4,6-dideoxy-alpha-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_AGL
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
 AGL  C1    C  CH1   0   0.233  6.4782  15.0168  42.1001
 AGL  C2    C  CH1   0   0.019  6.9541  14.6250  43.4965
 AGL  C3    C  CH1   0  -0.004  7.4315  15.8534  44.2610
 AGL  C4    C  CH1   0  -0.110  8.5120  16.5727  43.4570
 AGL  C5    C  CH1   0   0.053  7.9649  16.8892  42.0617
 AGL  C6    C  CH3   0  -0.694  9.0071  17.4926  41.1412
 AGL  O1    O  OH1   0  -0.662  5.3102  15.7631  42.2176
 AGL  O2    O  OH1   0  -0.668  5.9184  13.9492  44.1587
 AGL  O3    O  OH1   0  -0.676  7.9227  15.4111  45.5144
 AGL  N4    N  NH2   0  -0.813  8.8829  17.8068  44.1308
 AGL  O5    O  O2    0  -0.502  7.4994  15.7018  41.4292
 AGL  H1    H  HCH1  0   0.229  6.3080  14.1136  41.5013
 AGL  H2    H  HCH1  0   0.210  7.8217  13.9621  43.3499
 AGL  H3    H  HCH1  0   0.221  6.5908  16.5447  44.4040
 AGL  H4    H  HCH1  0   0.203  9.3608  15.8783  43.3356
 AGL  H5    H  HCH1  0   0.206  7.1407  17.6050  42.1793
 AGL  H61   H  HCH3  0   0.242  8.5956  17.6510  40.1439
 AGL  H62   H  HCH3  0   0.231  9.3361  18.4636  41.5099
 AGL  H63   H  HCH3  0   0.225  9.8821  16.8460  41.0550
 AGL  HO1   H  HOH1  0   0.458  4.8991  15.8392  41.3497
 AGL  HO2   H  HOH1  0   0.445  6.2430  13.7167  45.0348
 AGL  HO3   H  HOH1  0   0.458  7.6357  16.0211  46.1987
 AGL  HN41  H  HNH2  0   0.350  9.7170  18.1926  43.7069
 AGL  HN42  H  HNH2  0   0.344  9.1490  17.5977  45.0853

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
 AGL  C1  C2    single  1.526  0.020  1.526
 AGL  C1  O1    single  1.391  0.020  1.391
 AGL  C1  O5    single  1.401  0.020  1.401
 AGL  C1  H1    single  0.970  0.020  1.090
 AGL  C2  C3    single  1.524  0.020  1.524
 AGL  C2  O2    single  1.403  0.020  1.403
 AGL  C2  H2    single  0.970  0.020  1.090
 AGL  C3  C4    single  1.527  0.020  1.527
 AGL  C3  O3    single  1.417  0.020  1.417
 AGL  C3  H3    single  0.970  0.020  1.090
 AGL  C4  C5    single  1.532  0.020  1.532
 AGL  C4  N4    single  1.454  0.020  1.454
 AGL  C4  H4    single  0.970  0.020  1.090
 AGL  C5  C6    single  1.516  0.020  1.516
 AGL  C5  O5    single  1.424  0.020  1.424
 AGL  C5  H5    single  0.970  0.020  1.090
 AGL  C6  H61   single  0.970  0.020  1.090
 AGL  C6  H62   single  0.970  0.020  1.090
 AGL  C6  H63   single  0.970  0.020  1.090
 AGL  O1  HO1   single  0.850  0.020  0.980
 AGL  O2  HO2   single  0.850  0.020  0.980
 AGL  O3  HO3   single  0.850  0.020  0.980
 AGL  N4  HN41  single  0.890  0.020  1.040
 AGL  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
 AGL  H1    C1  O5    104.74  3.000
 AGL  H1    C1  O1    110.95  3.000
 AGL  O5    C1  O1    112.97  3.000
 AGL  H1    C1  C2    109.66  3.000
 AGL  O5    C1  C2    109.66  3.000
 AGL  O1    C1  C2    108.80  3.000
 AGL  H2    C2  O2    110.76  3.000
 AGL  H2    C2  C3    107.77  3.000
 AGL  O2    C2  C3    112.51  3.000
 AGL  H2    C2  C1    106.15  3.000
 AGL  O2    C2  C1    108.98  3.000
 AGL  C3    C2  C1    110.47  3.000
 AGL  H3    C3  O3    110.29  3.000
 AGL  H3    C3  C4    108.29  3.000
 AGL  O3    C3  C4    111.56  3.000
 AGL  H3    C3  C2    109.46  3.000
 AGL  O3    C3  C2    107.51  3.000
 AGL  C4    C3  C2    109.72  3.000
 AGL  H4    C4  N4    112.88  3.000
 AGL  H4    C4  C5    107.74  3.000
 AGL  N4    C4  C5    109.74  3.000
 AGL  H4    C4  C3    107.81  3.000
 AGL  N4    C4  C3    109.65  3.000
 AGL  C5    C4  C3    108.92  3.000
 AGL  H5    C5  O5    110.24  3.000
 AGL  H5    C5  C6    108.76  3.000
 AGL  O5    C5  C6    106.68  3.000
 AGL  H5    C5  C4    107.77  3.000
 AGL  O5    C5  C4    110.43  3.000
 AGL  C6    C5  C4    112.94  3.000
 AGL  H63   C6  H62   108.22  3.000
 AGL  H63   C6  H61   108.44  3.000
 AGL  H62   C6  H61   107.10  3.000
 AGL  H63   C6  C5    111.31  3.000
 AGL  H62   C6  C5    110.91  3.000
 AGL  H61   C6  C5    110.72  3.000
 AGL  HO1   O1  C1    108.95  3.000
 AGL  HO2   O2  C2    107.28  3.000
 AGL  HO3   O3  C3    109.17  3.000
 AGL  HN42  N4  HN41  104.89  3.000
 AGL  HN42  N4  C4    109.18  3.000
 AGL  HN41  N4  C4    109.85  3.000
 AGL  C5    O5  C1    115.69  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
 AGL  chir_01  C1  C2  O1  O5  negativ
 AGL  chir_02  C2  O2  C1  C3  negativ
 AGL  chir_03  C3  O3  C2  C4  positiv
 AGL  chir_04  C4  N4  C3  C5  negativ
 AGL  chir_05  C5  O5  C4  C6  negativ

