Stereochemistry with JSME (Molecule Editor in JavaScript)

Q

Can JSME (Molecule Editor in JavaScript) be used to do Stereochemistry?

✍: Guest

A

Yes. JSME (Molecule Editor in JavaScript) can be used to stereochemistry. You can create a molecule structure with wedges and hatches provide stereoinformation on bonds.

Here is an example with 1 wedge and 1 hatch:

Molecule with Tetrahedral Stereocenter
Molecule with Tetrahedral Stereocenter

You can then write the structure into a SDF/Mol V2000 file, FYI-002.sdf. The wedge is stored as Stereo code "1" and the hatch is stored as Stereo code "6". In other words, only 2D stereoinformation is recorded.

[H][C@](C)(F)Cl
JME 2017-02-26 Wed Feb 03 20:27:39 GMT+800 2021

  5  4  0  0  0  0  0  0  0  0999 V2000
    1.2481    1.1538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.5195    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6481    1.1469    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.2376    2.5537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  6  0  0  0
  1  4  1  1  0  0  0
  1  5  1  0  0  0  0
M  END

You can also write the structure into a SDF/Mol V3000 file, FYI-002.sd3. Note that "CFG=3" in V3000 is the same as Stereo Code of "6" in V2000 format.

[H][C@](C)(F)Cl
JME 2017-02-26 Wed Feb 03 20:29:08 GMT+800 2021

  0  0  0  0  0  0  0  0  0  0999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 5 4 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.2481 1.1538 0.0000 0
M  V30 2 Cl 0.0000 0.5195 0.0000 0
M  V30 3 H 2.6481 1.1469 0.0000 0
M  V30 4 F 2.0411 0.0000 0.0000 0
M  V30 5 C 1.2376 2.5537 0.0000 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 1 3 CFG=3
M  V30 3 1 1 4 CFG=1
M  V30 4 1 1 5
M  V30 END BOND
M  V30 END CTAB
M  END

JSME can also read stereoinformation from SDF/Mol files.

 

SDF/Mol File FAQ

Stereoinformation in SDF/Mol V3000 Files

Stereochemistry, Chirality, Parity

⇑⇑ SDF/Mol File FAQ

2021-02-06, 135👍, 0💬