# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 06:25:51 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 4-deoxy-alpha-D-xylo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1C[C@H](O)[C@@H](O)[C@@H](O)O1
#
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
 G4D  G4D  4-deoxy-alpha-D-xylo-hexopyranose  D-saccharide  23  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 GRAND
;

data_comp_G4D
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
 G4D  C1   C  CH1   0   0.232  66.0785  93.9763   8.9345
 G4D  C2   C  CH1   0   0.021  67.4052  93.9175   9.6905
 G4D  C3   C  CH1   0   0.016  68.4487  94.7891   9.0056
 G4D  C4   C  CH2   0  -0.495  68.5654  94.3599   7.5478
 G4D  C5   C  CH1   0   0.016  67.1996  94.4020   6.8745
 G4D  C6   C  CH2   0  -0.179  67.2113  93.9134   5.4418
 G4D  O1   O  OH1   0  -0.662  65.5461  95.2550   9.0724
 G4D  O2   O  OH1   0  -0.669  67.1696  94.2827  11.0247
 G4D  O3   O  OH1   0  -0.672  69.6553  94.6206   9.7197
 G4D  O5   O  O2    0  -0.502  66.2626  93.6106   7.5953
 G4D  O6   O  OH1   0  -0.667  67.6906  92.5920   5.3817
 G4D  H1   H  HCH1  0   0.229  65.3946  93.2197   9.3387
 G4D  H2   H  HCH1  0   0.209  67.7528  92.8740   9.6230
 G4D  H3   H  HCH1  0   0.209  68.1223  95.8375   9.0489
 G4D  H4   H  HCH2  0   0.240  69.2522  95.0221   7.0128
 G4D  H42  H  HCH2  0   0.234  68.9799  93.3495   7.5013
 G4D  H5   H  HCH1  0   0.219  66.8583  95.4454   6.8360
 G4D  H61  H  HCH2  0   0.209  66.1940  93.9950   5.0358
 G4D  H62  H  HCH2  0   0.202  67.8398  94.6048   4.8660
 G4D  HO1  H  HOH1  0   0.458  64.6339  95.2473   8.7624
 G4D  HO2  H  HOH1  0   0.447  68.0100  94.2414  11.4925
 G4D  HO3  H  HOH1  0   0.452  70.2740  95.3025   9.4413
 G4D  HO6  H  HOH1  0   0.455  67.7697  92.3432   4.4570

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
 G4D  C1  C2   single  1.528  0.020  1.528
 G4D  C1  O1   single  1.392  0.020  1.392
 G4D  C1  O5   single  1.400  0.020  1.400
 G4D  C1  H1   single  0.970  0.020  1.090
 G4D  C2  C3   single  1.522  0.020  1.522
 G4D  C2  O2   single  1.403  0.020  1.403
 G4D  C2  H2   single  0.970  0.020  1.090
 G4D  C3  C4   single  1.524  0.020  1.524
 G4D  C3  O3   single  1.412  0.020  1.412
 G4D  C3  H3   single  0.970  0.020  1.090
 G4D  C4  C5   single  1.523  0.020  1.523
 G4D  C4  H4   single  0.970  0.020  1.090
 G4D  C4  H42  single  0.970  0.020  1.090
 G4D  C5  C6   single  1.514  0.020  1.514
 G4D  C5  O5   single  1.423  0.020  1.423
 G4D  C5  H5   single  0.970  0.020  1.090
 G4D  C6  O6   single  1.407  0.020  1.407
 G4D  C6  H61  single  0.970  0.020  1.090
 G4D  C6  H62  single  0.970  0.020  1.090
 G4D  O1  HO1  single  0.850  0.020  0.980
 G4D  O2  HO2  single  0.850  0.020  0.980
 G4D  O3  HO3  single  0.850  0.020  0.980
 G4D  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
 G4D  H1   C1  O5   104.73  3.000
 G4D  H1   C1  O1   111.01  3.000
 G4D  O5   C1  O1   112.64  3.000
 G4D  H1   C1  C2   109.41  3.000
 G4D  O5   C1  C2   110.42  3.000
 G4D  O1   C1  C2   108.56  3.000
 G4D  H2   C2  O2   110.96  3.000
 G4D  H2   C2  C3   107.36  3.000
 G4D  O2   C2  C3   113.20  3.000
 G4D  H2   C2  C1   106.26  3.000
 G4D  O2   C2  C1   108.34  3.000
 G4D  C3   C2  C1   110.52  3.000
 G4D  H3   C3  O3   110.34  3.000
 G4D  H3   C3  C4   109.22  3.000
 G4D  O3   C3  C4   112.63  3.000
 G4D  H3   C3  C2   108.96  3.000
 G4D  O3   C3  C2   106.85  3.000
 G4D  C4   C3  C2   108.76  3.000
 G4D  H42  C4  H4   107.50  3.000
 G4D  H42  C4  C5   110.29  3.000
 G4D  H4   C4  C5   109.27  3.000
 G4D  H42  C4  C3   109.27  3.000
 G4D  H4   C4  C3   110.21  3.000
 G4D  C5   C4  C3   110.26  3.000
 G4D  H5   C5  O5   109.97  3.000
 G4D  H5   C5  C6   106.01  3.000
 G4D  O5   C5  C6   107.76  3.000
 G4D  H5   C5  C4   108.68  3.000
 G4D  O5   C5  C4   110.56  3.000
 G4D  C6   C5  C4   113.73  3.000
 G4D  H62  C6  H61  106.84  3.000
 G4D  H62  C6  O6   111.97  3.000
 G4D  H61  C6  O6   111.68  3.000
 G4D  H62  C6  C5   107.31  3.000
 G4D  H61  C6  C5   108.58  3.000
 G4D  O6   C6  C5   110.25  3.000
 G4D  HO1  O1  C1   108.84  3.000
 G4D  HO2  O2  C2   107.72  3.000
 G4D  HO3  O3  C3   108.58  3.000
 G4D  C5   O5  C1   115.21  3.000
 G4D  HO6  O6  C6   108.20  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
 G4D  chir_01  C1  C2  O1  O5  negativ
 G4D  chir_02  C2  O2  C1  C3  negativ
 G4D  chir_03  C3  O3  C2  C4  positiv
 G4D  chir_04  C5  O5  C6  C4  positiv

