pKa variation with structure representation

I am finding that depending on how I draw ethyl cyanoacetate, it is giving me wildly different pKa values, none of which are correct (C(2) should be 9).  JChem gives this structure a pKa of 18.8:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5"

          elementType="R C C R O"

          sgroupRef="sg1 0 0 sg2 0"

          x2="-12.368124961853027 -11.034445840024992 -9.546920067539826 -9.148338738081945 -8.21324094571179"

          y2="3.4649999141693115 4.234999914169311 3.836418584711429 2.3488928122262642 4.606418584711429"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="1" />

        <bond atomRefs2="a2 a3" order="1" />

        <bond atomRefs2="a3 a4" order="1" />

        <bond atomRefs2="a3 a5" order="2" />

      </bondArray>

      <molecule id="sg1" role="SuperatomSgroup" title="CN" leftName="NC" molID="m2">

        <atomArray

            atomID="a6 a7"

            elementType="C N"

            attachmentPoint="1 0"

            x2="-23.099999847412107 -24.63999984741211"

            y2="6.545000076293945 6.545000076293945"

            />

        <bondArray>

          <bond atomRefs2="a6 a7" order="3" />

        </bondArray>

      </molecule>

      <molecule id="sg2" role="SuperatomSgroup" title="OEt" leftName="EtO" molID="m3">

        <atomArray

            atomID="a8 a9 a10"

            elementType="O C C"

            attachmentPoint="1 0 0"

            x2="-9.185212253046169 -10.518891374874205 -11.852570496702239"

            y2="1.6959749752363447 0.9259749752363442 1.6959749752363438"

            />

        <bondArray>

          <bond atomRefs2="a9 a8" order="1" />

          <bond atomRefs2="a10 a9" order="1" />

        </bondArray>

      </molecule>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

Likewise this structure with all groups ungrouped:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5 a6 a7 a8"

          elementType="C C C O O N C C"

          x2="-11.68346822604581 -10.349789104217773 -8.862263331732608 -8.463682002274727 -7.528584209904572 -13.017147347873847 -9.55262644530201 -11.040152217787172"

          y2="3.9576949021652466 4.727694902165247 4.3291135727073655 2.8415878002222 5.099113572707365 4.72769490216525 1.7526433571949167 2.151224686652799"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="1" />

        <bond atomRefs2="a2 a3" order="1" />

        <bond atomRefs2="a3 a4" order="1" />

        <bond atomRefs2="a3 a5" order="2" />

        <bond atomRefs2="a1 a6" order="3" />

        <bond atomRefs2="a7 a4" order="1" />

        <bond atomRefs2="a8 a7" order="1" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

But for this structure it gives a pKa of 13.8 -- still not correct, but better:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3"

          elementType="R C R"

          sgroupRef="sg1 0 sg2"

          x2="-4.090624809265137 -2.756945687437101 -1.4232665656090655"

          y2="1.5881249904632568 0.8181249904632569 1.5881249904632568"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="1" />

        <bond atomRefs2="a2 a3" order="1" />

      </bondArray>

      <molecule id="sg1" role="SuperatomSgroup" title="CN" leftName="NC" molID="m2">

        <atomArray

            atomID="a4 a5"

            elementType="C N"

            attachmentPoint="1 0"

            x2="-5.678749980926513 -7.218749980926514"

            y2="3.0799999237060547 3.0799999237060547"

            />

        <bondArray>

          <bond atomRefs2="a4 a5" order="3" />

        </bondArray>

      </molecule>

      <molecule id="sg2" role="SuperatomSgroup" title="CO2Et"

                leftName="EtO2C" molID="m3">

        <atomArray

            atomID="a6 a7 a8 a9 a10"

            elementType="C C O C O"

            attachmentPoint="1 0 0 0 0"

            x2="0.9240000762939449 3.2340000762939445 1.6940000762939444 4.004000076293944 -0.6159999237060552"

            y2="1.8205567502212876 0.486877628393251 0.4868776283932519 -0.8468014934347838 1.8205567502212876"

            />

        <bondArray>

          <bond atomRefs2="a8 a6" order="1" />

          <bond atomRefs2="a6 a10" order="2" />

          <bond atomRefs2="a9 a7" order="1" />

          <bond atomRefs2="a7 a8" order="1" />

        </bondArray>

      </molecule>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

And now expand this structure, and it still gives me a pKa of 13.8, even though it seems identical to the second one:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5 a6 a7 a8"

          elementType="C C C N C O C O"

          x2="-5.257594040864667 -3.923914919036632 -2.5902357972085968 -5.257594040864669 -1.2565566753805604 -1.256556675380561 0.07712244644747424 -2.5902357972085968"

          y2="1.8127083237965897 1.0427083237965897 1.8127083237965897 3.3527083237965907 -0.4972916762034103 1.0427083237965902 -1.267291676203409 3.3527083237965902"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="1" />

        <bond atomRefs2="a2 a3" order="1" />

        <bond atomRefs2="a1 a4" order="3" />

        <bond atomRefs2="a6 a3" order="1" />

        <bond atomRefs2="a3 a8" order="2" />

        <bond atomRefs2="a7 a5" order="1" />

        <bond atomRefs2="a5 a6" order="1" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

This is happening in both JChem 5.3 and 5.2.  Can you explain and fix?

Hi,

I have fixed these bugs.

Thanks for sending report.

Jozsi

Thanks.  When will the fix be available?

Hi,

The fix will be available at the begening of the next week.

Jozsi