[Ambit-users] Fwd: Issues with my SMIRKS reaction

---------- Forwarded message ----------
From: Yannick .Djoumbou <y.d...@gm...>
Date: Sun, Jul 10, 2016 at 7:57 PM
Subject: Issues with my SMIRKS reaction
To: amb...@li..., Nikolay Kochev <ni...@un...>,
Nina Jeliazkova <jel...@gm...>


Hi all,

I have some issues with my SMIRKS manager.
have written the SMIKRS below that I am applying on one compounds:

[#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[#8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1


I am trying to join two atoms here to form a cycle, The C7 and the O3.  In
 the reactant, O3 can be linked to a Hydrogen atom (case 1)  or can be
negatively charged (case 2). The problem is that in the product, the O3 has
a valence of 3 (with an implicit H) (case 1), or a valence of 2 (case 2).

The examples are illustrated in the attached file.


Could anyone help?


Thanks.


Regards,