ioChem-BD

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geometry ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceGronOR cml
idgeometry
xml:basegeometry.xml

Input ​

 OpenMolcas header from Seward (integral module)
 (No title provided by user)                                                    
 Integrals generated by Gateway/Seward, Wed Apr 28 15:27:59 2021                

      Atom          x             y             z          Znuc     s  p  d  f  g  h  i

   1  C1        1.31805374   -4.61433703    0.00000000     6.00     5  4  2  1  0  0  0
   2  C2       -1.31805374   -4.61433703    0.00000000     6.00     5  4  2  1  0  0  0
   3  C3        1.34559649   -0.33656778    0.00000000     6.00     5  4  2  1  0  0  0
   4  C4       -1.34559649   -0.33656778    0.00000000     6.00     5  4  2  1  0  0  0
   5  N1        2.68867587   -2.46206748    0.00000000     7.00     5  4  2  1  0  0  0
   6  N2       -2.68867587   -2.46206748    0.00000000     7.00     5  4  2  1  0  0  0
   7  N3        0.00000000    4.41598571    0.00000000     7.00     5  4  2  1  0  0  0
   8  H1        2.38164640   -6.38284667    0.00000000     1.00     3  2  1  0  0  0  0
   9  H2       -2.38164640   -6.38284667    0.00000000     1.00     3  2  1  0  0  0  0
  10  S1        2.64782377    2.70477067    0.00000000    16.00     6  5  2  1  0  0  0
  11  S2       -2.64782377    2.70477067    0.00000000    16.00     6  5  2  1  0  0  0
  12  C5        6.98723211   -4.61433703    5.66917837     6.00     5  4  2  1  0  0  0
  13  C6        4.35112464   -4.61433703    5.66917837     6.00     5  4  2  1  0  0  0
  14  C7        7.01477487   -0.33656778    5.66917837     6.00     5  4  2  1  0  0  0
  15  C8        4.32358188   -0.33656778    5.66917837     6.00     5  4  2  1  0  0  0
  16  N4        8.35785425   -2.46206748    5.66917837     7.00     5  4  2  1  0  0  0
  17  N5        2.98050250   -2.46206748    5.66917837     7.00     5  4  2  1  0  0  0
  18  N6        5.66917837    4.41598571    5.66917837     7.00     5  4  2  1  0  0  0
  19  H3        8.05082478   -6.38284667    5.66917837     1.00     3  2  1  0  0  0  0
  20  H4        3.28753197   -6.38284667    5.66917837     1.00     3  2  1  0  0  0  0
  21  S3        8.31700215    2.70477067    5.66917837    16.00     6  5  2  1  0  0  0
  22  S4        3.02135460    2.70477067    5.66917837    16.00     6  5  2  1  0  0  0

