Hi Greg,
I am having problems working with biomocules such as B12 (sdf attached). If
I read the file RDKit will return an error message complaining about
valences which are greater than permitted, in this case atom # 1 N. I
suspect the problem is due to metal coordination (in this case a Cobalt
atom) which occurs in the structure. This problems occurs in most
Porphyrin-like molecules.
Adrian
B12.sdf
-ISIS- 3D
179189 0 0 0 0 0 0 0 0 1 V2000
-4.6140 -0.3070 -0.0150 Co 0 0 0 0 0
-4.5660 0.8550 1.3000 N 0 0 0 0 0
-5.5540 0.7210 -1.1640 N 0 0 0 0 0
-5.0460 -1.9120 -0.5820 N 0 0 0 0 0
-2.8290 -0.5950 0.0710 N 0 0 0 0 0
-3.3670 0.5590 2.0470 C 0 0 0 0 0
-3.6260 -0.4890 3.1320 C 0 0 0 0 0
-2.9890 1.9330 2.6490 C 0 0 0 0 0
-2.4570 1.7830 4.0760 C 0 0 0 0 0
-1.9810 2.6660 1.7620 C 0 0 0 0 0
-1.6920 4.0250 2.3460 C 0 0 0 0 0
-2.3240 4.4210 3.3020 O 0 0 0 0 0
-0.7310 4.8010 1.8060 N 0 0 0 0 0
-4.3810 2.6520 2.6400 C 0 0 0 0 0
-5.1860 2.2990 3.8920 C 0 0 0 0 0
-6.4820 3.1120 3.9110 C 0 0 0 0 0
-7.2750 2.7640 5.1450 C 0 0 0 0 0
-6.8460 1.9470 5.9310 O 0 0 0 0 0
-8.4610 3.3620 5.3740 N 0 0 0 0 0
-5.0200 2.0780 1.4090 C 0 0 0 0 0
-5.7290 2.6340 0.3230 C 0 0 0 0 0
-6.3850 3.9790 0.4990 C 0 0 0 0 0
-5.8470 1.9940 -0.8940 C 0 0 0 0 0
-6.4780 2.5440 -2.1580 C 0 0 0 0 0
-7.8540 3.1430 -1.8600 C 0 0 0 0 0
-5.5660 3.5870 -2.8080 C 0 0 0 0 0
-4.2060 2.9830 -3.0520 C 0 0 0 0 0
-4.0000 1.8210 -2.7710 O 0 0 0 0 0
-3.2210 3.7340 -3.5810 N 0 0 0 0 0
-6.6100 1.2830 -3.0610 C 0 0 0 0 0
-8.0330 1.1530 -3.6080 C 0 0 0 0 0
-8.0700 0.0590 -4.6760 C 0 0 0 0 0
-9.4390 0.0180 -5.3060 C 0 0 0 0 0
-10.3000 0.7880 -4.9360 O 0 0 0 0 0
-9.7060 -0.8740 -6.2800 N 0 0 0 0 0
-6.2940 0.1570 -2.0990 C 0 0 0 0 0
-6.6760 -1.1900 -2.1360 C 0 0 0 0 0
-6.1330 -2.1570 -1.3180 C 0 0 0 0 0
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-7.2470 -3.8700 0.1280 C 0 0 0 0 0
-7.0430 -4.2450 -2.3580 C 0 0 0 0 0
-4.9390 -4.1530 -0.9190 C 0 0 0 0 0
-4.8500 -5.0430 0.3220 C 0 0 0 0 0
-3.4510 -5.6560 0.4120 C 0 0 0 0 0
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-4.3970 -6.8400 2.2200 O 0 0 0 0 0
-2.2670 -7.3110 1.8180 N 0 0 0 0 0
-4.1400 -2.8730 -0.7270 C 0 0 0 0 0
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-1.9270 -3.9270 -1.2270 C 0 0 0 0 0
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M END
$$$$
