# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:20:03 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 2,6-dideoxy-4-O-methyl-beta-D-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@@H](C)O[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
 DRI  DRI  2,6-dideoxy-4-O-methyl-beta-D-arabino-hexopyranose  D-saccharide  25  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 PERFECT
;

data_comp_DRI
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
 DRI  O1   O  OH1   0  -0.653  8.5365   7.6749  -5.0841
 DRI  C1   C  CH1   0   0.286  7.2913   7.7885  -5.6689
 DRI  C5   C  CH1   0   0.001  6.1993   8.7724  -7.5195
 DRI  C2   C  CH2   0  -0.508  6.3224   8.3856  -4.6657
 DRI  C3   C  CH1   0   0.027  4.9723   8.6077  -5.3265
 DRI  O3   O  OH1   0  -0.664  4.1264   9.2536  -4.4055
 DRI  C4   C  CH1   0   0.008  5.1544   9.4280  -6.6042
 DRI  O4   O  O2    0  -0.492  3.9225   9.6992  -7.2391
 DRI  CME  C  CH3   0  -0.423  3.2718   8.6216  -7.8803
 DRI  O5   O  O2    0  -0.496  7.4071   8.6295  -6.7965
 DRI  C6   C  CH3   0  -0.679  6.4910   9.5946  -8.7581
 DRI  HO1  H  HOH1  0   0.457  9.0929   7.1084  -5.6297
 DRI  H1   H  HCH1  0   0.178  6.9115   6.8063  -6.0033
 DRI  H5   H  HCH1  0   0.213  5.8446   7.7744  -7.8254
 DRI  H2   H  HCH2  0   0.238  6.7202   9.3391  -4.3031
 DRI  H22  H  HCH2  0   0.251  6.2150   7.7162  -3.8088
 DRI  H3   H  HCH1  0   0.201  4.5643   7.6204  -5.5970
 DRI  HO3  H  HOH1  0   0.445  3.2940   9.4470  -4.8493
 DRI  H4   H  HCH1  0   0.233  5.5420  10.4136  -6.3167
 DRI  H41  H  HCH3  0   0.216  3.1730   7.7361  -7.2461
 DRI  H42  H  HCH3  0   0.215  3.7698   8.3198  -8.8067
 DRI  H43  H  HCH3  0   0.240  2.2695   8.9633  -8.1359
 DRI  H61  H  HCH3  0   0.237  5.6037   9.6895  -9.3818
 DRI  H62  H  HCH3  0   0.240  7.2662   9.1201  -9.3602
 DRI  H63  H  HCH3  0   0.229  6.8268  10.5986  -8.4938

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
 DRI  O1   C1   single  1.380  0.020  1.380
 DRI  O1   HO1  single  0.850  0.020  0.980
 DRI  C1   C2   single  1.517  0.020  1.517
 DRI  C1   O5   single  1.411  0.020  1.411
 DRI  C1   H1   single  0.970  0.020  1.090
 DRI  C5   C4   single  1.536  0.020  1.536
 DRI  C5   O5   single  1.415  0.020  1.415
 DRI  C5   C6   single  1.515  0.020  1.515
 DRI  C5   H5   single  0.970  0.020  1.090
 DRI  C2   C3   single  1.519  0.020  1.519
 DRI  C2   H2   single  0.970  0.020  1.090
 DRI  C2   H22  single  0.970  0.020  1.090
 DRI  C3   O3   single  1.407  0.020  1.407
 DRI  C3   C4   single  1.529  0.020  1.529
 DRI  C3   H3   single  0.970  0.020  1.090
 DRI  O3   HO3  single  0.850  0.020  0.980
 DRI  C4   O4   single  1.412  0.020  1.412
 DRI  C4   H4   single  0.970  0.020  1.090
 DRI  O4   CME  single  1.413  0.020  1.413
 DRI  CME  H41  single  0.970  0.020  1.090
 DRI  CME  H42  single  0.970  0.020  1.090
 DRI  CME  H43  single  0.970  0.020  1.090
 DRI  C6   H61  single  0.970  0.020  1.090
 DRI  C6   H62  single  0.970  0.020  1.090
 DRI  C6   H63  single  0.970  0.020  1.090

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
 DRI  HO1  O1   C1   109.24  3.000
 DRI  H1   C1   O5   108.42  3.000
 DRI  H1   C1   C2   109.30  3.000
 DRI  O5   C1   C2   110.26  3.000
 DRI  H1   C1   O1   111.41  3.000
 DRI  O5   C1   O1   108.27  3.000
 DRI  C2   C1   O1   109.17  3.000
 DRI  H5   C5   C6   109.05  3.000
 DRI  H5   C5   O5   108.97  3.000
 DRI  C6   C5   O5   107.95  3.000
 DRI  H5   C5   C4   109.44  3.000
 DRI  C6   C5   C4   112.74  3.000
 DRI  O5   C5   C4   108.62  3.000
 DRI  H22  C2   H2   108.03  3.000
 DRI  H22  C2   C3   110.07  3.000
 DRI  H2   C2   C3   109.85  3.000
 DRI  H22  C2   C1   109.90  3.000
 DRI  H2   C2   C1   109.25  3.000
 DRI  C3   C2   C1   109.72  3.000
 DRI  H3   C3   C4   108.64  3.000
 DRI  H3   C3   O3   110.44  3.000
 DRI  C4   C3   O3   111.85  3.000
 DRI  H3   C3   C2   107.74  3.000
 DRI  C4   C3   C2   109.63  3.000
 DRI  O3   C3   C2   108.45  3.000
 DRI  HO3  O3   C3   108.06  3.000
 DRI  H4   C4   O4   104.68  3.000
 DRI  H4   C4   C3   107.76  3.000
 DRI  O4   C4   C3   112.01  3.000
 DRI  H4   C4   C5   107.41  3.000
 DRI  O4   C4   C5   114.05  3.000
 DRI  C3   C4   C5   110.48  3.000
 DRI  CME  O4   C4   117.34  3.000
 DRI  H43  CME  H42  107.85  3.000
 DRI  H43  CME  H41  107.87  3.000
 DRI  H42  CME  H41  107.98  3.000
 DRI  H43  CME  O4   106.92  3.000
 DRI  H42  CME  O4   112.65  3.000
 DRI  H41  CME  O4   113.34  3.000
 DRI  C5   O5   C1   113.47  3.000
 DRI  H63  C6   H62  108.38  3.000
 DRI  H63  C6   H61  108.02  3.000
 DRI  H62  C6   H61  107.52  3.000
 DRI  H63  C6   C5   111.14  3.000
 DRI  H62  C6   C5   110.62  3.000
 DRI  H61  C6   C5   111.03  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DRI  Var_01  H41  CME  O4  C4  50.45  30.0  3

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
 DRI  chir_01  C1  O1  C2  O5  negativ
 DRI  chir_02  C5  O5  C4  C6  negativ
 DRI  chir_03  C3  O3  C2  C4  positiv
 DRI  chir_04  C4  O4  C5  C3  positiv