Output text ​

xml
<comment class="example.output" id="geometry">
      <molecule id="molgeom">
          <atomArray>
              <atom id="C1" elementType="C" x3="0.69748405" y3="-2.44180218" z3="0.00000000" />
              <atom id="C2" elementType="C" x3="-0.69748405" y3="-2.44180218" z3="0.00000000" />
              <atom id="C3" elementType="C" x3="0.71205905" y3="-0.17810401" z3="0.00000000" />
              <atom id="C4" elementType="C" x3="-0.71205905" y3="-0.17810401" z3="0.00000000" />
              <atom id="N1" elementType="N" x3="1.42278610" y3="-1.30287010" z3="0.00000000" />
              <atom id="N2" elementType="N" x3="-1.42278610" y3="-1.30287010" z3="0.00000000" />
              <atom id="N3" elementType="N" x3="0.00000000" y3="2.33683917" z3="0.00000000" />
              <atom id="H1" elementType="H" x3="1.26031309" y3="-3.37765724" z3="0.00000000" />
              <atom id="H2" elementType="H" x3="-1.26031309" y3="-3.37765724" z3="0.00000000" />
              <atom id="S1" elementType="S" x3="1.40116810" y3="1.43130310" z3="0.00000000" />
              <atom id="S2" elementType="S" x3="-1.40116810" y3="1.43130310" z3="0.00000000" />
              <atom id="C5" elementType="C" x3="3.69748427" y3="-2.44180218" z3="3.00000021" />
              <atom id="C6" elementType="C" x3="2.30251617" y3="-2.44180218" z3="3.00000021" />
              <atom id="C7" elementType="C" x3="3.71205927" y3="-0.17810401" z3="3.00000021" />
              <atom id="C8" elementType="C" x3="2.28794117" y3="-0.17810401" z3="3.00000021" />
              <atom id="N4" elementType="N" x3="4.42278632" y3="-1.30287010" z3="3.00000021" />
              <atom id="N5" elementType="N" x3="1.57721411" y3="-1.30287010" z3="3.00000021" />
              <atom id="N6" elementType="N" x3="3.00000021" y3="2.33683917" z3="3.00000021" />
              <atom id="H3" elementType="H" x3="4.26031331" y3="-3.37765724" z3="3.00000021" />
              <atom id="H4" elementType="H" x3="1.73968712" y3="-3.37765724" z3="3.00000021" />
              <atom id="S3" elementType="S" x3="4.40116832" y3="1.43130310" z3="3.00000021" />
              <atom id="S4" elementType="S" x3="1.59883212" y3="1.43130310" z3="3.00000021" />
          </atomArray>
          <formula concise=" C  8 N  6 H  4 S  4">
              <atomArray elementType=" C  N  H  S " count="  8.0  6.0  4.0  4.0" />
          </formula>
          <bondArray>
              <bond atomRefs2="C1 C2" order="S" />
              <bond atomRefs2="C1 N1" order="S" />
              <bond atomRefs2="C1 H1" order="S" />
              <bond atomRefs2="C2 N2" order="S" />
              <bond atomRefs2="C2 H2" order="S" />
              <bond atomRefs2="C3 C4" order="S" />
              <bond atomRefs2="C3 N1" order="S" />
              <bond atomRefs2="C3 S1" order="S" />
              <bond atomRefs2="C4 N2" order="S" />
              <bond atomRefs2="C4 S2" order="S" />
              <bond atomRefs2="N3 S1" order="S" />
              <bond atomRefs2="N3 S2" order="S" />
              <bond atomRefs2="C5 C6" order="S" />
              <bond atomRefs2="C5 N4" order="S" />
              <bond atomRefs2="C5 H3" order="S" />
              <bond atomRefs2="C6 N5" order="S" />
              <bond atomRefs2="C6 H4" order="S" />
              <bond atomRefs2="C7 C8" order="S" />
              <bond atomRefs2="C7 N4" order="S" />
              <bond atomRefs2="C7 S3" order="S" />
              <bond atomRefs2="C8 N5" order="S" />
              <bond atomRefs2="C8 S4" order="S" />
              <bond atomRefs2="N6 S3" order="S" />
              <bond atomRefs2="N6 S4" order="S" />
          </bondArray>
      </molecule> 
      <module dictRef="gr:atomicBasisSet">
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C1</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C2</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C3</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C4</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">N1</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">N2</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">N3</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">H1</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="3">s|p|d</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="3">3 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">H2</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="3">s|p|d</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="3">3 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">S1</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">6 5 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">S2</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">6 5 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C5</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C6</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C7</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">C8</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">N4</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">N5</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">N6</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">5 4 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">H3</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="3">s|p|d</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="3">3 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">H4</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="3">s|p|d</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="3">3 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">S3</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">6 5 2 1</array>
        </list>
        <list dictRef="gr:contracted">
            <scalar dataType="xsd:string" dictRef="gr:atomLabel">S4</scalar>
            <array dataType="xsd:string" dictRef="gr:shells" delimiter="|" size="4">s|p|d|f</array>
            <array dataType="xsd:integer" dictRef="gr:contractedFunctions" size="4">6 5 2 1</array>
        </list>
      </module> 
  </comment>