# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:07:19 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 2-amino-2-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@@H](O)O[C@H](CO)[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
 PA1  PA1  2-amino-2-deoxy-alpha-D-glucopyranose  D-saccharide  25  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PA1
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
 PA1  C1    C  CH1   0   0.250   1.5963   0.1786   0.5164
 PA1  O1    O  OH1   0  -0.664   1.9414  -1.1656   0.6082
 PA1  C2    C  CH1   0  -0.138   0.5371   0.5011   1.5663
 PA1  N2    N  NH2   0  -0.811   0.9845   0.1141   2.8932
 PA1  C3    C  CH1   0   0.033  -0.7778  -0.2005   1.2264
 PA1  O3    O  OH1   0  -0.675  -1.8047   0.1940   2.1100
 PA1  C4    C  CH1   0   0.008  -1.2076   0.1551  -0.1881
 PA1  O4    O  OH1   0  -0.670  -2.3407  -0.6167  -0.5136
 PA1  C5    C  CH1   0  -0.013  -0.0594  -0.1243  -1.1684
 PA1  O5    O  O2    0  -0.502   1.1284   0.5303  -0.7583
 PA1  C6    C  CH2   0  -0.162  -0.3868   0.3701  -2.5617
 PA1  O6    O  OH1   0  -0.670   0.6414  -0.0174  -3.4412
 PA1  H1    H  HCH1  0   0.230   2.4734   0.8201   0.6727
 PA1  HO1   H  HOH1  0   0.460   2.7101  -1.3257   0.0504
 PA1  H2    H  HCH1  0   0.221   0.3620   1.5854   1.4799
 PA1  HN21  H  HNH2  0   0.349   1.8969   0.5153   3.0762
 PA1  HN22  H  HNH2  0   0.346   0.3729   0.5338   3.5820
 PA1  H3    H  HCH1  0   0.214  -0.6217  -1.2872   1.2797
 PA1  HO3   H  HOH1  0   0.454  -1.7433  -0.3389   2.9078
 PA1  H4    H  HCH1  0   0.217  -1.4404   1.2301  -0.2197
 PA1  HO4   H  HOH1  0   0.456  -2.8945  -0.1203  -1.1214
 PA1  H5    H  HCH1  0   0.218   0.0935  -1.2119  -1.2110
 PA1  H61   H  HCH2  0   0.198  -1.3493  -0.0595  -2.8630
 PA1  H62   H  HCH2  0   0.196  -0.5139   1.4617  -2.5359
 PA1  HO6   H  HOH1  0   0.456   0.3991   0.2706  -4.3257

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
 PA1  C1  O1    single  1.391  0.020  1.391
 PA1  C1  C2    single  1.526  0.020  1.526
 PA1  C1  O5    single  1.403  0.020  1.403
 PA1  C1  H1    single  0.970  0.020  1.090
 PA1  O1  HO1   single  0.850  0.020  0.980
 PA1  C2  N2    single  1.453  0.020  1.453
 PA1  C2  C3    single  1.529  0.020  1.529
 PA1  C2  H2    single  0.970  0.020  1.090
 PA1  N2  HN21  single  0.890  0.020  1.040
 PA1  N2  HN22  single  0.890  0.020  1.040
 PA1  C3  O3    single  1.411  0.020  1.411
 PA1  C3  C4    single  1.520  0.020  1.520
 PA1  C3  H3    single  0.970  0.020  1.090
 PA1  O3  HO3   single  0.850  0.020  0.980
 PA1  C4  O4    single  1.409  0.020  1.409
 PA1  C4  C5    single  1.535  0.020  1.535
 PA1  C4  H4    single  0.970  0.020  1.090
 PA1  O4  HO4   single  0.850  0.020  0.980
 PA1  C5  O5    single  1.417  0.020  1.417
 PA1  C5  C6    single  1.514  0.020  1.514
 PA1  C5  H5    single  0.970  0.020  1.090
 PA1  C6  O6    single  1.407  0.020  1.407
 PA1  C6  H61   single  0.970  0.020  1.090
 PA1  C6  H62   single  0.970  0.020  1.090
 PA1  O6  HO6   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
 PA1  H1    C1  O5    104.44  3.000
 PA1  H1    C1  C2    109.46  3.000
 PA1  O5    C1  C2    109.92  3.000
 PA1  H1    C1  O1    110.92  3.000
 PA1  O5    C1  O1    112.65  3.000
 PA1  C2    C1  O1    109.34  3.000
 PA1  HO1   O1  C1    108.69  3.000
 PA1  H2    C2  C3    107.31  3.000
 PA1  H2    C2  N2    112.50  3.000
 PA1  C3    C2  N2    110.22  3.000
 PA1  H2    C2  C1    105.33  3.000
 PA1  C3    C2  C1    110.31  3.000
 PA1  N2    C2  C1    111.00  3.000
 PA1  HN22  N2  HN21  104.88  3.000
 PA1  HN22  N2  C2    108.96  3.000
 PA1  HN21  N2  C2    109.68  3.000
 PA1  H3    C3  C4    108.46  3.000
 PA1  H3    C3  O3    110.45  3.000
 PA1  C4    C3  O3    108.15  3.000
 PA1  H3    C3  C2    108.71  3.000
 PA1  C4    C3  C2    110.04  3.000
 PA1  O3    C3  C2    111.00  3.000
 PA1  HO3   O3  C3    108.56  3.000
 PA1  H4    C4  C5    108.52  3.000
 PA1  H4    C4  O4    111.00  3.000
 PA1  C5    C4  O4    110.74  3.000
 PA1  H4    C4  C3    108.36  3.000
 PA1  C5    C4  C3    109.88  3.000
 PA1  O4    C4  C3    108.31  3.000
 PA1  HO4   O4  C4    109.07  3.000
 PA1  H5    C5  C6    108.51  3.000
 PA1  H5    C5  O5    110.59  3.000
 PA1  C6    C5  O5    107.26  3.000
 PA1  H5    C5  C4    107.99  3.000
 PA1  C6    C5  C4    111.49  3.000
 PA1  O5    C5  C4    110.98  3.000
 PA1  C5    O5  C1    115.27  3.000
 PA1  H62   C6  H61   107.10  3.000
 PA1  H62   C6  O6    111.87  3.000
 PA1  H61   C6  O6    111.21  3.000
 PA1  H62   C6  C5    109.13  3.000
 PA1  H61   C6  C5    108.34  3.000
 PA1  O6    C6  C5    109.10  3.000
 PA1  HO6   O6  C6    107.96  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
 PA1  chir_01  C1  O1  C2  O5  positiv
 PA1  chir_02  C2  N2  C3  C1  positiv
 PA1  chir_03  C3  O3  C2  C4  positiv
 PA1  chir_04  C4  O4  C5  C3  positiv
 PA1  chir_05  C5  O5  C4  C6  negativ

