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dominiquesydow/check_sdf_dummy_atoms.ipynb

Created June 8, 2020 11:13
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check_sdf_dummy_atoms.ipynb
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Raw
fragments.sdf
RDKit 3D
34 41 0 0 0 0 0 0 0 0999 V2000
0.4371 12.7505 36.9853 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2642 12.9079 38.2277 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1139 14.4529 38.7161 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.1199 15.2058 37.5393 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4629 14.9015 39.2347 C 0 0 1 0 0 0 0 0 0 0 0 0
1.5348 14.4683 40.5302 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7584 14.1638 38.7160 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5866 16.4121 39.2693 N 0 0 0 0 0 0 0 0 0 0 0 0
1.0672 17.1163 40.3752 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4388 16.7898 41.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0627 15.6155 42.0329 N 0 0 0 0 0 0 0 0 0 0 0 0
0.3466 14.2770 41.1661 C 0 0 1 0 0 0 0 0 0 0 0 0
-0.7124 14.4810 39.9151 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5317 15.7088 43.1974 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0207 14.7348 44.0079 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6224 14.9462 45.2351 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6961 16.3400 45.6074 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1686 17.3033 44.7665 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5705 17.0948 43.5370 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0309 17.8151 42.4832 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3331 19.1308 42.1573 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0635 20.4186 42.8468 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4789 20.5149 43.9799 O 0 0 0 0 0 0 0 0 0 0 0 0
0.9404 19.4457 41.0616 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0638 20.8782 40.9989 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4914 21.3888 42.1763 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3044 18.4545 40.1286 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9344 18.5389 38.9159 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1268 17.2037 38.4036 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7069 17.0197 37.1928 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4033 19.5492 38.2013 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0259 19.4173 36.9909 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1866 18.0888 36.4700 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1680 12.0345 39.2648 R 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 6
3 5 1 0
3 13 1 0
5 6 1 0
5 7 1 6
5 8 1 0
6 12 1 0
8 9 1 0
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9 10 2 0
9 27 1 0
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14 15 2 0
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16 17 2 0
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19 20 1 0
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21 24 1 0
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24 25 1 0
24 27 2 0
25 26 1 0
27 28 1 0
28 29 2 0
28 31 1 0
29 30 1 0
30 33 2 0
31 32 2 0
32 33 1 0
2 34 1 0
M ISO 1 34 2
M END
$$$$
RDKit 3D
3 2 0 0 0 0 0 0 0 0999 V2000
0.1680 12.0345 39.2648 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2860 10.5972 39.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2642 12.9079 38.2277 R 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
3 1 1 0
M ISO 1 3 1
M END
$$$$
Raw
fragments2.sdf
RDKit 3D
34 41 0 0 0 0 0 0 0 0999 V2000
0.4371 12.7505 36.9853 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2642 12.9079 38.2277 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1139 14.4529 38.7161 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.1199 15.2058 37.5393 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4629 14.9015 39.2347 C 0 0 1 0 0 0 0 0 0 0 0 0
1.5348 14.4683 40.5302 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7584 14.1638 38.7160 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5866 16.4121 39.2693 N 0 0 0 0 0 0 0 0 0 0 0 0
1.0672 17.1163 40.3752 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4388 16.7898 41.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0627 15.6155 42.0329 N 0 0 0 0 0 0 0 0 0 0 0 0
0.3466 14.2770 41.1661 C 0 0 1 0 0 0 0 0 0 0 0 0
