# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:48:36 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: (2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)CC[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
 CDR  CDR  (2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol  D-saccharide  21  9  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CDR
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
 CDR  O1   O  OH1   0  -0.656   8.3665  -2.6068  3.7152
 CDR  C1   C  CH1   0   0.298   7.7905  -2.4724  4.9645
 CDR  C2   C  CH2   0  -0.490   7.0836  -3.7608  5.3375
 CDR  C3   C  CH2   0  -0.485   6.5573  -3.6669  6.7641
 CDR  C4   C  CH1   0   0.058   7.6593  -3.2505  7.7248
 CDR  O4   O  OH1   0  -0.668   7.0782  -3.0562  8.9947
 CDR  C5   C  CH1   0   0.021   8.3422  -1.9751  7.2099
 CDR  O5   O  O2    0  -0.500   8.8155  -2.1896  5.8932
 CDR  C6   C  CH3   0  -0.697   9.5224  -1.5449  8.0580
 CDR  HO1  H  HOH1  0   0.455   8.6376  -1.7394  3.3956
 CDR  H1   H  HCH1  0   0.171   7.0625  -1.6411  4.9840
 CDR  H2   H  HCH2  0   0.244   6.2628  -3.9485  4.6423
 CDR  H22  H  HCH2  0   0.231   7.7871  -4.5943  5.2455
 CDR  H3   H  HCH2  0   0.225   5.7498  -2.9273  6.8108
 CDR  H32  H  HCH2  0   0.247   6.1291  -4.6223  7.0742
 CDR  H4   H  HCH1  0   0.197   8.4198  -4.0465  7.7588
 CDR  HO4  H  HOH1  0   0.450   7.7779  -3.0119  9.6530
 CDR  H5   H  HCH1  0   0.199   7.5888  -1.1688  7.2109
 CDR  H61  H  HCH3  0   0.243   9.9966  -0.6558  7.6413
 CDR  H62  H  HCH3  0   0.229   9.2052  -1.2933  9.0699
 CDR  H63  H  HCH3  0   0.228  10.2737  -2.3346  8.1233

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
 CDR  O1  C1   single  1.382  0.020  1.382
 CDR  O1  HO1  single  0.850  0.020  0.980
 CDR  C1  C2   single  1.516  0.020  1.516
 CDR  C1  O5   single  1.412  0.020  1.412
 CDR  C1  H1   single  0.970  0.020  1.090
 CDR  C2  C3   single  1.523  0.020  1.523
 CDR  C2  H2   single  0.970  0.020  1.090
 CDR  C2  H22  single  0.970  0.020  1.090
 CDR  C3  C4   single  1.520  0.020  1.520
 CDR  C3  H3   single  0.970  0.020  1.090
 CDR  C3  H32  single  0.970  0.020  1.090
 CDR  C4  O4   single  1.410  0.020  1.410
 CDR  C4  C5   single  1.536  0.020  1.536
 CDR  C4  H4   single  0.970  0.020  1.090
 CDR  O4  HO4  single  0.850  0.020  0.980
 CDR  C5  O5   single  1.415  0.020  1.415
 CDR  C5  C6   single  1.516  0.020  1.516
 CDR  C5  H5   single  0.970  0.020  1.090
 CDR  C6  H61  single  0.970  0.020  1.090
 CDR  C6  H62  single  0.970  0.020  1.090
 CDR  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
 CDR  HO1  O1  C1   109.25  3.000
 CDR  H1   C1  O5   108.41  3.000
 CDR  H1   C1  C2   109.13  3.000
 CDR  O5   C1  C2   110.30  3.000
 CDR  H1   C1  O1   111.32  3.000
 CDR  O5   C1  O1   108.15  3.000
 CDR  C2   C1  O1   109.52  3.000
 CDR  H22  C2  H2   107.38  3.000
 CDR  H22  C2  C3   110.35  3.000
 CDR  H2   C2  C3   110.31  3.000
 CDR  H22  C2  C1   109.07  3.000
 CDR  H2   C2  C1   109.87  3.000
 CDR  C3   C2  C1   109.82  3.000
 CDR  H32  C3  H3   106.82  3.000
 CDR  H32  C3  C4   110.15  3.000
 CDR  H3   C3  C4   108.80  3.000
 CDR  H32  C3  C2   110.33  3.000
 CDR  H3   C3  C2   109.63  3.000
 CDR  C4   C3  C2   111.00  3.000
 CDR  H4   C4  C5   107.67  3.000
 CDR  H4   C4  O4   110.88  3.000
 CDR  C5   C4  O4   111.77  3.000
 CDR  H4   C4  C3   108.79  3.000
 CDR  C5   C4  C3   109.75  3.000
 CDR  O4   C4  C3   107.95  3.000
 CDR  HO4  O4  C4   108.85  3.000
 CDR  H5   C5  C6   108.88  3.000
 CDR  H5   C5  O5   109.87  3.000
 CDR  C6   C5  O5   107.64  3.000
 CDR  H5   C5  C4   107.63  3.000
 CDR  C6   C5  C4   113.23  3.000
 CDR  O5   C5  C4   109.56  3.000
 CDR  C5   O5  C1   113.54  3.000
 CDR  H63  C6  H62  108.16  3.000
 CDR  H63  C6  H61  108.26  3.000
 CDR  H62  C6  H61  107.04  3.000
 CDR  H63  C6  C5   111.34  3.000
 CDR  H62  C6  C5   111.00  3.000
 CDR  H61  C6  C5   110.87  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
 CDR  Var_01  C4  C3  C2  C1  -52.33  30.0  1

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
 CDR  chir_01  C1  O1  C2  O5  negativ
 CDR  chir_02  C4  O4  C5  C3  positiv
 CDR  chir_03  C5  O5  C4  C6  negativ

