The sdf is an rdkit reading of the original smiles string, which if wrong would
explain the funky charge settings in the mol block for atoms 84 and 85. I
modified these to 5 and 3 respectively to make the correct charge states,
however, that did not resolve the issue. Perhaps the bonding info is also
incorrect. The file is on a remote server so I will repost with attachment if
I continue to have problems.
Brian
________________________________
From: Chris Earnshaw <cgearns...@gmail.com>
Sent: Thursday, October 5, 2017 12:04:02 AM
To: Bennion, Brian; RDKit Discuss (rdkit-discuss@lists.sourceforge.net)
Subject: Re: [Rdkit-discuss] nitrogen valence issues
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<mailto: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<mailto: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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