Dear Greg,
I generate ugly 3D structures from connectivities with the (slightly
modified) algorithm by Carhardt
(Journal of Chemical Information and Computer Sciences, Vol. 16, No. 2,
1976, p.88)
and I wanted to refine them using the UFF force field and minimizer from RDKit.
From
*********************
OUTLSD
16 18 0 0 0 0 0 0 0 0 0 V2000
0.0944 -1.8500 -0.3995 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8074 -0.6908 0.3874 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6686 0.7271 0.6756 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2579 -1.4765 -0.6386 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6067 0.5659 1.6728 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7205 -0.5363 1.2149 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1323 -3.0282 0.1008 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6066 3.3566 -1.6966 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3897 1.7467 -0.3835 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1573 -0.5722 -0.7163 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2656 1.7746 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2064 0.6865 -0.6065 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7845 2.8497 -0.5281 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1332 1.0065 2.6743 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9229 4.0000 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6269 -2.2090 -1.5153 O 0 0 0 0 0 0 0 0 0 0 0 0
1 16 1 0 0 0 0
1 7 1 0 0 0 0
1 4 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 6 1 0 0 0 0
3 11 1 0 0 0 0
3 5 1 0 0 0 0
4 10 1 0 0 0 0
5 14 1 0 0 0 0
5 6 1 0 0 0 0
8 13 1 0 0 0 0
9 11 1 0 0 0 0
9 13 1 0 0 0 0
9 12 1 0 0 0 0
10 12 1 0 0 0 0
11 13 1 0 0 0 0
13 15 1 0 0 0 0
M END
*******************************
I got
*************************************
1
RDKit 3D
42 44 0 0 0 0 0 0 0 0999 V2000
0.0944 -1.8500 -0.3995 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8074 -0.6908 0.3874 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6686 0.7271 0.6756 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2579 -1.4765 -0.6386 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6067 0.5659 1.6728 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7205 -0.5363 1.2149 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1323 -3.0282 0.1008 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6066 3.3566 -1.6966 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3897 1.7467 -0.3835 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1573 -0.5722 -0.7163 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2656 1.7746 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2064 0.6865 -0.6065 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7845 2.8497 -0.5281 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1332 1.0065 2.6743 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9229 4.0000 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6269 -2.2090 -1.5153 O 0 0 0 0 0 0 0 0 0 0 0 0
0.4326 -1.4205 -0.3454 H 0 0 0 0 0 0 0 0 0 0 0 0
-8.3414 2.9862 -5.5505 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3746 -1.9121 -1.6419 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.4463 -1.5427 0.4431 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9118 1.4425 2.2316 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6340 -1.2865 2.0147 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7033 -0.6584 0.7361 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1301 -2.9606 1.1987 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7480 -3.5969 -0.2333 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0473 -3.5392 -0.2333 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2438 4.3902 -1.5966 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1356 2.7591 -2.2464 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5594 3.3540 -2.2464 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4715 1.5951 -0.5128 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5690 -0.7363 -1.7231 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5416 -0.7553 0.2980 H 0 0 0 0 0 0 0 0 0 0 0 0
9.2828 0.3655 6.5524 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9394 0.8039 0.2054 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1723 0.8298 -1.6966 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6362 0.5906 3.5631 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1966 0.7253 2.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0465 2.1165 2.6929 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9106 3.8979 1.1033 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0969 4.6539 -0.3085 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.8804 4.4393 -0.3085 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4342 -2.7532 -1.3357 H 0 0 0 0 0 0 0 0 0 0 0 0
1 16 1 0
1 7 1 0
1 4 1 0
1 2 1 0
2 3 1 0
2 6 1 0
3 11 1 0
3 5 1 0
4 10 1 0
5 14 1 0
5 6 1 0
8 13 1 0
9 11 1 0
9 13 1 0
9 12 1 0
10 12 1 0
11 13 1 0
13 15 1 0
2 17 1 0
3 18 1 0
4 19 1 0
4 20 1 0
5 21 1 0
6 22 1 0
6 23 1 0
7 24 1 0
7 25 1 0
7 26 1 0
8 27 1 0
8 28 1 0
8 29 1 0
9 30 1 0
10 31 1 0
10 32 1 0
11 33 1 0
12 34 1 0
12 35 1 0
14 36 1 0
14 37 1 0
14 38 1 0
15 39 1 0
15 40 1 0
15 41 1 0
16 42 1 0
M END
*****************************************
Two hydrogen atoms have been placed very far from the C atom they are
bonded with.
Can something be done? Maybe my starting point is too far from a structure
of minimal energy.
I many other cases, I got correct 3D structures.
I used the code from MinimizeCLI.cpp.
Best regards,
Jean-Marc
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry
CNRS UMR 6229
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax :33 3 26 91 31 66
http://www.univ-reims.fr/ICMR
http://www.univ-reims.fr/LSD/JmnSoft
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