# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:10:32 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 2-amino-2-deoxy-beta-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
 GCS  GCS  2-amino-2-deoxy-beta-D-glucopyranose  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 OK
;

data_comp_GCS
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
 GCS  C1    C  CH1   0   0.307  20.2600  45.8887  45.7377
 GCS  C2    C  CH1   0  -0.153  21.0149  44.5663  45.8253
 GCS  C3    C  CH1   0   0.039  21.4254  44.1563  44.4180
 GCS  C4    C  CH1   0   0.001  20.2324  44.1526  43.4685
 GCS  C5    C  CH1   0  -0.017  19.5149  45.5055  43.5397
 GCS  C6    C  CH2   0  -0.160  18.2572  45.5335  42.6975
 GCS  N2    N  NH2   0  -0.804  22.1970  44.7380  46.6500
 GCS  O1    O  OH1   0  -0.656  19.7986  46.2190  46.9959
 GCS  O3    O  OH1   0  -0.667  22.0325  42.8891  44.4922
 GCS  O4    O  OH1   0  -0.671  20.7362  43.8891  42.1764
 GCS  O5    O  O2    0  -0.496  19.1524  45.7684  44.8780
 GCS  O6    O  OH1   0  -0.664  17.7185  46.8331  42.7208
 GCS  H1    H  HCH1  0   0.177  20.9449  46.6596  45.3417
 GCS  H2    H  HCH1  0   0.217  20.3131  43.8082  46.2123
 GCS  H3    H  HCH1  0   0.201  22.1429  44.9088  44.0490
 GCS  H4    H  HCH1  0   0.219  19.5309  43.3678  43.7869
 GCS  H5    H  HCH1  0   0.214  20.2044  46.2834  43.1694
 GCS  H61   H  HCH2  0   0.200  18.5164  45.2260  41.6773
 GCS  H62   H  HCH2  0   0.198  17.5504  44.7884  43.0885
 GCS  HN21  H  HNH2  0   0.349  22.7373  43.8825  46.6466
 GCS  HN22  H  HNH2  0   0.346  21.9197  44.8866  47.6114
 GCS  HO1   H  HOH1  0   0.460  19.5629  47.1527  47.0159
 GCS  HO3   H  HOH1  0   0.448  22.3481  42.6584  43.6124
 GCS  HO4   H  HOH1  0   0.459  20.0686  43.4242  41.6649
 GCS  HO6   H  HOH1  0   0.454  16.9233  46.8370  42.1807

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
 GCS  C1  C2    single  1.525  0.020  1.525
 GCS  C1  O1    single  1.380  0.020  1.380
 GCS  C1  O5    single  1.407  0.020  1.407
 GCS  C1  H1    single  0.970  0.020  1.090
 GCS  C2  C3    single  1.522  0.020  1.522
 GCS  C2  N2    single  1.452  0.020  1.452
 GCS  C2  H2    single  0.970  0.020  1.090
 GCS  C3  C4    single  1.525  0.020  1.525
 GCS  C3  O3    single  1.407  0.020  1.407
 GCS  C3  H3    single  0.970  0.020  1.090
 GCS  C4  C5    single  1.533  0.020  1.533
 GCS  C4  O4    single  1.412  0.020  1.412
 GCS  C4  H4    single  0.970  0.020  1.090
 GCS  C5  C6    single  1.514  0.020  1.514
 GCS  C5  O5    single  1.411  0.020  1.411
 GCS  C5  H5    single  0.970  0.020  1.090
 GCS  C6  O6    single  1.407  0.020  1.407
 GCS  C6  H61   single  0.970  0.020  1.090
 GCS  C6  H62   single  0.970  0.020  1.090
 GCS  N2  HN21  single  0.890  0.020  1.040
 GCS  N2  HN22  single  0.890  0.020  1.040
 GCS  O1  HO1   single  0.850  0.020  0.980
 GCS  O3  HO3   single  0.850  0.020  0.980
 GCS  O4  HO4   single  0.850  0.020  0.980
 GCS  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
 GCS  H1    C1  O5    109.18  3.000
 GCS  H1    C1  O1    111.53  3.000
 GCS  O5    C1  O1    108.31  3.000
 GCS  H1    C1  C2    108.59  3.000
 GCS  O5    C1  C2    110.52  3.000
 GCS  O1    C1  C2    108.70  3.000
 GCS  H2    C2  N2    113.58  3.000
 GCS  H2    C2  C3    108.11  3.000
 GCS  N2    C2  C3    109.73  3.000
 GCS  H2    C2  C1    107.52  3.000
 GCS  N2    C2  C1    109.46  3.000
 GCS  C3    C2  C1    108.29  3.000
 GCS  H3    C3  O3    110.57  3.000
 GCS  H3    C3  C4    107.59  3.000
 GCS  O3    C3  C4    111.61  3.000
 GCS  H3    C3  C2    107.51  3.000
 GCS  O3    C3  C2    108.07  3.000
 GCS  C4    C3  C2    111.43  3.000
 GCS  H4    C4  O4    111.06  3.000
 GCS  H4    C4  C5    108.53  3.000
 GCS  O4    C4  C5    111.98  3.000
 GCS  H4    C4  C3    108.70  3.000
 GCS  O4    C4  C3    106.93  3.000
 GCS  C5    C4  C3    109.58  3.000
 GCS  H5    C5  O5    110.32  3.000
 GCS  H5    C5  C6    108.63  3.000
 GCS  O5    C5  C6    108.10  3.000
 GCS  H5    C5  C4    108.31  3.000
 GCS  O5    C5  C4    109.19  3.000
 GCS  C6    C5  C4    112.29  3.000
 GCS  H62   C6  H61   107.03  3.000
 GCS  H62   C6  O6    111.97  3.000
 GCS  H61   C6  O6    111.40  3.000
 GCS  H62   C6  C5    108.90  3.000
 GCS  H61   C6  C5    108.42  3.000
 GCS  O6    C6  C5    109.03  3.000
 GCS  HN22  N2  HN21  105.89  3.000
 GCS  HN22  N2  C2    109.52  3.000
 GCS  HN21  N2  C2    109.44  3.000
 GCS  HO1   O1  C1    109.43  3.000
 GCS  HO3   O3  C3    108.00  3.000
 GCS  HO4   O4  C4    109.24  3.000
 GCS  C5    O5  C1    113.15  3.000
 GCS  HO6   O6  C6    108.13  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
 GCS  chir_01  C1  C2  O1  O5  positiv
 GCS  chir_02  C2  N2  C3  C1  positiv
 GCS  chir_03  C3  O3  C2  C4  positiv
 GCS  chir_04  C4  O4  C5  C3  positiv
 GCS  chir_05  C5  O5  C4  C6  negativ