-0.7124 14.4810 39.9151 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5317 15.7088 43.1974 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0207 14.7348 44.0079 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6224 14.9462 45.2351 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6961 16.3400 45.6074 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1686 17.3033 44.7665 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5705 17.0948 43.5370 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0309 17.8151 42.4832 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3331 19.1308 42.1573 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0635 20.4186 42.8468 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4789 20.5149 43.9799 O 0 0 0 0 0 0 0 0 0 0 0 0
0.9404 19.4457 41.0616 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0638 20.8782 40.9989 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4914 21.3888 42.1763 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3044 18.4545 40.1286 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9344 18.5389 38.9159 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1268 17.2037 38.4036 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7069 17.0197 37.1928 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4033 19.5492 38.2013 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0259 19.4173 36.9909 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1866 18.0888 36.4700 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1680 12.0345 39.2648 * 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 6
3 5 1 0
3 13 1 0
5 6 1 0
5 7 1 6
5 8 1 0
6 12 1 0
8 9 1 0
8 29 1 0
9 10 2 0
9 27 1 0
10 11 1 0
10 20 1 0
11 12 1 0
11 14 1 0
12 13 1 6
14 15 2 0
14 19 1 0
15 16 1 0
16 17 2 0
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21 22 1 0
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22 26 1 0
24 25 1 0
24 27 2 0
25 26 1 0
27 28 1 0
28 29 2 0
28 31 1 0
29 30 1 0
30 33 2 0
31 32 2 0
32 33 1 0
2 34 1 0
V 34 *
M END
$$$$
RDKit 3D
3 2 0 0 0 0 0 0 0 0999 V2000
0.1680 12.0345 39.2648 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2860 10.5972 39.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2642 12.9079 38.2277 * 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
3 1 1 0
V 3 *
M END
$$$$
Raw
fragments3.sdf
RDKit 3D
34 41 0 0 0 0 0 0 0 0999 V2000
0.4371 12.7505 36.9853 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2642 12.9079 38.2277 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1139 14.4529 38.7161 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.1199 15.2058 37.5393 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4629 14.9015 39.2347 C 0 0 1 0 0 0 0 0 0 0 0 0
1.5348 14.4683 40.5302 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7584 14.1638 38.7160 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5866 16.4121 39.2693 N 0 0 0 0 0 0 0 0 0 0 0 0
1.0672 17.1163 40.3752 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4388 16.7898 41.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0627 15.6155 42.0329 N 0 0 0 0 0 0 0 0 0 0 0 0
0.3466 14.2770 41.1661 C 0 0 1 0 0 0 0 0 0 0 0 0
-0.7124 14.4810 39.9151 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5317 15.7088 43.1974 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0207 14.7348 44.0079 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6224 14.9462 45.2351 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6961 16.3400 45.6074 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1686 17.3033 44.7665 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5705 17.0948 43.5370 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0309 17.8151 42.4832 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3331 19.1308 42.1573 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0635 20.4186 42.8468 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4789 20.5149 43.9799 O 0 0 0 0 0 0 0 0 0 0 0 0
0.9404 19.4457 41.0616 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0638 20.8782 40.9989 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4914 21.3888 42.1763 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3044 18.4545 40.1286 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9344 18.5389 38.9159 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1268 17.2037 38.4036 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7069 17.0197 37.1928 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4033 19.5492 38.2013 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0259 19.4173 36.9909 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1866 18.0888 36.4700 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1680 12.0345 39.2648 * 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 6
