# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 20:02:08 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 2-amino-2-deoxy-alpha-D-galactopyranose
#   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
 X6X  X6X  2-amino-2-deoxy-alpha-D-galactopyranose  D-saccharide  25  12  .  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_X6X
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
 X6X  O4    O  OH1   0  -0.675   -9.8918   0.8251  13.8293
 X6X  C4    C  CH1   0  -0.004   -8.7078   1.0241  13.0917
 X6X  C3    C  CH1   0   0.045   -8.1567  -0.3303  12.6621
 X6X  O3    O  OH1   0  -0.672   -9.1496  -1.0218  11.9376
 X6X  C2    C  CH1   0  -0.137   -7.6771  -1.1243  13.8774
 X6X  N2    N  NH2   0  -0.813   -7.1125  -2.3977  13.4577
 X6X  C1    C  CH1   0   0.246   -6.6480  -0.2996  14.6522
 X6X  O1    O  OH1   0  -0.660   -5.4799  -0.1950  13.9018
 X6X  O5    O  O2    0  -0.505   -7.1808   0.9527  14.9917
 X6X  C5    C  CH1   0  -0.002   -7.6273   1.7452  13.9033
 X6X  C6    C  CH2   0  -0.195   -8.0966   3.0521  14.5225
 X6X  O6    O  OH1   0  -0.668   -8.5687   3.8844  13.4894
 X6X  HO4   H  HOH1  0   0.454  -10.4099   1.6347  13.8018
 X6X  H4    H  HCH1  0   0.232   -8.9038   1.6130  12.1866
 X6X  H3    H  HCH1  0   0.217   -7.2897  -0.1299  12.0182
 X6X  HO3   H  HOH1  0   0.449   -8.7138  -1.6665  11.3725
 X6X  H2    H  HCH1  0   0.224   -8.5263  -1.2525  14.5640
 X6X  HN21  H  HNH2  0   0.347   -6.6725  -2.8540  14.2487
 X6X  HN22  H  HNH2  0   0.345   -7.8656  -3.0176  13.1869
 X6X  H1    H  HCH1  0   0.226   -6.4482  -0.7820  15.6180
 X6X  HO1   H  HOH1  0   0.457   -4.7847   0.1695  14.4600
 X6X  H5    H  HCH1  0   0.217   -6.7951   1.9648  13.2201
 X6X  H61   H  HCH2  0   0.216   -7.2539   3.5080  15.0577
 X6X  H62   H  HCH2  0   0.200   -8.8735   2.8437  15.2691
 X6X  HO6   H  HOH1  0   0.458   -8.9098   4.6917  13.8838

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
 X6X  O3  C3    single  1.410  0.020  1.410
 X6X  C3  C4    single  1.524  0.020  1.524
 X6X  C3  C2    single  1.529  0.020  1.529
 X6X  C4  O4    single  1.409  0.020  1.409
 X6X  C4  C5    single  1.532  0.020  1.532
 X6X  N2  C2    single  1.455  0.020  1.455
 X6X  O6  C6    single  1.408  0.020  1.408
 X6X  C5  C6    single  1.520  0.020  1.520
 X6X  C5  O5    single  1.418  0.020  1.418
 X6X  C2  C1    single  1.530  0.020  1.530
 X6X  O1  C1    single  1.392  0.020  1.392
 X6X  C1  O5    single  1.403  0.020  1.403
 X6X  O4  HO4   single  0.850  0.020  0.980
 X6X  C4  H4    single  0.970  0.020  1.090
 X6X  C3  H3    single  0.970  0.020  1.090
 X6X  O3  HO3   single  0.850  0.020  0.980
 X6X  C2  H2    single  0.970  0.020  1.090
 X6X  N2  HN21  single  0.890  0.020  1.040
 X6X  N2  HN22  single  0.890  0.020  1.040
 X6X  C1  H1    single  0.970  0.020  1.090
 X6X  O1  HO1   single  0.850  0.020  0.980
 X6X  C5  H5    single  0.970  0.020  1.090
 X6X  C6  H61   single  0.970  0.020  1.090
 X6X  C6  H62   single  0.970  0.020  1.090
 X6X  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
 X6X  HO4   O4  C4    108.60  3.000
 X6X  H4    C4  C5    108.08  3.000
 X6X  H4    C4  C3    107.99  3.000
 X6X  C5    C4  C3    108.22  3.000
 X6X  H4    C4  O4    110.95  3.000
 X6X  C5    C4  O4    112.45  3.000
 X6X  C3    C4  O4    109.02  3.000
 X6X  H3    C3  C2    108.25  3.000
 X6X  H3    C3  O3    110.12  3.000
 X6X  C2    C3  O3    112.00  3.000
 X6X  H3    C3  C4    106.77  3.000
 X6X  C2    C3  C4    110.54  3.000
 X6X  O3    C3  C4    109.03  3.000
 X6X  HO3   O3  C3    108.16  3.000
 X6X  H2    C2  C1    105.43  3.000
 X6X  H2    C2  N2    112.20  3.000
 X6X  C1    C2  N2    110.91  3.000
 X6X  H2    C2  C3    108.34  3.000
 X6X  C1    C2  C3    109.49  3.000
 X6X  N2    C2  C3    110.31  3.000
 X6X  HN22  N2  HN21  104.84  3.000
 X6X  HN22  N2  C2    108.93  3.000
 X6X  HN21  N2  C2    109.72  3.000
 X6X  H1    C1  O5    104.39  3.000
 X6X  H1    C1  O1    110.76  3.000
 X6X  O5    C1  O1    112.46  3.000
 X6X  H1    C1  C2    109.34  3.000
 X6X  O5    C1  C2    110.39  3.000
 X6X  O1    C1  C2    109.39  3.000
 X6X  HO1   O1  C1    108.76  3.000
 X6X  C5    O5  C1    115.64  3.000
 X6X  H5    C5  C6    108.38  3.000
 X6X  H5    C5  O5    110.50  3.000
 X6X  C6    C5  O5    105.37  3.000
 X6X  H5    C5  C4    107.39  3.000
 X6X  O5    C5  C4    111.44  3.000
 X6X  C6    C5  C4    113.75  3.000
 X6X  H62   C6  H61   106.90  3.000
 X6X  H62   C6  O6    111.96  3.000
 X6X  H61   C6  O6    111.70  3.000
 X6X  H62   C6  C5    109.41  3.000
 X6X  H61   C6  C5    108.58  3.000
 X6X  O6    C6  C5    108.22  3.000
 X6X  HO6   O6  C6    108.33  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
 X6X  chir_01  C4  C3  O4  C5  negativ
 X6X  chir_02  C3  O3  C2  C4  positiv
 X6X  chir_03  C2  N2  C1  C3  negativ
 X6X  chir_04  C1  O5  O1  C2  positiv
 X6X  chir_05  C5  O5  C6  C4  positiv

