Hi Sam:
You can define a SMILES string, put that in coot, and it will create
coordinates.
Similarly, within phenix, you can do this with elbow.builder and then optimize
is either with built-in forcefields or with an external QM program. It will
give you a reasonable (usually) cif file that you can then use for refinements
in phenix or refmac.
Do you actually keep ligands of mass destruction on hand in the lab? Cool.
Bill
On Wed, 5 Sep 2007 19:21:45 +0000
U Sam <[EMAIL PROTECTED]> wrote:
Hi,
Thanks for the reply to my earlier query.
I am looking for the coordinates of few organophosphates which can bond
covalently to protein as follows .
1) Para-oxon: O,O-Diethyl-O-para-nitrophenyl phosphate
2) Sarin: 2-(fluoro-methyl-phosphoryl)oxypropane
3) Soman: 3-(fluoro-methyl-phosphoryl)oxy-2,2-dimethyl-butane
4) Tabun: Ethyl N,N-dimethylphosphoramidocyanidate
5) DFP: 2-(fluoro-(1-methylethoxy)phosphoryl)oxypropane
6) VX: O-ethyl-S-[2(diisopropylamino)ethyl] methylphosphonothiolate
I would like to know if anybody know the correct "hiccup' site. I searched
a similar site though google, but I did not find any good hit.
JL Susman and Charles Millard groups did some studies with few of these
organophosphates, but I donot see any complete structure of the
organophosphates in their submitted PDBs.
Appreciate suggestion/notes.
Sam
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