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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