On 16/03/2011 17:41, nms_uk wrote:
The significance of different stereochemistry in biological systems is immense. The drug Thalidomide is a case where one isomer was benign and one a teratogen, with serious consequences for more than 10,000 people.Dear all, I'm using openbabel to compare 2 molfiles. It tells me that the 2 molfiles has different sp3 stereochemistry. When I display the molfiles, they look exactly the same. I have 2 questions: 1- Can 2 molecules with different sp3 stereochemistry be similar (how significant is it for a chemist)?
2- If not, Why do they look the same when displayed?
OpenBabel can display 2D structures: obabel molfile1.mol molfile2.mol -O out.svg The output is attached (view in a browser (not IE)).The parity of the chiral centre with the hash bond is indeed different in the two molecules, as is reported by the k format.
obabel molfile1.mol molfile2.mol -okTo see this, if you look up the hash bond in molfile1, the order of the other attached atoms in a clockwise direction is N C H. The H is not drawn but can be taken to be opposite the hash bond. Doing the same with molfile2, the order is N H C - the opposite parity.
Chris
I draw using http://pubchem.ncbi.nlm.nih.gov/edit2/index.html you can import the molfile and display it. And here are the 2 molfiles: molfile1 25 24 0 0 0 0 0 0 0 0999 V2000 -2.3278 -0.8381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7678 -1.1081 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3178 -0.3281 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7378 -1.1781 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7378 -1.6981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1478 -0.8681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5778 -1.1881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5678 -1.8581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0178 -0.8681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0078 -0.3381 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0078 -2.1981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5622 -1.0881 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.5822 0.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0022 -2.8581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1622 -0.8381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1722 -0.1881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1522 0.4619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5722 -3.1981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7322 -1.1781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7322 -1.6981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7222 0.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5722 -3.8481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3022 -0.8581 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.3022 -0.1981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8722 -1.1781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15 16 1 6 16 13 1 0 16 21 1 0 16 17 1 0 1 2 2 0 1 3 1 0 1 4 1 0 19 15 1 0 19 20 2 0 19 23 1 0 15 12 1 0 18 14 1 0 18 22 1 0 14 11 1 0 11 8 1 0 8 7 1 0 7 6 1 0 7 9 1 0 6 4 1 0 9 12 1 0 9 10 2 0 25 23 1 0 24 23 1 0 5 4 1 0 M END ***************************************************** molfile2 25 24 0 0 0 0 0 0 0 0999 V2000 -3.5724 -0.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8579 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1434 -0.6187 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.4289 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7145 -0.6187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7145 -0.6187 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.4289 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1434 -0.6187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8579 -1.0313 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.1434 0.2062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8579 -1.8563 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.8563 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4289 -1.8563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1434 0.2062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5724 -0.6187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8579 -1.8563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7145 -2.2687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1434 -2.2687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4289 -2.6812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7145 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.6187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.4437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7145 1.8563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7145 2.6812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 2 0 3 2 1 0 4 3 1 0 5 4 1 0 6 5 1 0 7 6 1 0 8 7 1 0 9 8 1 0 10 9 1 0 3 11 1 0 2 12 1 0 6 13 2 0 8 14 1 6 9 15 2 0 10 16 1 0 10 17 1 0 14 18 1 0 14 19 1 0 14 20 1 0 5 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 M END -- View this message in context: http://forums.openbabel.org/openbabel-comparison-sp3-stereochemistry-tp3382484p3382484.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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