Hi
Be aware that there is a problem with one of the azide groups in
CHEMBL592333 - in SMILES it's '-N=[NH+]-[NH-]' rather than '-N=[N+]=[N-].
This doesn't render the structure chemically invalid but it's probably
wrong.
What's the provenance of your SD file? It isn't the same as as a fresh
download of this structure from CHEMBL, which can be processed by RDkit
quite happily (allowing for the structure being wrong!). Is it possible
that your file has got corrupted by some other processing step?
Regards,
Chris
On 5 October 2017 at 03:28, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Brian,
>
> When you pasted that into the email the formatting of the mol block did
> end up screwed up, which makes this hard to reproduce.
> Could you please attach the mol block to the message as a file?
>
> -greg
>
> On Thu, Oct 5, 2017 at 2:21 AM, Bennion, Brian <benni...@llnl.gov> wrote:
>
>> Hello,
>>
>> After looking at the email list and seeing that this error has cropped up
>> several times for aromatic/aliphatic heterocyclic nitrogens I still haven’t
>> been able to resolve the valence =4 error for one of the azo groups in a
>> molecule that has 7. The first couple of azo groups seem to be interpreted
>> fine.
>>
>> Am I doing something incorrect here or is the mol file not formatted
>> properly?
>>
>> Thanks
>>
>> Brian
>>
>>
>>
>>
>>
>> [16:50:29] Explicit valence for atom # 85 N, 4, is greater than permitted
>>
>> [16:50:29] ERROR: Could not sanitize molecule ending on line 206
>>
>> [16:50:29] ERROR: Explicit valence for atom # 85 N, 4, is greater than
>> permitted
>>
>>
>>
>> CHEMBL592333
>>
>> 3D
>>
>>
>>
>> 91 98 0 0 0 0 0 0 0 0999 V2000
>>
>> 8.3826 -4.1789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 7.6967 -2.8968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 8.5551 -1.5926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 9.9817 -1.6449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 10.7075 -3.0051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 9.8956 -4.2577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 9.5145 2.2882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 9.8798 0.8284 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 11.3118 0.3983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 12.3905 1.3820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 12.0187 2.9205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 10.6272 3.3273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 9.8204 4.3866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 7.9490 5.4779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 8.5179 4.0883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 4.3822 5.0511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 7.6673 2.8820 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 6.4150 5.6541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 5.5680 4.4264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 6.1262 3.0849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 11.0958 -0.9118 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 4.5054 -4.0612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 6.0427 -3.9376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 6.8866 -5.1186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 6.3028 -6.4902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 4.7637 -6.6458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 3.9029 -5.4182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 2.7159 -5.9831 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 0.6356 -5.6026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 1.9599 -4.8851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 3.1331 3.3333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 3.0734 4.8222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 1.8216 2.5373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -2.1064 -0.8835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -1.6580 0.6255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -1.8630 -3.0392 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -1.1133 -1.9528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 0.5294 3.2743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 1.7976 5.5400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 0.4790 4.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -0.1940 0.9129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -0.2800 2.2297 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 0.3560 -1.6364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 0.7840 -0.1761 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 2.0400 -3.4362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -0.6446 -4.