# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 13:37:17 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (2~{R},3~{S},4~{R})-2-(hydroxymethyl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OCC[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
 7D1  7D1  (2~{R},3~{S},4~{R})-2-(hydroxymethyl)oxane-3,4-diol  D-saccharide  22  10  .  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_7D1
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
 7D1  O4   O  OH1   0  -0.676   0.3648   2.1054   0.2241
 7D1  C4   C  CH1   0   0.033   0.4300   0.7891  -0.2706
 7D1  C5   C  CH1   0  -0.001  -0.8301   0.0457   0.1851
 7D1  C6   C  CH2   0  -0.159  -2.0881   0.6754  -0.3768
 7D1  O6   O  OH1   0  -0.672  -3.2077   0.0280   0.1808
 7D1  C3   C  CH1   0   0.022   1.6700   0.0625   0.2348
 7D1  O3   O  OH1   0  -0.676   2.7938   0.7464  -0.2799
 7D1  C2   C  CH2   0  -0.495   1.6227  -1.3998  -0.1845
 7D1  C1   C  CH2   0  -0.194   0.3099  -2.0136   0.2692
 7D1  O5   O  O2    0  -0.487  -0.7913  -1.2959  -0.2444
 7D1  H1   H  HOH1  0   0.451   1.1820   2.5517  -0.0212
 7D1  H2   H  HCH1  0   0.202   0.4546   0.7795  -1.3734
 7D1  H3   H  HCH1  0   0.209  -0.8738   0.0907   1.2872
 7D1  H4   H  HCH2  0   0.210  -2.0820   1.7441  -0.1397
 7D1  H5   H  HCH2  0   0.194  -2.0700   0.5880  -1.4723
 7D1  H6   H  HOH1  0   0.455  -3.9978   0.4615  -0.1535
 7D1  H7   H  HCH1  0   0.206   1.6611   0.1136   1.3344
 7D1  H8   H  HOH1  0   0.456   3.5710   0.4728   0.2163
 7D1  H9   H  HCH2  0   0.233   1.7164  -1.4775  -1.2720
 7D1  H10  H  HCH2  0   0.243   2.4583  -1.9508   0.2553
 7D1  H11  H  HCH2  0   0.243   0.2138  -3.0399  -0.0874
 7D1  H12  H  HCH2  0   0.203   0.2711  -2.0419   1.3678

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
 7D1  C6  O6   single  1.408  0.020  1.408
 7D1  C6  C5   single  1.515  0.020  1.515
 7D1  C5  O5   single  1.409  0.020  1.409
 7D1  C5  C4   single  1.532  0.020  1.532
 7D1  O5  C1   single  1.411  0.020  1.411
 7D1  C1  C2   single  1.519  0.020  1.519
 7D1  O4  C4   single  1.408  0.020  1.408
 7D1  C4  C3   single  1.524  0.020  1.524
 7D1  C3  C2   single  1.522  0.020  1.522
 7D1  C3  O3   single  1.413  0.020  1.413
 7D1  O4  H1   single  0.850  0.020  0.980
 7D1  C4  H2   single  0.970  0.020  1.090
 7D1  C5  H3   single  0.970  0.020  1.090
 7D1  C6  H4   single  0.970  0.020  1.090
 7D1  C6  H5   single  0.970  0.020  1.090
 7D1  O6  H6   single  0.850  0.020  0.980
 7D1  C3  H7   single  0.970  0.020  1.090
 7D1  O3  H8   single  0.850  0.020  0.980
 7D1  C2  H9   single  0.970  0.020  1.090
 7D1  C2  H10  single  0.970  0.020  1.090
 7D1  C1  H11  single  0.970  0.020  1.090
 7D1  C1  H12  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
 7D1  H1   O4  C4   107.73  3.000
 7D1  H2   C4  C3   108.02  3.000
 7D1  H2   C4  C5   108.14  3.000
 7D1  C3   C4  C5   109.83  3.000
 7D1  H2   C4  O4   111.13  3.000
 7D1  C3   C4  O4   111.53  3.000
 7D1  C5   C4  O4   108.12  3.000
 7D1  H3   C5  O5   110.13  3.000
 7D1  H3   C5  C6   108.69  3.000
 7D1  O5   C5  C6   107.80  3.000
 7D1  H3   C5  C4   108.04  3.000
 7D1  O5   C5  C4   110.40  3.000
 7D1  C6   C5  C4   111.77  3.000
 7D1  H5   C6  H4   107.06  3.000
 7D1  H5   C6  O6   111.79  3.000
 7D1  H4   C6  O6   111.56  3.000
 7D1  H5   C6  C5   108.84  3.000
 7D1  H4   C6  C5   108.71  3.000
 7D1  O6   C6  C5   108.80  3.000
 7D1  H6   O6  C6   107.97  3.000
 7D1  H7   C3  C2   108.64  3.000
 7D1  H7   C3  O3   110.36  3.000
 7D1  C2   C3  O3   112.92  3.000
 7D1  H7   C3  C4   107.62  3.000
 7D1  O3   C3  C4   107.20  3.000
 7D1  C2   C3  C4   109.97  3.000
 7D1  H8   O3  C3   108.49  3.000
 7D1  H10  C2  H9   107.37  3.000
 7D1  H10  C2  C1   109.68  3.000
 7D1  H9   C2  C1   110.01  3.000
 7D1  H10  C2  C3   110.47  3.000
 7D1  H9   C2  C3   109.84  3.000
 7D1  C1   C2  C3   109.45  3.000
 7D1  H12  C1  H11  107.41  3.000
 7D1  H12  C1  O5   110.43  3.000
 7D1  H11  C1  O5   106.91  3.000
 7D1  H12  C1  C2   109.84  3.000
 7D1  H11  C1  C2   111.03  3.000
 7D1  O5   C1  C2   111.12  3.000
 7D1  C1   O5  C5   113.25  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
 7D1  Var_01  C2  C1  O5  C5  -61.25  30.0  1
 7D1  Var_02  O5  C1  C2  C3   56.61  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
 7D1  chir_01  C4  C5  O4  C3  negativ
 7D1  chir_02  C5  O5  C6  C4  positiv
 7D1  chir_03  C3  O3  C4  C2  negativ