3 5 1 0
3 13 1 0
5 6 1 0
5 7 1 6
5 8 1 0
6 12 1 0
8 9 1 0
8 29 1 0
9 10 2 0
9 27 1 0
10 11 1 0
10 20 1 0
11 12 1 0
11 14 1 0
12 13 1 6
14 15 2 0
14 19 1 0
15 16 1 0
16 17 2 0
17 18 1 0
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21 22 1 0
21 24 1 0
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25 26 1 0
27 28 1 0
28 29 2 0
28 31 1 0
29 30 1 0
30 33 2 0
31 32 2 0
32 33 1 0
2 34 1 0
V 34 *
M END
$$$$
RDKit 3D
3 2 0 0 0 0 0 0 0 0999 V2000
0.1680 12.0345 39.2648 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2860 10.5972 39.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2642 12.9079 38.2277 * 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
3 1 1 0
V 3 *
M END
$$$$
Raw
ligand.mol2
@<TRIPOS>MOLECULE
4wsq.A
56 63 1 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 O3 0.4371 12.7505 36.9853 O.2 1 KSA -0.5700
2 C22 0.2642 12.9079 38.2277 C.2 1 KSA 0.6590
3 O5 0.1680 12.0345 39.2648 O.3 1 KSA -0.4300
4 C26 0.2860 10.5972 39.0005 C.3 1 KSA 0.0400
5 H261 0.1860 10.0464 39.9358 H 1 KSA 0.0800
6 H262 1.2599 10.3879 38.5580 H 1 KSA 0.0800
7 H263 -0.5000 10.2888 38.3113 H 1 KSA 0.0800
8 C1 0.1139 14.4529 38.7161 C.3 1 KSA 0.3410
9 O4 -0.1199 15.2058 37.5393 O.3 1 KSA -0.6800
10 H4 0.5771 14.9921 36.9147 H 1 KSA 0.4000
11 C2 1.4629 14.9015 39.2347 C.3 1 KSA 0.5356
12 O1 1.5348 14.4683 40.5302 O.3 1 KSA -0.5600
13 C25 2.7584 14.1638 38.7160 C.3 1 KSA -0.2400
14 H251 2.5899 13.0869 38.7211 H 1 KSA 0.0800
15 H252 3.5985 14.4032 39.3680 H 1 KSA 0.0800
16 H253 2.9814 14.4919 37.7008 H 1 KSA 0.0800
17 N1 1.5866 16.4121 39.2693 N.pl3 1 KSA 0.0476
18 C3 1.0672 17.1163 40.3752 C.ar 1 KSA -0.1516
19 C4 0.4388 16.7898 41.5210 C.ar 1 KSA -0.1516
20 N2 0.0627 15.6155 42.0329 N.pl3 1 KSA 0.0476
21 C24 0.3466 14.2770 41.1661 C.3 1 KSA 0.4556
22 H24 0.2989 13.3566 41.7481 H 1 KSA 0.0800
23 C27 -0.7124 14.4810 39.9151 C.3 1 KSA -0.1600
24 H271 -1.4436 13.6728 39.8959 H 1 KSA 0.0800
25 H272 -1.2294 15.4366 40.0022 H 1 KSA 0.0800
26 C17 -0.5317 15.7088 43.1974 C.ar 1 KSA -0.1516
27 C18 -1.0207 14.7348 44.0079 C.ar 1 KSA -0.1500
28 H18 -0.9328 13.7138 43.6668 H 1 KSA 0.1500
29 C19 -1.6224 14.9462 45.2351 C.ar 1 KSA -0.1500
30 H19 -2.0004 14.1467 45.8550 H 1 KSA 0.1500
31 C20 -1.6961 16.3400 45.6074 C.ar 1 KSA -0.1500
32 H20 -2.1611 16.6287 46.5385 H 1 KSA 0.1500
33 C21 -1.1686 17.3033 44.7665 C.ar 1 KSA -0.1500
34 H21 -1.2304 18.3267 45.1060 H 1 KSA 0.1500
35 C16 -0.5705 17.0948 43.5370 C.ar 1 KSA 0.0000
36 C5 0.0309 17.8151 42.4832 C.ar 1 KSA 0.0000
37 C6 0.3331 19.1308 42.1573 C.ar 1 KSA 0.0862
38 C15 0.0635 20.4186 42.8468 C.2 1 KSA 0.5438
39 O2 -0.4789 20.5149 43.9799 O.2 1 KSA -0.5700
40 C7 0.9404 19.4457 41.0616 C.ar 1 KSA -0.1435
41 C23 1.0638 20.8782 40.9989 C.3 1 KSA 0.2836
42 H231 0.5338 21.2623 40.1273 H 1 KSA 0.0800
43 H232 2.1146 21.1617 40.9393 H 1 KSA 0.0800
44 N3 0.4914 21.3888 42.1763 N.am 1 KSA -0.7301
45 H3 0.4346 22.3631 42.4364 H 1 KSA 0.3700
46 C8 1.3044 18.4545 40.1286 C.ar 1 KSA 0.0000
47 C9 1.9344 18.5389 38.9159 C.ar 1 KSA 0.0000
48 C10 2.1268 17.2037 38.4036 C.ar 1 KSA -0.1516
49 C11 2.7069 17.0197 37.1928 C.ar 1 KSA -0.1500
50 H11 2.7941 16.0216 36.7897 H 1 KSA 0.1500
51 C14 2.4033 19.5492 38.2013 C.ar 1 KSA -0.1500
52 H14 2.2864 20.5456 38.6012 H 1 KSA 0.1500
53 C13 3.0259 19.4173 36.9909 C.ar 1 KSA -0.1500
54 H13 3.3831 20.2795 36.4474 H 1 KSA 0.1500
55 C12 3.1866 18.0888 36.4700 C.ar 1 KSA -0.1500
56 H12 3.6783 17.9301 35.5216 H 1 KSA 0.1500
@<TRIPOS>BOND
1 1 2 2
2 2 3 1
3 2 8 1
4 3 4 1
5 4 5 1
6 4 6 1
7 4 7 1
8 8 9 1
9 8 11 1
10 8 23 1
11 9 10 1
12 11 12 1
13 11 13 1
14 11 17 1
15 12 21 1
16 13 14 1
17 13 15 1
18 13 16 1
19 17 18 1
20 17 48 1
21 18 19 ar
22 18 46 ar
23 19 20 1
24 19 36 ar
25 20 21 1
26 20 26 1
27 21 22 1
28 21 23 1
29 23 24 1
30 23 25 1
31 26 27 ar
32 26 35 ar
33 27 28 1
34 27 29 ar
35 29 30 1
36 29 31 ar
37 31 32 1
38 31 33 ar
39 33 34 1
40 33 35 ar
41 35 36 1
42 36 37 ar
43 37 38 1
44 37 40 ar
45 38 39 2
46 38 44 am
47 40 41 1
48 40 46 ar
49 41 42 1
50 41 43 1
51 41 44 1
52 44 45 1
53 46 47 1
54 47 48 ar
55 47 51 ar
56 48 49 ar
57 49 50 1
58 49 55 ar
59 51 52 1
60 51 53 ar
61 53 54 1
62 53 55 ar
63 55 56 1
@<TRIPOS>SUBSTRUCTURE
1 KSA 18 GROUP 4 A **** 0
# MOE 2012.10 (io_trps.svl 2012.10)
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