# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:34:23 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{S},6~{S})-3-methoxy-6-methyl-5-[(1~{R})-1-oxidanylethoxy]oxane-2,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@H](O)O[C@@H](C)[C@@H](O[C@H](C)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
 8PK  8PK  (2~{R},3~{S},4~{R},5~{S},6~{S})-3-methoxy-6-methyl-5-[(1~{R})-1-oxidanylethoxy]oxane-2,4-diol  L-saccharide  33  15  .  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_8PK
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
 8PK  O9   O  OH1   0  -0.659   3.6309  -0.0780   0.3929
 8PK  C8   C  CH1   0   0.264   2.6747   0.8609  -0.0098
 8PK  C10  C  CH3   0  -0.710   3.1241   1.6782  -1.2032
 8PK  O4   O  O2    0  -0.503   1.4631   0.2505  -0.3636
 8PK  C4   C  CH1   0  -0.008   0.7219  -0.3347   0.6846
 8PK  C5   C  CH1   0   0.021   0.2406  -1.7179   0.2573
 8PK  C6   C  CH3   0  -0.687   1.3626  -2.6433  -0.1627
 8PK  O5   O  O2    0  -0.503  -0.6580  -1.6152  -0.8424
 8PK  C3   C  CH1   0   0.034  -0.4922   0.5244   1.0193
 8PK  O3   O  OH1   0  -0.668  -0.0586   1.8106   1.3817
 8PK  C2   C  CH1   0  -0.001  -1.4397   0.5636  -0.1748
 8PK  O2   O  O2    0  -0.497  -2.5532   1.3321   0.2001
 8PK  C7   C  CH3   0  -0.406  -3.3449   1.7811  -0.8734
 8PK  C1   C  CH1   0   0.236  -1.8155  -0.8571  -0.6167
 8PK  O1   O  OH1   0  -0.664  -2.6485  -1.4087   0.3509
 8PK  H1   H  HOH1  0   0.446   3.8639  -0.6292  -0.3636
 8PK  H2   H  HCH1  0   0.207   2.5378   1.5108   0.8601
 8PK  H3   H  HCH3  0   0.230   3.2390   1.0505  -2.0900
 8PK  H4   H  HCH3  0   0.237   2.4002   2.4595  -1.4324
 8PK  H5   H  HCH3  0   0.235   4.0812   2.1546  -0.9945
 8PK  H6   H  HCH1  0   0.248   1.3350  -0.4562   1.5869
 8PK  H7   H  HCH1  0   0.220  -0.2725  -2.1604   1.1207
 8PK  H8   H  HCH3  0   0.230   2.1056  -2.7214   0.6311
 8PK  H9   H  HCH3  0   0.238   0.9795  -3.6447  -0.3592
 8PK  H10  H  HCH3  0   0.228   1.8631  -2.2850  -1.0618
 8PK  H11  H  HCH1  0   0.211  -1.0099   0.0403   1.8613
 8PK  H12  H  HOH1  0   0.448  -0.8399   2.3538   1.5299
 8PK  H13  H  HCH1  0   0.227  -0.9163   1.0378  -1.0181
 8PK  H14  H  HCH3  0   0.209  -2.7488   2.3134  -1.6233
 8PK  H15  H  HCH3  0   0.211  -3.8751   0.9660  -1.3758
 8PK  H16  H  HCH3  0   0.239  -4.0875   2.4689  -0.4708
 8PK  H17  H  HCH1  0   0.226  -2.3133  -0.8294  -1.5937
 8PK  H18  H  HOH1  0   0.460  -3.0271  -2.2251   0.0073

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
 8PK  O3   C3   single  1.405  0.020  1.405
 8PK  C7   O2   single  1.407  0.020  1.407
 8PK  C10  C8   single  1.515  0.020  1.515
 8PK  C8   O9   single  1.399  0.020  1.399
 8PK  C8   O4   single  1.402  0.020  1.402
 8PK  O2   C2   single  1.404  0.020  1.404
 8PK  C3   C2   single  1.525  0.020  1.525
 8PK  C3   C4   single  1.525  0.020  1.525
 8PK  C2   C1   single  1.535  0.020  1.535
 8PK  O4   C4   single  1.411  0.020  1.411
 8PK  C4   C5   single  1.526  0.020  1.526
 8PK  C1   O1   single  1.391  0.020  1.391
 8PK  C1   O5   single  1.402  0.020  1.402
 8PK  C5   O5   single  1.424  0.020  1.424
 8PK  C5   C6   single  1.514  0.020  1.514
 8PK  O9   H1   single  0.850  0.020  0.980
 8PK  C8   H2   single  0.970  0.020  1.090
