# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:58:12 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 4-amino-4-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@H](O)[C@@H](O)[C@@H](O)O[C@@H]1CO
#
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
 GDA  GDA  4-amino-4-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 GRAND
;

data_comp_GDA
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
 GDA  C1    C  CH1   0   0.235  -2.5660   1.3701   0.0810
 GDA  C2    C  CH1   0   0.018  -1.8352   0.6540  -1.0503
 GDA  C3    C  CH1   0  -0.001  -0.3303   0.6990  -0.8247
 GDA  C4    C  CH1   0  -0.144   0.1437   2.1426  -0.6252
 GDA  C5    C  CH1   0   0.005  -0.6849   2.8007   0.4778
 GDA  C6    C  CH2   0  -0.160  -0.4086   4.2887   0.6014
 GDA  N4    N  NH2   0  -0.794   1.5573   2.2631  -0.3134
 GDA  O2    O  OH1   0  -0.673  -2.3295  -0.6570  -1.1408
 GDA  O3    O  OH1   0  -0.675   0.2767   0.0994  -1.9523
 GDA  O5    O  O2    0  -0.515  -2.0747   2.6783   0.2025
 GDA  O6    O  OH1   0  -0.669  -1.1148   4.8871   1.6628
 GDA  O1    O  OH1   0  -0.663  -2.4187   0.6298   1.2470
 GDA  HA_1  H  HCH1  0   0.237  -3.6241   1.4943  -0.1792
 GDA  HA    H  HCH1  0   0.215  -2.0560   1.2195  -1.9695
 GDA  HB    H  HCH1  0   0.214  -0.0875   0.1308   0.0852
 GDA  HC    H  HCH1  0   0.232  -0.0354   2.6928  -1.5575
 GDA  H5    H  HCH1  0   0.213  -0.4452   2.3206   1.4377
 GDA  H6C1  H  HCH2  0   0.193  -0.6302   4.7755  -0.3591
 GDA  H6C2  H  HCH2  0   0.230   0.6529   4.4296   0.7988
 GDA  H4N1  H  HNH2  0   0.352   2.1165   1.9717  -1.1044
 GDA  H4N2  H  HNH2  0   0.342   1.8004   1.6449   0.4527
 GDA  H2    H  HOH1  0   0.449  -1.8526  -1.0970  -1.8522
 GDA  H3    H  HOH1  0   0.455   1.1263  -0.2657  -1.6912
 GDA  H6    H  HOH1  0   0.445  -2.0553   4.7671   1.4976
 GDA  H1    H  HOH1  0   0.462  -3.0158   0.9806   1.9166

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
 GDA  C1  C2    single  1.525  0.020  1.525
 GDA  C1  O5    single  1.403  0.020  1.403
 GDA  C1  O1    single  1.389  0.020  1.389
 GDA  C1  HA_1  single  0.970  0.020  1.090
 GDA  C2  C3    single  1.522  0.020  1.522
 GDA  C2  O2    single  1.404  0.020  1.404
 GDA  C2  HA    single  0.970  0.020  1.090
 GDA  C3  C4    single  1.532  0.020  1.532
 GDA  C3  O3    single  1.414  0.020  1.414
 GDA  C3  HB    single  0.970  0.020  1.090
 GDA  C4  C5    single  1.528  0.020  1.528
 GDA  C4  N4    single  1.453  0.020  1.453
 GDA  C4  HC    single  0.970  0.020  1.090
 GDA  C5  C6    single  1.518  0.020  1.518
 GDA  C5  O5    single  1.422  0.020  1.422
 GDA  C5  H5    single  0.970  0.020  1.090
 GDA  C6  O6    single  1.408  0.020  1.408
 GDA  C6  H6C1  single  0.970  0.020  1.090
 GDA  C6  H6C2  single  0.970  0.020  1.090
 GDA  N4  H4N1  single  0.890  0.020  1.040
 GDA  N4  H4N2  single  0.890  0.020  1.040
 GDA  O2  H2    single  0.850  0.020  0.980
 GDA  O3  H3    single  0.850  0.020  0.980
 GDA  O6  H6    single  0.850  0.020  0.980
 GDA  O1  H1    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
 GDA  HA_1  C1  O1    111.22  3.000
 GDA  HA_1  C1  O5    104.65  3.000
 GDA  O1    C1  O5    112.78  3.000
 GDA  HA_1  C1  C2    109.85  3.000
 GDA  O1    C1  C2    108.76  3.000
 GDA  O5    C1  C2    109.53  3.000
 GDA  HA    C2  O2    110.79  3.000
 GDA  HA    C2  C3    107.85  3.000
 GDA  O2    C2  C3    112.65  3.000
 GDA  HA    C2  C1    106.37  3.000
 GDA  O2    C2  C1    108.51  3.000
 GDA  C3    C2  C1    110.48  3.000
 GDA  HB    C3  O3    110.24  3.000
 GDA  HB    C3  C4    108.10  3.000
 GDA  O3    C3  C4    111.74  3.000
 GDA  HB    C3  C2    109.00  3.000
 GDA  O3    C3  C2    107.08  3.000
 GDA  C4    C3  C2    110.66  3.000
 GDA  HC    C4  N4    107.43  3.000
 GDA  HC    C4  C5    107.98  3.000
 GDA  N4    C4  C5    109.69  3.000
 GDA  HC    C4  C3    108.14  3.000
 GDA  N4    C4  C3    114.02  3.000
 GDA  C5    C4  C3    109.38  3.000
 GDA  H5    C5  O5    110.15  3.000
 GDA  H5    C5  C6    108.48  3.000
 GDA  O5    C5  C6    106.14  3.000
 GDA  H5    C5  C4    108.89  3.000
 GDA  O5    C5  C4    110.68  3.000
 GDA  C6    C5  C4    112.46  3.000
 GDA  H6C2  C6  H6C1  107.32  3.000
 GDA  H6C2  C6  O6    107.29  3.000
 GDA  H6C1  C6  O6    111.66  3.000
 GDA  H6C2  C6  C5    108.60  3.000
 GDA  H6C1  C6  C5    109.03  3.000
 GDA  O6    C6  C5    112.73  3.000
 GDA  H4N2  N4  H4N1  106.42  3.000
 GDA  H4N2  N4  C4    110.18  3.000
 GDA  H4N1  N4  C4    110.26  3.000
 GDA  H2    O2  C2    107.46  3.000
 GDA  H3    O3  C3    108.90  3.000
 GDA  C5    O5  C1    116.06  3.000
 GDA  H6    O6  C6    107.92  3.000
 GDA  H1    O1  C1    108.88  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
 GDA  chir_01  C1  C2  O5  O1  positiv
 GDA  chir_02  C2  O2  C1  C3  negativ
 GDA  chir_03  C3  O3  C2  C4  positiv
 GDA  chir_04  C4  N4  C5  C3  positiv
 GDA  chir_05  C5  O5  C4  C6  negativ

