Hi folks
Can anyone help with this?
I must have missed something in the documentation, because I don’t understand
why the .mol and .sdf files downloaded from
https://www.ebi.ac.uk/chebi
seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now
since I solved any small molecule structures, but something around 1.395Å rings
a faint bell).
I need to have ligands that have realistic sizes, and while I’m perfectly at
ease scaling the models to what I think are sensible sizes, I can’t help but
think that this isn’t necessary and I’ve missed something somewhere.
Here’s an example of a molecule that I used this morning -
https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0
contents of downloaded file -
>
> Marvin 01140911122D
>
> 15 15 0 0 0 0 999 V2000
> -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7145 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4992 0.6674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4992 -0.6675 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1.9841 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.4289 -0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0001 1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0001 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.7541 1.4520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.0809 -1.5365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 10 1 2 0 0 0 0
> 1 2 1 0 0 0 0
> 14 2 1 0 0 0 0
> 8 3 1 0 0 0 0
> 4 3 2 0 0 0 0
> 7 4 1 0 0 0 0
> 1 5 1 0 0 0 0
> 5 3 1 0 0 0 0
> 12 5 1 0 0 0 0
> 6 2 1 0 0 0 0
> 6 4 1 0 0 0 0
> 11 6 2 0 0 0 0
> 9 7 1 0 0 0 0
> 13 7 1 0 0 0 0
> 9 8 2 0 0 0 0
> M END
>
Harry
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