# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:12:09 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)CC[C@H]1OC(C)=O
#
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
 ARI  ARI  '(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate'  D-saccharide  26  12  .  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_ARI
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
 ARI  O1   O  OH1   0  -0.655   8.4987  3.1373   -4.7335
 ARI  C1   C  CH1   0   0.295   9.2570  2.3503   -5.5783
 ARI  C2   C  CH2   0  -0.486   8.5207  2.1625   -6.8908
 ARI  C3   C  CH2   0  -0.490   9.4044  1.4006   -7.8738
 ARI  C4   C  CH1   0   0.015  10.7817  2.0379   -7.9935
 ARI  O4   O  O2    0  -0.462  10.6888  3.3272   -8.6164
 ARI  CME  C  CH3   0  -0.769  10.5522  4.8319  -10.3986
 ARI  CO4  C  C     0   0.566  10.6712  3.4070   -9.9435
 ARI  OC4  O  O     0  -0.450  10.7399  2.4514  -10.6749
 ARI  C5   C  CH1   0   0.016  11.3784  2.2523   -6.6067
 ARI  O5   O  O2    0  -0.496  10.4947  2.9976   -5.7944
 ARI  C6   C  CH3   0  -0.682  12.7245  2.9477   -6.6204
 ARI  HO1  H  HOH1  0   0.456   8.8650  3.0925   -3.8435
 ARI  H1   H  HCH1  0   0.174   9.4580  1.3581   -5.1345
 ARI  H2   H  HCH2  0   0.246   7.5950  1.6105   -6.7171
 ARI  H22  H  HCH2  0   0.236   8.2466  3.1402   -7.2966
 ARI  H3   H  HCH2  0   0.244   9.5492  0.3750   -7.5205
 ARI  H32  H  HCH2  0   0.260   8.9246  1.3212   -8.8502
 ARI  H4   H  HCH1  0   0.260  11.4517  1.3928   -8.5677
 ARI  H41  H  HCH3  0   0.259  10.6252  4.8932  -11.4806
 ARI  H42  H  HCH3  0   0.272   9.5928  5.2467  -10.0859
 ARI  H43  H  HCH3  0   0.268  11.3310  5.4487   -9.9503
 ARI  H5   H  HCH1  0   0.217  11.5138  1.2423   -6.1856
 ARI  H61  H  HCH3  0   0.241  13.1472  2.9815   -5.6164
 ARI  H62  H  HCH3  0   0.232  13.4214  2.4011   -7.2562
 ARI  H63  H  HCH3  0   0.233  12.6509  3.9680   -6.9950

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
 ARI  O1   C1   single  1.381  0.020  1.381
 ARI  O1   HO1  single  0.850  0.020  0.980
 ARI  C1   C2   single  1.517  0.020  1.517
 ARI  C1   O5   single  1.413  0.020  1.413
 ARI  C1   H1   single  0.970  0.020  1.090
 ARI  C2   C3   single  1.526  0.020  1.526
 ARI  C2   H2   single  0.970  0.020  1.090
 ARI  C2   H22  single  0.970  0.020  1.090
 ARI  C3   C4   single  1.522  0.020  1.522
 ARI  C3   H3   single  0.970  0.020  1.090
 ARI  C3   H32  single  0.970  0.020  1.090
 ARI  C4   O4   single  1.435  0.020  1.435
 ARI  C4   C5   single  1.525  0.020  1.525
 ARI  C4   H4   single  0.970  0.020  1.090
 ARI  O4   CO4  single  1.330  0.020  1.330
 ARI  CME  CO4  single  1.501  0.020  1.501
 ARI  CME  H41  single  0.970  0.020  1.090
 ARI  CME  H42  single  0.970  0.020  1.090
 ARI  CME  H43  single  0.970  0.020  1.090
 ARI  CO4  OC4  double  1.205  0.020  1.205
 ARI  C5   O5   single  1.413  0.020  1.413
 ARI  C5   C6   single  1.515  0.020  1.515
 ARI  C5   H5   single  0.970  0.020  1.090
 ARI  C6   H61  single  0.970  0.020  1.090
 ARI  C6   H62  single  0.970  0.020  1.090
 ARI  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
 ARI  HO1  O1   C1   109.25  3.000
 ARI  H1   C1   O5   108.25  3.000
 ARI  H1   C1   C2   108.94  3.000
 ARI  O5   C1   C2   110.46  3.000
 ARI  H1   C1   O1   111.46  3.000
 ARI  O5   C1   O1   108.26  3.000
 ARI  C2   C1   O1   109.47  3.000
 ARI  H22  C2   H2   107.38  3.000
 ARI  H22  C2   C3   110.65  3.000
 ARI  H2   C2   C3   109.94  3.000
 ARI  H22  C2   C1   109.40  3.000
 ARI  H2   C2   C1   109.66  3.000
 ARI  C3   C2   C1   109.77  3.000
 ARI  H32  C3   H3   106.20  3.000
 ARI  H32  C3   C4   110.98  3.000
 ARI  H3   C3   C4   107.34  3.000
 ARI  H32  C3   C2   110.99  3.000
 ARI  H3   C3   C2   109.67  3.000
 ARI  C4   C3   C2   111.45  3.000
 ARI  H4   C4   C5   108.72  3.000
 ARI  H4   C4   O4   109.99  3.000
 ARI  C5   C4   O4   107.09  3.000
 ARI  H4   C4   C3   110.41  3.000
 ARI  C5   C4   C3   109.96  3.000
 ARI  O4   C4   C3   110.59  3.000
 ARI  CO4  O4   C4   119.22  3.000
 ARI  H43  CME  H42  107.18  3.000
 ARI  H43  CME  H41  109.25  3.000
 ARI  H42  CME  H41  108.85  3.000
 ARI  H43  CME  CO4  110.85  3.000
 ARI  H42  CME  CO4  110.12  3.000
 ARI  H41  CME  CO4  110.51  3.000
 ARI  OC4  CO4  CME  124.98  3.000
 ARI  OC4  CO4  O4   123.87  3.000
 ARI  CME  CO4  O4   111.15  3.000
 ARI  H5   C5   C6   108.35  3.000
 ARI  H5   C5   O5   109.90  3.000
 ARI  C6   C5   O5   108.58  3.000
 ARI  H5   C5   C4   105.46  3.000
 ARI  C6   C5   C4   113.83  3.000
 ARI  O5   C5   C4   110.63  3.000
 ARI  C5   O5   C1   113.20  3.000
 ARI  H63  C6   H62  108.19  3.000
 ARI  H63  C6   H61  108.30  3.000
 ARI  H62  C6   H61  107.75  3.000
 ARI  H63  C6   C5   111.90  3.000
 ARI  H62  C6   C5   110.06  3.000
 ARI  H61  C6   C5   110.52  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
 ARI  Var_01  C4   C3   C2   C1  -51.38  30.0  1
 ARI  Var_02  CME  CO4  O4   C4  179.24  30.0  3
 ARI  Var_03  H41  CME  CO4  O4  175.10  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
 ARI  chir_01  C1  O1  C2  O5  negativ
 ARI  chir_02  C4  O4  C5  C3  negativ
 ARI  chir_03  C5  O5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 ARI  plan-1  O4   0.020
 ARI  plan-1  CME  0.020
 ARI  plan-1  CO4  0.020
 ARI  plan-1  OC4  0.020

