# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:38:36 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC[C@@H](O)[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
 AH2  AH2  (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)oxane-3,4,5-triol  D-saccharide  23  11  .  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_AH2
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
 AH2  O3   O  OH1   0  -0.673  -2.4502  -1.2518  -0.0611
 AH2  C4   C  CH1   0   0.026  -0.1106  -0.9351  -0.2170
 AH2  C5   C  CH1   0  -0.001   1.0604  -0.0689   0.2593
 AH2  O4   O  OH1   0  -0.676   0.1762  -2.2708   0.1287
 AH2  C6   C  CH2   0  -0.157   2.3426  -0.4143  -0.4688
 AH2  O5   O  O2    0  -0.483   0.7910   1.2959   0.0338
 AH2  O6   O  OH1   0  -0.672   3.4021   0.3153   0.1040
 AH2  C3   C  CH1   0   0.010  -1.4014  -0.4628   0.4459
 AH2  C2   C  CH1   0  -0.014  -1.6096   1.0322   0.2290
 AH2  O2   O  OH1   0  -0.668  -1.8656   1.2526  -1.1373
 AH2  C1   C  CH2   0  -0.229  -0.3569   1.7535   0.7069
 AH2  H32  H  HOH1  0   0.456  -3.2224  -1.1383   0.5015
 AH2  H41  H  HCH1  0   0.211  -0.2088  -0.8247  -1.3073
 AH2  H5   H  HCH1  0   0.209   1.2002  -0.2522   1.3388
 AH2  H42  H  HOH1  0   0.452  -0.5636  -2.8160  -0.1582
 AH2  H61  H  HCH2  0   0.210   2.5072  -1.4941  -0.3937
 AH2  H62  H  HCH2  0   0.195   2.2152  -0.1815  -1.5352
 AH2  H63  H  HOH1  0   0.456   4.2101   0.0766  -0.3583
 AH2  H31  H  HCH1  0   0.215  -1.2879  -0.6139   1.5304
 AH2  H21  H  HCH1  0   0.222  -2.4521   1.3702   0.8523
 AH2  H22  H  HOH1  0   0.452  -1.9888   2.1971  -1.2745
 AH2  H12  H  HCH2  0   0.209  -0.2579   1.6234   1.7948
 AH2  H11  H  HCH2  0   0.250  -0.4333   2.8268   0.5172

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
 AH2  C1  O5   single  1.407  0.020  1.407
 AH2  C1  C2   single  1.522  0.020  1.522
 AH2  O5  C5   single  1.409  0.020  1.409
 AH2  C2  C3   single  1.525  0.020  1.525
 AH2  C2  O2   single  1.407  0.020  1.407
 AH2  C5  C6   single  1.514  0.020  1.514
 AH2  C5  C4   single  1.533  0.020  1.533
 AH2  C3  C4   single  1.526  0.020  1.526
 AH2  C3  O3   single  1.407  0.020  1.407
 AH2  C6  O6   single  1.408  0.020  1.408
 AH2  C4  O4   single  1.409  0.020  1.409
 AH2  O3  H32  single  0.850  0.020  0.980
 AH2  C4  H41  single  0.970  0.020  1.090
 AH2  C5  H5   single  0.970  0.020  1.090
 AH2  O4  H42  single  0.850  0.020  0.980
 AH2  C6  H61  single  0.970  0.020  1.090
 AH2  C6  H62  single  0.970  0.020  1.090
 AH2  O6  H63  single  0.850  0.020  0.980
 AH2  C3  H31  single  0.970  0.020  1.090
 AH2  C2  H21  single  0.970  0.020  1.090
 AH2  O2  H22  single  0.850  0.020  0.980
 AH2  C1  H12  single  0.970  0.020  1.090
 AH2  C1  H11  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
 AH2  H32  O3  C3   108.75  3.000
 AH2  H41  C4  C3   108.90  3.000
 AH2  H41  C4  O4   110.88  3.000
 AH2  C3   C4  O4   111.04  3.000
 AH2  H41  C4  C5   108.63  3.000
 AH2  O4   C4  C5   107.70  3.000
 AH2  C3   C4  C5   109.66  3.000
 AH2  H5   C5  O5   109.96  3.000
 AH2  H5   C5  C6   108.97  3.000
 AH2  O5   C5  C6   107.81  3.000
 AH2  H5   C5  C4   107.87  3.000
 AH2  C6   C5  C4   111.63  3.000
 AH2  O5   C5  C4   110.59  3.000
 AH2  H42  O4  C4   107.89  3.000
 AH2  H62  C6  H61  107.03  3.000
 AH2  H62  C6  O6   111.85  3.000
 AH2  H61  C6  O6   111.71  3.000
 AH2  H62  C6  C5   108.67  3.000
 AH2  H61  C6  C5   108.62  3.000
 AH2  O6   C6  C5   108.86  3.000
 AH2  C1   O5  C5   113.23  3.000
 AH2  H63  O6  C6   107.95  3.000
 AH2  H31  C3  C2   106.78  3.000
 AH2  H31  C3  C4   107.35  3.000
 AH2  C2   C3  C4   110.92  3.000
 AH2  H31  C3  O3   110.78  3.000
 AH2  C4   C3  O3   107.48  3.000
 AH2  C2   C3  O3   113.38  3.000
 AH2  H21  C2  C1   107.85  3.000
 AH2  H21  C2  O2   111.24  3.000
 AH2  C1   C2  O2   112.35  3.000
 AH2  H21  C2  C3   108.96  3.000
 AH2  O2   C2  C3   108.44  3.000
 AH2  C1   C2  C3   107.91  3.000
 AH2  H22  O2  C2   108.38  3.000
 AH2  H11  C1  H12  107.11  3.000
 AH2  H11  C1  C2   110.69  3.000
 AH2  H12  C1  C2   109.17  3.000
 AH2  H11  C1  O5   107.07  3.000
 AH2  H12  C1  O5   111.17  3.000
 AH2  C2   C1  O5   111.53  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
 AH2  Var_01  C2  C1  O5  C5  -62.40  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
 AH2  chir_01  C4  C5  C3  O4  positiv
 AH2  chir_02  C5  O5  C4  C6  negativ
 AH2  chir_03  C3  O3  C4  C2  negativ
 AH2  chir_04  C2  O2  C3  C1  negativ

