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Datawarrior Protonates the Oxygen in a Phosphorous Oxygen Double Bond. [message #568]

Wed, 22 May 2019 16:55

SMolnar
Messages: 2
Registered: January 2018
Location: United States

Junior Member

I have a series of organophosphorous compounds containing a Phosphorous-Oxygen double bond (pentavalent phosphorous). When I import the sdf file into Datawarrior (v-5.0.0) the the P=O bond is converted to a P-OH bond.

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Re: Datawarrior Protonates the Oxygen in a Phosphorous Oxygen Double Bond. [message #571 is a reply to message #568]

Tue, 28 May 2019 11:02

thomas
Messages: 715
Registered: June 2014

Senior Member

I tried with the following sdf example, which works fine. Can you send me an sdf record that does not work? Thanks in advance, Thomas
---------------------

Actelion Java MolfileCreator 1.0

7 6 0 0 0 0 0 0 0 0999 V2000
3.7717 -5.8584 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0579 -6.6301 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3442 -5.8584 -0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
7.6304 -6.6301 -0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.9166 -5.8584 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3442 -4.3584 -0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.6495 -5.1193 -0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
3 6 2 0 0 0 0
3 7 1 0 0 0 0
M END
$$$$

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