How can I find full formula of the ligand in PDB files?

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6.9 years ago

srdjanmasirevic2 ▴ 10

Hello I have many pdb files and I am trying to find full formula of an ligand in each pdb file without considering brackets?

So, I know that under FORMUL I can find a formula with considering brackets.

If the formula is 10(C5 N10 O5 H1) I need this version C50 N100 O50 H10. Or in other way how can I do this calculation for number of files?

pdb • 1.9k views

ADD COMMENT • link updated 4.4 years ago by Biostar 20 • written 6.9 years ago by srdjanmasirevic2 ▴ 10

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For example for ligand ID FGA that I extracted from protein PDB with ID 2MTZ.pdb the formula is FORMUL 2 FGA 6(C5 H9 N O4) and when I searched the same compound in PDBeChem database for same compound under Formula it is written C5 H9 N O4. Which one is correct and how do I know if this compound has 30 carbon atoms or just 5?

ADD REPLY • link 6.9 years ago by srdjanmasirevic2 ▴ 10

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Why do you want to do this ? (as a friendly question)

ADD REPLY • link 6.8 years ago by cdsouthan ★ 1.9k

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