A question about conversion from SDF into PDB

[langren-2]

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Dear there,
I am currently working on molecular docking of a particular ligand, phenethyl isothiocyanate. The SDF file can be found in  ChemBank, and what I need to do is simply to change the file into PDB file. But when the conversion was done, I found all the double bonds (in benzole or S=C=N-) were missing. I have no idea what is going on, and how should I deal with that.
Thanks in advance.
 
The SDF code is shown below
 
1049672
  SMI2MOL
 11 11  0  0  0  0  0  0  0  0999 V2000
   -3.0700    2.5700    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1900    2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3100    1.5500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4300    2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4500    1.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3300    2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1800    1.5300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0600    2.0400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0700    3.0500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2000    3.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3300    3.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6 11  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <ChembankId>
1049672
> <SMILES>
S=C=NCCc1ccccc1
> <InChI>
1/C9H9NS/c11-8-10-7-6-9-4-2-1-3-5-9/h1-5H,6-7H2
$$$$

 
 

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[baoilleach]

Hello langren,

Please attach the SDF in your email to the mailing list. Please also
attach the resulting PDB file, and explain what the correct PDB file
should contain.

This will help us find the problem.

Regards,
   Noel

2009/10/12 langren <langren0101@...>:

> Dear there,
> I am currently working on molecular docking of a particular ligand,
> phenethyl isothiocyanate. The SDF file can be found in  ChemBank, and what I
> need to do is simply to change the file into PDB file. But when
> the conversion was done, I found all the double bonds (in benzole or S=C=N-)
> were missing. I have no idea what is going on, and how should I deal with
> that.
> Thanks in advance.
>
> The SDF code is shown below
>
> 1049672
>   SMI2MOL
>  11 11  0  0  0  0  0  0  0  0999 V2000
>    -3.0700    2.5700    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
>    -2.1900    2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -1.3100    1.5500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
>    -0.4300    2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     0.4500    1.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     1.3300    2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     2.1800    1.5300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     3.0600    2.0400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     3.0700    3.0500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     2.2000    3.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     1.3300    3.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  2  0  0  0  0
>   2  3  2  0  0  0  0
>   3  4  1  0  0  0  0
>   4  5  1  0  0  0  0
>   5  6  1  0  0  0  0
>   6 11  2  0  0  0  0
>   6  7  1  0  0  0  0
>   7  8  2  0  0  0  0
>   8  9  1  0  0  0  0
>   9 10  2  0  0  0  0
>  10 11  1  0  0  0  0
> M  END
>> <ChembankId>
> 1049672
>> <SMILES>
> S=C=NCCc1ccccc1
>> <InChI>
> 1/C9H9NS/c11-8-10-7-6-9-4-2-1-3-5-9/h1-5H,6-7H2
> $$$$
>
>
>
>
> ________________________________
> 聊天+搜索+邮箱 想要轻松出游,手机MSN帮你搞定! 立刻下载！
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

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Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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_______________________________________________
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