# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:17:27 2021
#   Inital geometry file: a 63 line input string
#   Ligand name: 4,6-dideoxy-2,3-di-O-methyl-alpha-D-xylo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1C[C@@H](C)O[C@H](O)[C@@H]1OC
#
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
 RVM  RVM  4,6-dideoxy-2,3-di-O-methyl-alpha-D-xylo-hexopyranose  D-saccharide  28  12  .  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_RVM
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
 RVM  C4   C  CH2   0  -0.479  31.7089  7.3582  38.6478
 RVM  C5   C  CH1   0   0.033  32.2053  6.8878  40.0078
 RVM  O5   O  O2    0  -0.499  31.1338  6.8645  40.9521
 RVM  C6   C  CH3   0  -0.682  33.2754  7.7966  40.5749
 RVM  C3   C  CH1   0   0.059  30.5541  6.4917  38.1693
 RVM  O3   O  O2    0  -0.499  30.0396  6.9902  36.9532
 RVM  C3O  C  CH3   0  -0.407  29.9301  6.0352  35.9258
 RVM  C2   C  CH1   0  -0.014  29.4674  6.4965  39.2333
 RVM  O2   O  O2    0  -0.504  28.4370  5.5928  38.9010
 RVM  C2O  C  CH3   0  -0.403  27.1729  6.1790  38.6938
 RVM  C1   C  CH1   0   0.258  30.0325  6.0975  40.6045
 RVM  H41  H  HCH2  0   0.248  32.5320  7.3163  37.9304
 RVM  H42  H  HCH2  0   0.230  31.3862  8.4031  38.7151
 RVM  H5   H  HCH1  0   0.218  32.6210  5.8781  39.8991
 RVM  H61  H  HCH3  0   0.239  33.6361  7.4336  41.5377
 RVM  H62  H  HCH3  0   0.232  34.1264  7.8388  39.8951
 RVM  H63  H  HCH3  0   0.226  32.8996  8.8128  40.7064
 RVM  H3   H  HCH1  0   0.215  30.9190  5.4641  38.0344
 RVM  H8   H  HCH3  0   0.228  29.4965  6.5317  35.0577
 RVM  H9   H  HCH3  0   0.206  30.9054  5.6290  35.6339
 RVM  H10  H  HCH3  0   0.208  29.2825  5.1974  36.2006
 RVM  H2   H  HCH1  0   0.230  29.0783  7.5206  39.3213
 RVM  H12  H  HCH3  0   0.233  26.4710  5.3761  38.4712
 RVM  H13  H  HCH3  0   0.211  26.8130  6.7122  39.5801
 RVM  H14  H  HCH3  0   0.213  27.1785  6.8762  37.8508
 RVM  H1   H  HCH1  0   0.218  29.2745  6.3038  41.3735
 RVM  O1   O  OH1   0  -0.671  30.4023  4.7451  40.6310
 RVM  HO1  H  HOH1  0   0.452  29.6732  4.2272  40.2703

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
 RVM  C4   C3   single  1.521  0.020  1.521
 RVM  C4   C5   single  1.522  0.020  1.522
 RVM  C5   O5   single  1.428  0.020  1.428
 RVM  C5   C6   single  1.514  0.020  1.514
 RVM  O5   C1   single  1.386  0.020  1.386
 RVM  C3   O3   single  1.411  0.020  1.411
 RVM  C3   C2   single  1.521  0.020  1.521
 RVM  O3   C3O  single  1.407  0.020  1.407
 RVM  C2   O2   single  1.410  0.020  1.410
 RVM  C2   C1   single  1.536  0.020  1.536
 RVM  O2   C2O  single  1.409  0.020  1.409
 RVM  C4   H41  single  0.970  0.020  1.090
 RVM  C4   H42  single  0.970  0.020  1.090
 RVM  C5   H5   single  0.970  0.020  1.090
 RVM  C6   H61  single  0.970  0.020  1.090
