state text is centered in the residue shape

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ModificationResidueExporter.java

@@ -240,6 +240,13 @@ public class ModificationResidueExporter {
 
   public BoundingBox createBoundingBoxForModificationText(ModificationResidue mr) {
     BoundingBox result = createBoundingBoxForModification(mr);
+    if (mr instanceof ModificationSite) {
+      result.getPosition().setY(result.getPosition().getY() - DEFAULT_MODIFICATION_DIAMETER);
+    }
+    result.getPosition().setX(result.getPosition().getX() + 2);
+    result.getPosition().setY(result.getPosition().getY() + 2);
+    result.getDimensions().setWidth(result.getDimensions().getWidth() - 4);
+    result.getDimensions().setHeight(result.getDimensions().getHeight() - 4);
     result.getPosition().setZ(result.getPosition().getZ() + 1);
     return result;
   }