# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 17:58:09 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 2-deoxy-beta-D-erythro-pentofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)C[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
 2DR  2DR  2-deoxy-beta-D-erythro-pentofuranose  D-saccharide  19  9  .  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_2DR
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
 2DR  C2    C  CH2   0  -0.592   1.2551   0.6290  -0.6975
 2DR  C3    C  CR15  0   0.026   0.0797   1.4854  -0.2449
 2DR  C4    C  CR15  0  -0.044  -0.8091   0.4403   0.4195
 2DR  C5    C  CH2   0  -0.151  -1.7200  -0.2565  -0.5750
 2DR  O1    O  OH1   0  -0.665   1.5303  -1.7041  -0.3017
 2DR  O3    O  OH1   0  -0.673   0.4445   2.4270   0.7398
 2DR  O4    O  O     0  -0.507   0.0987  -0.4529   1.0427
 2DR  O5    O  OH1   0  -0.670  -2.4608  -1.2365   0.1106
 2DR  C1    C  CR15  0   0.302   1.3265  -0.4877   0.3440
 2DR  H21C  H  HCH2  0   0.255   1.0514   0.2020  -1.6818
 2DR  H22C  H  HCH2  0   0.270   2.1872   1.1903  -0.7744
 2DR  H3    H  HCR5  0   0.231  -0.4195   1.9720  -1.0919
 2DR  H1    H  HCR5  0   0.209   2.1168  -0.3179   1.0842
 2DR  H4    H  HCR5  0   0.246  -1.4275   0.8911   1.2034
 2DR  HA    H  HOH1  0   0.451   1.1066   3.0127   0.3603
 2DR  H51C  H  HCH2  0   0.200  -2.3721   0.5033  -1.0266
 2DR  H52C  H  HCH2  0   0.198  -1.1292  -0.6933  -1.3908
 2DR  H5    H  HOH1  0   0.455  -3.0383  -1.6723  -0.5222
 2DR  HB    H  HOH1  0   0.456   1.7553  -2.3731   0.3533

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
 2DR  C2  C3    single  1.523  0.020  1.523
 2DR  C2  C1    single  1.529  0.020  1.529
 2DR  C3  C4    single  1.524  0.020  1.524
 2DR  C3  O3    single  1.410  0.020  1.410
 2DR  C4  C5    single  1.518  0.020  1.518
 2DR  C4  O4    single  1.418  0.020  1.418
 2DR  C5  O5    single  1.407  0.020  1.407
 2DR  O1  C1    single  1.392  0.020  1.392
 2DR  O4  C1    single  1.413  0.020  1.413
 2DR  C2  H21C  single  0.970  0.020  1.090
 2DR  C2  H22C  single  0.970  0.020  1.090
 2DR  C3  H3    single  0.970  0.020  1.090
 2DR  C1  H1    single  0.970  0.020  1.090
 2DR  C4  H4    single  0.970  0.020  1.090
 2DR  O3  HA    single  0.850  0.020  0.980
 2DR  C5  H51C  single  0.970  0.020  1.090
 2DR  C5  H52C  single  0.970  0.020  1.090
 2DR  O5  H5    single  0.850  0.020  0.980
 2DR  O1  HB    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
 2DR  H22C  C2  H21C  107.28  3.000
 2DR  H22C  C2  C1    112.58  3.000
 2DR  H21C  C2  C1    109.71  3.000
 2DR  H22C  C2  C3    113.02  3.000
 2DR  H21C  C2  C3    110.10  3.000
 2DR  C1    C2  C3    104.15  3.000
 2DR  H3    C3  O3    111.14  3.000
 2DR  H3    C3  C4    112.04  3.000
 2DR  O3    C3  C4    107.71  3.000
 2DR  H3    C3  C2    111.79  3.000
 2DR  O3    C3  C2    112.53  3.000
 2DR  C4    C3  C2    101.18  3.000
 2DR  H4    C4  O4    107.83  3.000
 2DR  H4    C4  C5    108.60  3.000
 2DR  O4    C4  C5    112.52  3.000
 2DR  H4    C4  C3    111.03  3.000
 2DR  O4    C4  C3    104.49  3.000
 2DR  C5    C4  C3    112.27  3.000
 2DR  H52C  C5  H51C  106.81  3.000
 2DR  H52C  C5  O5    111.61  3.000
 2DR  H51C  C5  O5    111.69  3.000
 2DR  H52C  C5  C4    110.27  3.000
 2DR  H51C  C5  C4    107.94  3.000
 2DR  O5    C5  C4    108.45  3.000
 2DR  HB    O1  C1    109.01  3.000
 2DR  HA    O3  C3    108.00  3.000
 2DR  C1    O4  C4    110.77  3.000
 2DR  H5    O5  C5    108.14  3.000
 2DR  H1    C1  O4    106.78  3.000
 2DR  H1    C1  O1    110.07  3.000
 2DR  O4    C1  O1    112.21  3.000
 2DR  H1    C1  C2    112.38  3.000
 2DR  O4    C1  C2    106.15  3.000
 2DR  O1    C1  C2    109.21  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
 2DR  chir_01  C3  C2  C4  O3  negativ
 2DR  chir_02  C4  O4  C3  C5  negativ
 2DR  chir_03  C1  O4  O1  C2  negativ

