Same structures behaving differently in substructural search

User 0e345a0616

10-02-2015 06:13:31

Hello Sir

I am doing sub structural search in jchem but here same structures behaving different.

For eq i have two structures both are same named as Test1.mol and Test2.mol .But when i am doing substructural search ,

Test1.mol is giving no hits whereas

Test2.mol is giving 42 hits.

Don't know why this problem arise. Both are drawn in chem draw. Structures are attached here

Please reply sir


User 0e345a0616

10-02-2015 06:14:34

As per my query the 2nd structure is attached here

ChemAxon 4f0b8a99b5

10-02-2015 19:12:00


thanks for those examples, they both have calculated different mol weights, I will look into it further tomorrow. thanks for patience.

Best regards,


ChemAxon 26d92e5dcd

11-02-2015 12:57:29

Hello Monica,

after investigating the difference in the files themselves, the structures are not identical. The Test1.mol file contains a charge on the structure's functional group and hence, together with implicit hydrogens will give different molecular weights (2 hydrogens difference). 

The charge definition can be seen in the Test1.mol file:

M  CHG  2   6   1   8  -1

More so, as the structures are not equivalent, the search will behave differently for both of them. That is why, one structure will give you hits and the other one will not. You have to decide which molecule you want to take as the correct one and keep that one in the database. 

You can easily see the difference between the 2 molecules, if you right click inside of Marvin and select "Expand Groups". See the attached screenshot.

I hope this explains why the behaviour was different.

Wishing all the best