[Chimera-users] Information regarding double bonds

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 18 08:30:04 PST 2022 

Hi Naima
I don't use Maestro, but it looks like the 2D diagram is showing the neutral form of the compound.  My guess is that there is not any problem, because the 3D structures are the same compound -- the hydrogens are different simply because the 3D structures are in a more reasonable protonation state for the pH in biological systems, with negatively charged phosphate groups.  The 2D diagram is probably just meant to show what compound you have, not to suggest which protonation state should be used. 
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 18, 2022, at 7:47 AM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> Thank you so much. I have just one concern that in 2D diagram it is showing phosphate group having 3 OHs while in my result.pdbqt and igp.mol does not have any hydrogen in phosphate end so is maestro reading it wrong or is there any problem in my files.
> 
> Thank you
> 
> 
> On Thursday, November 17, 2022 at 05:05:45 PM EST, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 
> Hi Naima,
> I don't understand which hydrogen(s) in which file you think are wrong.  The 3D structure of igp.mol2 including the hydrogens looks correct to me,  and it is the same compound as shown in your 2D chemical diagram except corrected to a reasonable protonation state (negative phosphate group, etc.).  Chemical diagrams like that do not show all the hydrogens on carbon atoms; they are simplified to make the diagram easier to understand.  However, you would not expect the real compound to only have the atoms shown in the diagram -- in other words, there is no compound that would just have those carbons without any hydrogens on them.
> 
> If you mean the pdbqt file, that is created by the autodock prep script and does not have hydrogens on the carbons because they are not needed by the docking method.  The real compound would have hydrogens on those carbons.
> Best,
> Elaine
> 
> > On Nov 17, 2022, at 1:46 PM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hello, I tried it but still the results are same. I will share my file and let me know where i am wrong. Even, i attached the file of maestro where it is showing hydrogen which is not present in my file.
> > 
> > 
> > 
> > On Monday, November 14, 2022 at 05:13:37 PM EST, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 
> > 
> > Hi Naima,
> > Probably the bond was abnormally long for a double bond and Chimera guessed it was a single bond (since it does not use bond-order information from the input file, only the atomic coordinates).
> > 
> > If you want to add hydrogens/charges in Chimera (e.g. if you want to use dock prep), then how to fix this is to:
> > (1) remove hydrogens from that molecule
> > (2) check the atom types on the end of the bond and change them to the correct atom type (e.g. from sp3 carbon which is type C3, to sp2 carbon which is type C2)
> > (3) then re-run dock prep
> > 
> > More details on each step:
> > (1) How to delete hydrogens from that molecule.  I don't know what model number or residue name this molecule has, so it is difficult to be specific.  If it were model #2.53, for example, you could use command 
> > 
> > delete H & #2.53
> > 
> > Or you could select just that molecule and then use command
> > 
> > delete H & sel
> > 
> > (2) You would probably want to show atom types as labels so you can see which ones are wrong.  If you have that molecule selected, for example, menu:  Actions... Label... IDATM type
> > 
> > Here is the explanation of the types so you can figure out which ones are wrong (presumably they are the ones next to the bond).
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>
> > 
> > If the ones next to the bond are C3 and C3, for example, you would need to change them to C2 and C2 instead.  If you select one atom you can change its type to C2 with command like
> > 
> > setattr a idatmType C2 sel
> > 
> > Then select the atom on the other side of the bond and repeat, or if it's N3 you may need to change to N2, if O3 change to O2, etc.  You would need to use menu: Actions... Label... IDATM type again to see the changes, as the labels will not update automatically.
> > 
> > (3) when the atom types are changed to what you want then you can re-run dock prep.
> > 
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.                      
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > 
> > 
> > 
> > > On Nov 14, 2022, at 1:55 PM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > > 
> > > Actually, I checked from 2 other softwares and when I checked via maestro it should they have hydrogen instead of double bond which initially was not present in my docked file
> > > 
> > > On Monday, November 14, 2022 at 04:15:10 PM EST, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > > 
> > > 
> > > How do you know it was lost?  Is it from the number of hydrogens added by dock prep? 
> > > Elaine
> > > 
> > > 
> > > > On Nov 14, 2022, at 1:10 PM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > > > 
> > > > Hello, 
> > > > 
> > > > Yes, but my question is that I know I have a double bond and I confirmed this double bond from PyMol software but after docking this was removed. Can you please tell me the reason. Actually when I just do dock prep, double bond was lost.
> > > > 
> > > > On Monday, November 14, 2022 at 04:04:35 PM EST, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > > > 
> > > > 
> > > > Hi Naima,
> > > > Chimera does not display double bonds with two lines, if that is what you mean.  I.e. it will be shown with one line or stick, but that does not mean it is a single bond unless you can somehow tell from other information such as number of added hydrogens.
> > > > I hope this helps,
> > > > Elaine
> > > > -----
> > > > Elaine C. Meng, Ph.D.                      
> > > > UCSF Chimera(X) team
> > > > Department of Pharmaceutical Chemistry
> > > > University of California, San Francisco
> > > > 
> > > > 
> > > > > On Nov 14, 2022, at 12:30 PM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > > > > 
> > > > > Hello,
> > > > > 
> > > > > I have one concern, before docking there is a double bond which i can check in pymol but after docking that double bond was lost. Can you please tell me how to fix this problem. 
> > > > > 
> > > > > Thank you
> > > 
> > > > 
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> > <3t44.mol2><igp.mol2><Result.pdbqt><2.pdb><Untitled.png>_______________________________________________
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