 8PK  C10  H3   single  0.970  0.020  1.090
 8PK  C10  H4   single  0.970  0.020  1.090
 8PK  C10  H5   single  0.970  0.020  1.090
 8PK  C4   H6   single  0.970  0.020  1.090
 8PK  C5   H7   single  0.970  0.020  1.090
 8PK  C6   H8   single  0.970  0.020  1.090
 8PK  C6   H9   single  0.970  0.020  1.090
 8PK  C6   H10  single  0.970  0.020  1.090
 8PK  C3   H11  single  0.970  0.020  1.090
 8PK  O3   H12  single  0.850  0.020  0.980
 8PK  C2   H13  single  0.970  0.020  1.090
 8PK  C7   H14  single  0.970  0.020  1.090
 8PK  C7   H15  single  0.970  0.020  1.090
 8PK  C7   H16  single  0.970  0.020  1.090
 8PK  C1   H17  single  0.970  0.020  1.090
 8PK  O1   H18  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
 8PK  H1   O9   C8   108.83  3.000
 8PK  H2   C8   O4   110.55  3.000
 8PK  H2   C8   C10  110.06  3.000
 8PK  O4   C8   C10  107.01  3.000
 8PK  H2   C8   O9   104.79  3.000
 8PK  O4   C8   O9   111.78  3.000
 8PK  C10  C8   O9   112.71  3.000
 8PK  H5   C10  H4   108.09  3.000
 8PK  H5   C10  H3   108.32  3.000
 8PK  H4   C10  H3   108.13  3.000
 8PK  H5   C10  C8   110.23  3.000
 8PK  H4   C10  C8   110.83  3.000
 8PK  H3   C10  C8   111.15  3.000
 8PK  C4   O4   C8   116.56  3.000
 8PK  H6   C4   C3   109.07  3.000
 8PK  H6   C4   C5   107.82  3.000
 8PK  C3   C4   C5   108.73  3.000
 8PK  H6   C4   O4   111.30  3.000
 8PK  C5   C4   O4   109.50  3.000
 8PK  C3   C4   O4   110.35  3.000
 8PK  H7   C5   O5   109.98  3.000
 8PK  H7   C5   C6   108.56  3.000
 8PK  O5   C5   C6   107.31  3.000
 8PK  H7   C5   C4   107.02  3.000
 8PK  C6   C5   C4   113.46  3.000
 8PK  O5   C5   C4   110.49  3.000
 8PK  H10  C6   H9   108.34  3.000
 8PK  H10  C6   H8   108.14  3.000
 8PK  H9   C6   H8   107.76  3.000
 8PK  H10  C6   C5   111.61  3.000
 8PK  H9   C6   C5   110.55  3.000
 8PK  H8   C6   C5   110.30  3.000
 8PK  C1   O5   C5   115.83  3.000
 8PK  H11  C3   C2   108.56  3.000
 8PK  H11  C3   O3   110.51  3.000
 8PK  C2   C3   O3   111.73  3.000
 8PK  H11  C3   C4   107.14  3.000
 8PK  C2   C3   C4   109.72  3.000
 8PK  O3   C3   C4   109.07  3.000
 8PK  H12  O3   C3   107.80  3.000
 8PK  H13  C2   C1   107.15  3.000
 8PK  H13  C2   O2   110.25  3.000
 8PK  C1   C2   O2   112.92  3.000
 8PK  H13  C2   C3   108.41  3.000
 8PK  C1   C2   C3   110.72  3.000
 8PK  O2   C2   C3   107.33  3.000
 8PK  C7   O2   C2   114.65  3.000
 8PK  H16  C7   H15  108.03  3.000
 8PK  H16  C7   H14  108.48  3.000
 8PK  H15  C7   H14  108.13  3.000
 8PK  H16  C7   O2   107.64  3.000
 8PK  H15  C7   O2   112.64  3.000
 8PK  H14  C7   O2   111.78  3.000
 8PK  H17  C1   O1   110.96  3.000
 8PK  H17  C1   C2   110.13  3.000
 8PK  O1   C1   C2   108.27  3.000
 8PK  H17  C1   O5   104.18  3.000
 8PK  O1   C1   O5   113.08  3.000
 8PK  C2   C1   O5   110.17  3.000
 8PK  H18  O1   C1   108.87  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
 8PK  Var_01  H14  C7  O2  C2  -53.42  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
 8PK  chir_01  C8  C10  O9  O4  positiv
 8PK  chir_02  C4  O4   C3  C5  negativ
 8PK  chir_03  C5  O5   C4  C6  positiv
 8PK  chir_04  C3  O3   C4  C2  positiv
 8PK  chir_05  C2  O2   C3  C1  negativ
 8PK  chir_06  C1  O5   O1  C2  negativ

