I have a molecule with the following SMILES:
ClearAll[sml];
sml = "O=C(NCC1=CC(NC(C2=CN=C3C=CC=CN23)=O)=C(C)C=C1)NC4=CC=CC(F)=C4";
The plot looks as follows:
sml // RightComposition[
Molecule[#, IncludeHydrogens -> True] &,
MoleculePlot[#, ImageSize -> Large] &
]
In particular, please note the presence of aromatic bonds.
Now, following the export example at the bottom of the page for PDB files in the help manual, I attempt to export the molecule to a PDB file:
ClearAll[coords, atoms];
{coords, atoms} = sml // RightComposition[
Molecule[#, IncludeHydrogens -> True] &,
{MoleculeValue[#, "AtomCoordinates"] &, AtomList /* Map[First]}, Through
];
Export[
FileNameJoin[{NotebookDirectory[], "mol.pdb"}],
{{QuantityMagnitude[UnitConvert[coords, "Picometers"]]}, {atoms}},
{{"AdditionalCoordinates", "AdditionalAtoms"}}
];
The export happens correctly (or at least so it appears), and I get a PDB file.
But when I load the PDB file, I find that the molecule has lost its aromatic bonds:
"mol.pdb" // RightComposition[
Import[FileNameJoin[{NotebookDirectory[], #}], {"PDB", "Molecule"}] &,
MoleculePlot[#, ImageSize -> Large] &
]
In addition, the oxygen atoms appear to have lost their double bonds as well.
What am I doing incorrectly?
Thanks in advance for your help.