You can also include pKa and logP values at data fields in Mol file or SDF. Data fields start with a header, which begins with a >. On the same line, the name of the data field is written in angular brackets. The name of the data field should be “apKa” (most acidic pKa), “bpKa” (most basic pKa), and “logP”, otherwise it will not be recognized (case- insensitive).
An example is shown below.
427_83
OpenBabel05201916532D
9 8 0 0 0 0 0 0 0999 V2000
0.5369 0.9749 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4030 0.4749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2690 0.9749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8015 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0044 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9590 1.5118 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8059 1.2849 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5790 0.4380 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.6649 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 9 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 5 1 0 0 0 0
3 6 1 0 0 0 0
3 7 1 0 0 0 0
3 8 1 0 0 0 0
M END
> <apKa>
3.64
> <bpKa>
7.45
> <logP>
-0.3
$$$$