There are only 30 atoms in this molecule, but the "M CHG" line is
referencing atom 31.
Craig
On Fri, Oct 4, 2013 at 1:53 PM, Mezei, Mihaly <mihaly.me...@mssm.edu> wrote:
> To follow up on my query a while ago (thanks, Craig James for a quick
> answer):
>
> When issued the command
>
> ]$ babel -isdf NC0747132.sdf -omol2 NC0747132.mol2
>
> I got
>
> ==============================
> *** Open Babel Error in ReadMolecule
> Error in line:
> M CHG 2 2 -1 31 1
> 0 molecules converted
> 1 errors 2 audit log messages 1 debugging messages
>
> The input file (also attached) was (downloaded from NCI):
> 747132
> SItclcactv03041212283D 0 0.00000 0.00000 1
>
> 30 30 0 0 0 0 0 0 0 0999 V2000
> 12.6807 1.6861 -0.7082 C 0 0 0 0 0 0 0 0 0 0 0 0
> 11.6744 2.1827 0.3596 C 0 0 0 0 0 0 0 0 0 0 0 0
> 11.6559 0.9900 1.3515 C 0 0 0 0 0 0 0 0 0 0 0 0
> 13.1168 0.4935 1.3254 C 0 0 0 0 0 0 0 0 0 0 0 0
> 13.7116 0.9526 0.0567 N 0 3 0 0 0 0 0 0 0 0 0 0
> 14.1733 -0.2053 -0.7204 C 0 0 0 0 0 0 0 0 0 0 0 0
> 15.2397 -0.9610 0.0751 C 0 0 0 0 0 0 0 0 0 0 0 0
> 15.7206 -2.1670 -0.7343 C 0 0 0 0 0 0 0 0 0 0 0 0
> 16.7869 -2.9227 0.0612 C 0 0 0 0 0 0 0 0 0 0 0 0
> 14.8464 1.8425 0.3363 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.1863 1.0194 -1.4147 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.1267 2.5318 -1.2317 H 0 0 0 0 0 0 0 0 0 0 0 0
> 12.0360 3.0890 0.8453 H 0 0 0 0 0 0 0 0 0 0 0 0
> 10.6886 2.3425 -0.0773 H 0 0 0 0 0 0 0 0 0 0 0 0
> 11.3805 1.3247 2.3516 H 0 0 0 0 0 0 0 0 0 0 0 0
> 10.9777 0.2105 1.0044 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.6668 0.9150 2.1667 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.1393 -0.5952 1.3729 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.3313 -0.8681 -0.9200 H 0 0 0 0 0 0 0 0 0 0 0 0
> 14.5983 0.1366 -1.6641 H 0 0 0 0 0 0 0 0 0 0 0 0
> 16.0817 -0.2982 0.2747 H 0 0 0 0 0 0 0 0 0 0 0 0
> 14.8147 -1.3029 1.0188 H 0 0 0 0 0 0 0 0 0 0 0 0
> 14.8786 -2.8297 -0.9340 H 0 0 0 0 0 0 0 0 0 0 0 0
> 16.1456 -1.8251 -1.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
> 17.1296 -3.7818 -0.5155 H 0 0 0 0 0 0 0 0 0 0 0 0
> 17.6290 -2.2599 0.2608 H 0 0 0 0 0 0 0 0 0 0 0 0
> 16.3620 -3.2646 1.0049 H 0 0 0 0 0 0 0 0 0 0 0 0
> 14.5030 2.6970 0.9195 H 0 0 0 0 0 0 0 0 0 0 0 0
> 15.6043 1.2987 0.9001 H 0 0 0 0 0 0 0 0 0 0 0 0
> 15.2739 2.1923 -0.6034 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 1 5 1 0 0 0 0
> 2 3 1 0 0 0 0
> 3 4 1 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 1 0 0 0 0
> 5 10 1 0 0 0 0
> 6 7 1 0 0 0 0
> 7 8 1 0 0 0 0
> 8 9 1 0 0 0 0
> 1 11 1 0 0 0 0
> 1 12 1 0 0 0 0
> 2 13 1 0 0 0 0
> 2 14 1 0 0 0 0
> 3 15 1 0 0 0 0
> 3 16 1 0 0 0 0
> 4 17 1 0 0 0 0
> 4 18 1 0 0 0 0
> 6 19 1 0 0 0 0
> 6 20 1 0 0 0 0
> 7 21 1 0 0 0 0
> 7 22 1 0 0 0 0
> 8 23 1 0 0 0 0
> 8 24 1 0 0 0 0
> 9 25 1 0 0 0 0
> 9 26 1 0 0 0 0
> 9 27 1 0 0 0 0
> 10 28 1 0 0 0 0
> 10 29 1 0 0 0 0
> 10 30 1 0 0 0 0
> M CHG 2 2 -1 31 1
> M END
> > <NSC>
> 747132
>
> > <Release>
> December 2010
>
> > <Structure Source>
> DTP/NCI DIS export via molfile
>
> > <Number of atom stereocenters>
> 0
>
> > <Number of bond stereocenters>
> 0
>
> > <Structure Evaluation>
> No Comparision - Unparameterized Atom - P(a2) connected atoms =[ C C F F F
> C ]
>
> > <Formula>
> C15H20?F18NP
>
> > <Molecular Weight>
> 587.2747
>
> > <DTP names>
> 1-Buty-1-methylpyrrollidinium tris(pentafluoroethyl)trifluorophosphate
>
> > <NCICADD_FICUS_ID>
> 8834DEE2301FF9DF-FICuS-01-81
>
> > <NCICADD_FICTS_ID>
> 8834DEE2301FF9DF-FICTS-01-60
>
> > <NCICADD_UUUUU_ID>
> 8834DEE2301FF9DF-uuuuu-01-30
>
> > <Standard InChI>
>
> InChI=1S/C9H20N.C6F18P/c1-3-4-7-10(2)8-5-6-9-10;7-1(8,9)4(16,17)25(22,23,24,5(18
>
> > <Standard InChIKey>
> InChIKey=KNGDDPFNUUIHKR-UHFFFAOYSA-N
>
> > <GUSAR Human Liver Microsomal Stability Prediction>
> N/A
>
> > <GUSAR Human Liver Microsomal Stability Prediction AD>
> N/A
>
> > <mol2-name>
> NC0747132.sdf
> $$$$
>
>
>
>
>
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