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -0.5472 -3.2855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 0.7300 -2.5970 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 8.1699 -5.4891 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -0.9196 6.9314 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 3.3718 -2.7438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 3.4375 -1.2457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 12.2233 -2.9903 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 7.3609 -7.5406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -1.9851 -5.4581 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 4.4420 2.6027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 13.8111 0.9358 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -3.5451 -1.3353 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 0.5839 -7.0998 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 10.5449 -5.6259 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 4.2197 -8.0395 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 13.2649 3.7658 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -0.8506 5.4331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -2.6861 1.6826 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 1.8710 1.0374 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 6.7424 4.5334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 8.1208 4.6949 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 5.0210 -4.9380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 4.8553 -6.2914 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 9.6021 -2.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 11.1193 -2.6926 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -0.3366 -0.2945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -1.8968 -0.3852 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 8.7855 6.7340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 5.3923 6.7330 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 10.8786 1.4957 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> 12.0747 2.2167 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>
>> -2.4480 -1.8457 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
>>
>> -3.5497 -2.9029 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0
>>
>> -2.2517 7.6211 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
>>
>> -3.5805 8.3170 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0
>>
>> 9.2243 5.6060 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
>>
>> 10.5994 6.3590 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0
>>
>> 13.4890 2.2193 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
>>
>> 15.0494 2.4295 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0
>>
>> 11.6943 -4.1991 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
>>
>> 12.8782 -5.1236 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0
>>
>> 3.4537 -7.0177 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
>>
>> 2.4539 -8.1103 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0
>>
>> 4.7687 -0.5531 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
>>
>> 6.1360 0.0648 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0
>>
>> 7 12 1 0 0 0 0
>>
>> 31 33 1 0 0 0 0
>>
>> 9 8 1 0 0 0 0
>>
>> 63 50 1 0 0 0 0
>>
>> 9 10 1 0 0 0 0
>>
>> 45 51 1 0 0 0 0
>>
>> 34 35 1 0 0 0 0
>>
>> 51 52 1 0 0 0 0
>>
>> 10 11 1 0 0 0 0
>>
>> 36 37 1 0 0 0 0
>>
>> 34 37 1 0 0 0 0
>>
>> 38 33 1 0 0 0 0
>>
>> 12 11 1 0 0 0 0
>>
>> 13 12 1 0 0 0 0
>>
>> 38 40 1 0 0 0 0
>>
>> 5 53 1 0 0 0 0
>>
>> 32 39 1 0 0 0 0
>>
>> 25 54 1 0 0 0 0
>>
>> 39 40 1 0 0 0 0
>>
>> 46 55 1 0 0 0 0
>>
>> 35 64 1 0 0 0 0
>>
>> 41 35 1 0 0 0 0
>>
>> 31 56 1 0 0 0 0
>>
>> 5 6 1 0 0 0 0
>>
>> 10 57 1 0 0 0 0
>>
>> 41 42 1 0 0 0 0
>>
>> 34 58 1 0 0 0 0
>>
>> 38 42 1 0 0 0 0
>>
>> 29 59 1 0 0 0 0
>>
>> 37 43 1 0 0 0 0
>>
>> 6 60 1 0 0 0 0
>>
>> 7 8 1 0 0 0 0
>>
>> 26 61 1 0 0 0 0
>>
>> 43 44 1 0 0 0 0
>>
>> 11 62 1 0 0 0 0
>>
>> 41 44 1 0 0 0 0
>>
>> 9 21 1 0 0 0 0
>>
>> 40 63 1 0 0 0 0
>>
>> 22 23 1 0 0 0 0
>>
>> 13 15 1 0 0 0 0
>>
>> 14 15 1 0 0 0 0
>>
>> 33 65 1 0 0 0 0
>>
>> 1 2 1 0 0 0 0
>>
>> 20 66 1 0 0 0 0
>>
>> 15 17 1 0 0 0 0
>>
>> 66 67 1 0 0 0 0
>>
>> 30 45 1 0 0 0 0
>>
>> 23 68 1 0 0 0 0
>>
>> 1 6 1 0 0 0 0
>>
>> 68 69 1 0 0 0 0
>>
>> 2 3 1 0 0 0 0
>>
>> 3 70 1 0 0 0 0
>>
>> 27 22 1 0 0 0 0
>>
>> 70 71 1 0 0 0 0
>>
>> 23 24 1 0 0 0 0
>>
>> 43 72 1 0 0 0 0
>>
>> 45 48 1 0 0 0 0
>>
>> 72 73 1 0 0 0 0
>>
>> 29 46 1 0 0 0 0
>>
>> 46 47 1 0 0 0 0
>>
>> 47 48 1 0 0 0 0
>>
>> 14 74 1 0 0 0 0
>>
>> 36 47 1 0 0 0 0
>>
>> 18 75 1 0 0 0 0
>>
>> 24 25 1 0 0 0 0
>>
>> 25 26 1 0 0 0 0
>>
>> 26 27 1 0 0 0 0
>>
>> 7 76 1 0 0 0 0
>>
>> 28 27 1 0 0 0 0
>>
>> 76 77 1 0 0 0 0
>>
>> 3 4 1 0 0 0 0
>>
>> 73 78 2 3 0 0 0
>>
>> 4 5 1 0 0 0 0
>>
>> 78 79 2 0 0 0 0
>>
>> 17 20 1 0 0 0 0
>>
>> 50 80 2 3 0 0 0
>>
>> 14 18 1 0 0 0 0
>>
>> 80 81 2 0 0 0 0
>>
>> 28 30 1 0 0 0 0
>>
>> 67 82 2 3 0 0 0
>>
>> 29 30 1 0 0 0 0
>>
>> 82 83 2 0 0 0 0
>>
>> 24 49 1 0 0 0 0
>>
>> 77 84 2 3 0 0 0
>>
>> 18 19 1 0 0 0 0
>>
>> 84 85 2 0 0 0 0
>>
>> 4 21 1 0 0 0 0
>>
>> 71 86 2 0 0 0 0
>>
>> 1 49 1 0 0 0 0
>>
>> 86 87 2 0 0 0 0
>>
>> 19 20 1 0 0 0 0
>>
>> 69 88 2 3 0 0 0
>>
>> 31 32 1 0 0 0 0
>>
>> 88 89 2 0 0 0 0
>>
>> 16 32 1 0 0 0 0
>>
>> 52 90 2 3 0 0 0
>>
>> 16 19 1 0 0 0 0
>>
>> 90 91 2 0 0 0 0
>>
>> M CHG 1 78 1
>>
>> M CHG 1 79 -1
>>
>> M CHG 1 80 1
>>
>> M CHG 1 81 -1
>>
>> M CHG 1 82 1
>>
>> M CHG 1 83 -1
>>
>> M CHG 1 84 1
>>
>> M CHG 1 85 -1
>>
>> M CHG 1 88 1
>>
>> M CHG 1 89 -1
>>
>> M CHG 1 90 1
>>
>> M CHG 1 91 -1
>>
>> M END
>>
>> > <chembl_id> (540484)
>>
>> CHEMBL592333
>>
>> $$$$
>>
>> ------------------------------------------------------------
>> ------------------
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>>
>>
>
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