Small molecule files are usually obtained as .sdf (PubChem, ZINC databases etc.) which can be converted to pdb file using OpenBabel software.

If 3D structure not available, Load the 2D structure in Avogadro software which will generate the 3D for the same.

Regards

PDB files are not meant for inorganic molecules.

"I am starting to learn computational chemistry..."

>> Nice that you are learning, therefore please focus and go through your course material and discuss your doubts with teachers, instead of asking them here.

Most of the classical coordinate files are plain text formats, that is, you can open them with a text editor to look at their content. Small molecule file formats like .sdf, .mol and .mol2 format contain not only the coordinates, but also information about the connectivity. They describe not only the identity and position of each atom in space but also which atom is bonded to which.

Caution: The .sdf format can be used for both 2D data and 3D data, do not mix up the two!!!

see: https://lifechemicals.com/order-and-supply/how-to-work-with-sd-files

and https://www.fda.gov/media/151718/download

https://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx

You can generate a 2D .sdf file by drawing the covalent structure of your molecule. These can be converted to a 3D structure by regularising the bond angles and lengths, and energy minimisation of the resulting structure: See https://chemoinfo.ipmc.cnrs.fr/LEA3D/drawonline.html for one online tool to do so

The .pdb format is a very old format that was defined for macromolecular structures at a time when computer memory was extremely restricted and expensive. It therefore took advantage of the fact that proteins and nucleic acids are made of a very limited repertoire of building blocks. The general properties of these building blocks , amino acids and nucleotides are not stored in the file itself, but encoded in a dictionary embedded in the interpreting program. Connectivity is deduced from interatomic distances. When working with complexes of proteins and small molecules, e.g. in molecular dynamics, you may have to provide the properties of these non-standard molecules in the form of additional forecefield and parameter files to augment the internal dictionary of the programs by the descriptions for these non-standard components

Check here for the definition of the .pdb format:

https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction

https://www.wwpdb.org/documentation/file-format

More recently, the protein databank is using an XML (extendable markup language format) format: PDBx/mmCIF format to allow the inclusion of additional data in a more controlled, machine-parsable fashion than the header of the original pdb files allowed. see:

https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner’s-guide-to-pdb-structures-and-the-pdbx-mmcif-format

You can find PDB files for small inorganic molecules such as nitric acid in a few different databases:

I hope this helps!

Hello

For any molecule you can find the sdf or mol format in pubchem or other chemical databases. You need to convert that file in your required format using some tools. You can use Open Babel tool.