 RVM  C6   H62  single  0.970  0.020  1.090
 RVM  C6   H63  single  0.970  0.020  1.090
 RVM  C3   H3   single  0.970  0.020  1.090
 RVM  C3O  H8   single  0.970  0.020  1.090
 RVM  C3O  H9   single  0.970  0.020  1.090
 RVM  C3O  H10  single  0.970  0.020  1.090
 RVM  C2   H2   single  0.970  0.020  1.090
 RVM  C2O  H12  single  0.970  0.020  1.090
 RVM  C2O  H13  single  0.970  0.020  1.090
 RVM  C2O  H14  single  0.970  0.020  1.090
 RVM  C1   H1   single  0.970  0.020  1.090
 RVM  C1   O1   single  1.402  0.020  1.402
 RVM  O1   HO1  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
 RVM  H42  C4   H41  107.38  3.000
 RVM  H42  C4   C3   109.82  3.000
 RVM  H41  C4   C3   110.09  3.000
 RVM  H42  C4   C5   109.63  3.000
 RVM  H41  C4   C5   109.22  3.000
 RVM  C3   C4   C5   110.65  3.000
 RVM  H5   C5   C6   108.76  3.000
 RVM  H5   C5   O5   109.55  3.000
 RVM  C6   C5   O5   107.00  3.000
 RVM  H5   C5   C4   108.63  3.000
 RVM  C6   C5   C4   112.30  3.000
 RVM  O5   C5   C4   110.55  3.000
 RVM  C1   O5   C5   116.05  3.000
 RVM  H63  C6   H62  107.94  3.000
 RVM  H63  C6   H61  108.51  3.000
 RVM  H62  C6   H61  107.78  3.000
 RVM  H63  C6   C5   111.14  3.000
 RVM  H62  C6   C5   109.96  3.000
 RVM  H61  C6   C5   111.38  3.000
 RVM  H3   C3   C2   109.04  3.000
 RVM  H3   C3   O3   110.22  3.000
 RVM  C2   C3   O3   109.95  3.000
 RVM  H3   C3   C4   108.61  3.000
 RVM  C2   C3   C4   108.70  3.000
 RVM  O3   C3   C4   110.28  3.000
 RVM  C3O  O3   C3   114.70  3.000
 RVM  H10  C3O  H9   108.05  3.000
 RVM  H10  C3O  H8   108.26  3.000
 RVM  H9   C3O  H8   108.10  3.000
 RVM  H10  C3O  O3   112.49  3.000
 RVM  H9   C3O  O3   112.13  3.000
 RVM  H8   C3O  O3   107.66  3.000
 RVM  H2   C2   C1   107.51  3.000
 RVM  H2   C2   O2   110.93  3.000
 RVM  C1   C2   O2   108.22  3.000
 RVM  H2   C2   C3   108.18  3.000
 RVM  C1   C2   C3   111.16  3.000
 RVM  O2   C2   C3   110.80  3.000
 RVM  C2O  O2   C2   115.07  3.000
 RVM  H14  C2O  H13  108.36  3.000
 RVM  H14  C2O  H12  108.40  3.000
 RVM  H13  C2O  H12  108.21  3.000
 RVM  H14  C2O  O2   111.96  3.000
 RVM  H13  C2O  O2   112.23  3.000
 RVM  H12  C2O  O2   107.55  3.000
 RVM  O1   C1   H1   110.47  3.000
 RVM  O1   C1   C2   111.38  3.000
 RVM  H1   C1   C2   108.79  3.000
 RVM  O1   C1   O5   108.62  3.000
 RVM  H1   C1   O5   105.58  3.000
 RVM  C2   C1   O5   111.86  3.000
 RVM  HO1  O1   C1   108.15  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
 RVM  Var_01  H8   C3O  O3  C3   178.30  30.0  3
 RVM  Var_02  H12  C2O  O2  C2  -178.61  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
 RVM  chir_01  C5  C4  O5  C6  positiv
 RVM  chir_02  C3  O3  C2  C4  positiv
 RVM  chir_03  C2  O2  C1  C3  negativ
 RVM  chir_04  C1  O5  O1  C2  positiv

