SMILES
SMILES should be entered in text format with one new line for each compound. If you want to include a compound name, you can put the compound name after SMILES with tab in between.
An example is shown below.
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CN1CCN(CC1)C(=O)OC1c2nccnc2C(=O)N1c1ccc(cn1)Cl Compound_1
COc1cc2nc([nH]c(=N)c2cc1OC)N1CCN(CC1)C(=O)C1CCCO1 Compound_2
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Mol file or SDF (Structure Data Format)
Put the 'Title' or 'ID' of your compounds in the first line of Mol file or SDF. If the first line is blank, the compound names are automatically assigned in order from Compound_1. 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 "> ". On the same line, 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.
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Compound_3
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
$$$$
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