PDB file format and double bonds

General Discussion
1

Hello,

can someone shed some light on how the double/triple bond is saved (avogadro1) in a pdb file type? If I save a molecule without hydrogens, I get all single bonds or all tripple bonds. Is this a bug in avogadro 1?

In the following pdb I made 1 CC single, 2, double, 3 tripple and fourth again single bond.

AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C LIG 1 -6.771 0.000 0.000 1.00 0.00 C
ATOM 2 C LIG 1 -5.240 0.000 0.000 1.00 0.00 C
HETATM 3 C LIG 2 -1.337 0.000 0.000 1.00 0.00 C
HETATM 4 C LIG 2 -0.006 0.000 0.000 1.00 0.00 C
HETATM 5 C LIG 3 3.808 0.000 0.000 1.00 0.00 C
HETATM 6 C LIG 3 5.000 0.000 0.000 1.00 0.00 C
HETATM 7 C LIG 4 8.843 0.000 0.000 1.00 0.00 C
HETATM 8 C LIG 4 10.374 0.000 0.000 1.00 0.00 C
CONECT 1 2
CONECT 2 1
CONECT 3 4
CONECT 4 3
CONECT 5 6
CONECT 6 5
CONECT 7 8
CONECT 8 7
MASTER 0 0 0 0 0 0 0 0 8 0 8 0
END

If i want a correct representation I have to manually add bonds, like

AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C LIG 1 -6.771 0.000 0.000 1.00 0.00 C
ATOM 2 C LIG 1 -5.240 0.000 0.000 1.00 0.00 C
HETATM 3 C LIG 2 -1.337 0.000 0.000 1.00 0.00 C
HETATM 4 C LIG 2 -0.006 0.000 0.000 1.00 0.00 C
HETATM 5 C LIG 3 3.808 0.000 0.000 1.00 0.00 C
HETATM 6 C LIG 3 5.000 0.000 0.000 1.00 0.00 C
HETATM 7 C LIG 4 8.843 0.000 0.000 1.00 0.00 C
HETATM 8 C LIG 4 10.374 0.000 0.000 1.00 0.00 C
CONECT 1 2
CONECT 2 1
CONECT 3 4 4
CONECT 4 3
CONECT 5 6 6
CONECT 6 5
CONECT 7 8 8
CONECT 8 7
MASTER 0 0 0 0 0 0 0 0 8 0 8 0
END

Avogadro1! is the only program out there, that does not change data in “remarks, Author and COMPND” fields, which is (to me) very important!

2

The PDB format does not support double and triple bonds. Avogadro (or more accurately the Open Babel library used for reading and writing files) must perceive bond orders when you use the PDB file format.

So no, it’s not a bug. If you want accurate atom typing, I suggest including the hydrogen atoms.

3

Ok, I understand.
Some of the online converters from mol to pdb, do a trick.
To present double bond in PDB, converter saves:

CONECT 1 2

Like

CONECT 1 2 2

And double bond apears. Its fake, but it works.

4

Older versions of Open Babel did this too. However, it’s clearly not valid PDB, and some software chokes on such CONECT records.

My suggestion is to use a different format, if possible - CML, Mol2, etc.