# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:45:18 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-deoxy-beta-D-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)C[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
 RR7  RR7  2-deoxy-beta-D-arabino-hexopyranose  D-saccharide  23  11  .  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_RR7
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
 RR7  C1   C  CH1   0   0.287   0.0975  33.8106  24.7965
 RR7  C2   C  CH2   0  -0.517  -0.8321  32.6793  24.3964
 RR7  C3   C  CH1   0   0.033  -0.0380  31.4036  24.1733
 RR7  C4   C  CH1   0   0.011   1.0888  31.6657  23.1817
 RR7  C5   C  CH1   0  -0.012   1.9296  32.8524  23.6743
 RR7  C6   C  CH2   0  -0.193   3.0835  33.2044  22.7608
 RR7  O1   O  OH1   0  -0.658  -0.6284  34.9815  24.8887
 RR7  O3   O  OH1   0  -0.670  -0.9182  30.4029  23.7206
 RR7  O4   O  OH1   0  -0.678   1.8620  30.4892  23.0874
 RR7  O5   O  O2    0  -0.502   1.1049  33.9892  23.8221
 RR7  O6   O  OH1   0  -0.672   2.6050  33.4444  21.4588
 RR7  H1   H  HCH1  0   0.183   0.5828  33.5638  25.7568
 RR7  H21  H  HCH2  0   0.255  -1.5787  32.5246  25.1789
 RR7  H22  H  HCH2  0   0.240  -1.3581  32.9553  23.4767
 RR7  H3   H  HCH1  0   0.201   0.4222  31.1056  25.1303
 RR7  H4   H  HCH1  0   0.221   0.6389  31.9230  22.2140
 RR7  H5   H  HCH1  0   0.218   2.3737  32.5777  24.6465
 RR7  H61  H  HCH2  0   0.219   3.5989  34.0807  23.1753
 RR7  H62  H  HCH2  0   0.207   3.8042  32.3787  22.7884
 RR7  HO1  H  HOH1  0   0.461  -0.1214  35.6318  25.3862
 RR7  HO3  H  HOH1  0   0.448  -0.4052  29.5985  23.5906
 RR7  HO4  H  HOH1  0   0.459   2.3010  30.4707  22.2322
 RR7  HO6  H  HOH1  0   0.459   3.3599  33.6108  20.8877

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
 RR7  O4  C4   single  1.411  0.020  1.411
 RR7  C1  C2   single  1.518  0.020  1.518
 RR7  C1  O1   single  1.381  0.020  1.381
 RR7  C1  O5   single  1.413  0.020  1.413
 RR7  C2  C3   single  1.519  0.020  1.519
 RR7  C3  O3   single  1.407  0.020  1.407
 RR7  C3  C4   single  1.524  0.020  1.524
 RR7  C4  C5   single  1.536  0.020  1.536
 RR7  C5  C6   single  1.513  0.020  1.513
 RR7  C5  O5   single  1.412  0.020  1.412
 RR7  C6  O6   single  1.408  0.020  1.408
 RR7  C1  H1   single  0.970  0.020  1.090
 RR7  C2  H21  single  0.970  0.020  1.090
 RR7  C2  H22  single  0.970  0.020  1.090
 RR7  C3  H3   single  0.970  0.020  1.090
 RR7  C4  H4   single  0.970  0.020  1.090
 RR7  C5  H5   single  0.970  0.020  1.090
 RR7  C6  H61  single  0.970  0.020  1.090
 RR7  C6  H62  single  0.970  0.020  1.090
 RR7  O1  HO1  single  0.850  0.020  0.980
 RR7  O3  HO3  single  0.850  0.020  0.980
 RR7  O6  HO6  single  0.850  0.020  0.980
 RR7  O4  HO4  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
 RR7  H1   C1  O5   108.35  3.000
 RR7  H1   C1  O1   111.26  3.000
 RR7  O5   C1  O1   108.28  3.000
 RR7  H1   C1  C2   109.38  3.000
 RR7  O5   C1  C2   110.43  3.000
 RR7  O1   C1  C2   109.12  3.000
 RR7  H22  C2  H21  108.00  3.000
 RR7  H22  C2  C3   109.84  3.000
 RR7  H21  C2  C3   110.09  3.000
 RR7  H22  C2  C1   109.14  3.000
 RR7  H21  C2  C1   109.59  3.000
 RR7  C3   C2  C1   110.15  3.000
 RR7  H3   C3  O3   110.36  3.000
 RR7  H3   C3  C4   107.62  3.000
 RR7  O3   C3  C4   112.05  3.000
 RR7  H3   C3  C2   108.51  3.000
 RR7  C4   C3  C2   109.74  3.000
 RR7  O3   C3  C2   108.50  3.000
 RR7  H4   C4  O4   111.17  3.000
 RR7  H4   C4  C5   109.03  3.000
 RR7  O4   C4  C5   111.46  3.000
 RR7  H4   C4  C3   108.11  3.000
 RR7  C5   C4  C3   109.22  3.000
 RR7  O4   C4  C3   107.78  3.000
 RR7  H5   C5  O5   110.07  3.000
 RR7  H5   C5  C6   106.43  3.000
 RR7  O5   C5  C6   108.74  3.000
 RR7  H5   C5  C4   108.09  3.000
 RR7  O5   C5  C4   109.63  3.000
 RR7  C6   C5  C4   113.81  3.000
 RR7  H62  C6  H61  106.44  3.000
 RR7  H62  C6  O6   112.03  3.000
 RR7  H61  C6  O6   111.88  3.000
 RR7  H62  C6  C5   108.11  3.000
 RR7  H61  C6  C5   108.40  3.000
 RR7  O6   C6  C5   109.80  3.000
 RR7  HO1  O1  C1   109.29  3.000
 RR7  HO3  O3  C3   107.71  3.000
 RR7  HO4  O4  C4   109.01  3.000
 RR7  C5   O5  C1   112.75  3.000
 RR7  HO6  O6  C6   108.19  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
 RR7  chir_01  C1  C2  O1  O5  positiv
 RR7  chir_02  C3  O3  C4  C2  negativ
 RR7  chir_03  C4  O4  C5  C3  positiv
 RR7  chir_04  C5  O5  C4  C6  negativ

