Hash Bond with Solid Line

Q

Why Hash Bond with a Solid Line used by Open Babel?

✍: FYIcenter.com

A

Sometimes, when a hash bond is located on a ring structure, Open Babel adds a solid line to the hash bond.

Here is an example SDF/Mol file, Hash-with-Solid-Line.sdf, that has 4 stereo centers on a ring structure.

Hash-with-Solid-Line
FYICenter.com

 15 16  0  0  0  0  0  0  0  0999 V2000
    3.6373    2.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    2.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4249    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8497    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0622    2.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4249    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6373    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8497    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4116    2.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0622    4.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8497    4.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6373    4.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4249    4.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    4.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  1  1  0  0  0  0
  4  5  1  0  0  0  0
  1  4  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  6  0  0  0
  3  6  1  6  0  0  0
  2  9  1  1  0  0  0
  5 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  5 11  1  0  0  0  0
 14 15  1  0  0  0  0
 13 14  1  0  0  0  0
  2 15  1  0  0  0  0
M  END

If we view this SDF/Mol with Open Babel, JSME and pccdb.org, we get 3 different results:

Stereo Centers with Ring Structure
Stereo Centers with Ring Structure

As you can see, 3 tools behaved differently:

  • Open Babel - Changed hash bonds to neighboring atoms. Hash style is changed by adding a solid line.
  • JSME - Kept everything as given in the input.
  • pccdb.org - Made the same changes on the hash bonds. and changed the formation of the ring structure.

So has bond with a solid line is a way to indicate a single bond on a ring going toward the back of the display screen.

By the way, pccdb.org changed the formation of the ring structure, because our input data does not match the real molecule structure. If we allow Open Babel to regenerate the 2D coordinates, it will give us a structure similar to pccdb.org's result.

fyicenter> obabel Hash-with-Solid-Line.sdf \
  -o svg -O output.svg --gen2D

fyicenter> chrome output.svg
2D Coordinates Regenerate by Open Babel
2D Coordinates Regenerate by Open Babel

 

Other Open Babel Commands

Custom Wedge/Hash with SVG output

Stereochemistry with Open Babel

⇑⇑ Open Babel Tutorials

2022-07-26, 489👍, 0💬