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I've just used Open Babel to convert .sdf and .mol2 files to SMARTS, and I'm a bit surprised the output can be different for the same structure. It's confusing me that one structure, one piece of information can be different depending on the file format in which it was saved.

I converted a ligand 1N7 in two available formats (.sdf and .mol2) of the 7RDX structure from RSCB PDB for chain N, and also for chain U. After the conversion, the SMARTS strings for the ligand in both chains are not the same for both input files types (i.e. the difference between the same ligand, from the same chain, just in two different formats available to download from RSCB PDB):

example no. 1:

[additional @H added in places, some square brackets added]

$ cat ./7rdx_N_1N7_from_mol2.smi

C1[C@@]2(C)[C@@H](C[C@@H](C1)O)[C][C]([C]1[C@H]3[C@]([C@H](C[C]21)O)([C@H](CC3)[C]([C])[C][C])C)O   1N7

$ cat ./7rdx_N_1N7_from_sdf.smi

C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CC)C)O   1N7

example no. 2:

[some square brackets added]

$ cat ./7rdx_U_1N7_from_mol2.smi

C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CCC(=O)NC[C][C][N+]([C])([C])[C])C)O 1N7

$ cat ./7rdx_U_1N7_from_sdf.smi

C1[C@@]2(C)[C@@H](C[C@@H](C1)O)C[C@H]([C@H]1[C@H]3[C@]([C@H](C[C@H]21)O)([C@H](CC3)[C@H](C)CCC(=O)NCCC[N+](C)(C)C)C)O   1N7

In both examples, the structures look quite similar to each other, but the difference is a little worrisome, because there is no chance to check every output by hand.

Is it a normal behaviour during the conversion?
Is it related to a different notation in the input files?
Which input format is better?

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    $\begingroup$ Mmmhhh be sure that each of the 3 modeled ligands correspond to the full one, could be that the density is poor and pdb shows only what is really ((??) there and not what they soaked the crystal with, actually 1N7 is CHAPSO I believe a detergent $\endgroup$
    – pippo1980
    Jan 2 at 19:59
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    $\begingroup$ Prior to grid freezing, 3-([3-cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate (CHAPSO, Anatrace) was added to the sample (8 mM final), resulting in a final complex concentration of 8 μM. The final buffer condition for the cryo-EM sample was 20 mM HEPES pH 8.0, 150 mM K-Acetate,10 mM MgCl2, 2 mM DTT, 1 mM ADP, 1 mM AlF3, 8 mM CHAPSO. $\endgroup$
    – pippo1980
    Jan 2 at 20:01

1 Answer 1

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to me your 2 strings seem different, no N in first molecule.

Here pictures, I used a PDB version of the original mmCIF file

but dindt use the RCSB PDB available one, imported .cif into

Biopython and parsed the resulting Struct object [so there could be mistakes].

so chain N --> A and chain U --> E

enter image description here

enter image description here

as per in my comment:

Mmmhhh be sure that each of the 3 modeled ligands correspond to the full one, could be that the density is poor and pdb shows only what is really ((??) there and not what they soaked the crystal with, actually 1N7 is CHAPSO I believe a detergent

... I could be wrong though, this mmCIF format is driving me crazy

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