How to create a molecule structure with custom atom positions?

You can create a molecule structure with custom atom positions using "obabel -i sdf -o svg" command as shown below.

1. Create a SDF file for your molecule structure. Take the L-Alanin-2D.sdf file used in other tutorials as an example.

2. Edit the SDF file by changing the coordinates of the 3rd and 5th atoms.

L-Alanin - Stretched
FYICenter.com
2D Stereoinformation: Stereo Code
  6  5  0  0  1  0  0  0  0  0999 V2000
    3.6373    2.1000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4249    1.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4249   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2124    2.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2124    4.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
M  END

3. Generate the SVG diagram with "obabel -i sdf -o svg" command.

fyicenter$ obabel L-Alanin-2D.sdf -O output.svg -xd

4. View output.svg, you will see a molecule diagram with 2 atoms stretched out.

⇒ "babel ... -o svg" - Two "svg" Tag Levels

⇐ "babel ... -o svg -xC" - Hide Terminal C in SVG

⇑ "babel ... -o svg" - Generating SVG Pictures

⇑⇑ Open Babel Tutorials