Hi guys, I want to make a protein-ligand docking from a PREDICTED protein structure (HSD17B2, calidris pugnax) (AlphaFold and D-I-TASSER) and I decided to use HADDOCK as it has been reported by many recent papers to be the overall best.
The ligand I want to use id TESTOSTERONE , so I went to pubchem database (https://pubchem.ncbi.nlm.nih.gov/compound/6013) and downloaded the 3D SDF file.
Then I converted this file with open.babel program to .PDB, but when I am submitting it in HADDOCK I get this:
Then, I read tons of tutorials that I have to do renumb and remove the HETAM of the ligand PDB or even take out repeated atoms... I tried the web PDB-tools but I it is not even recognizing the full ligand structure to begin with (when I press visualize), and in Pymol it looks super fine
the SDF content of the ligand is (i added the (#) here for better visualization purposes only) :
#> <PUBCHEM_SHAPE_MULTIPOLES>
420.43
9.43
2.1
1.06
1.16
0.42
0.43
-0.59
-2.56
-0.22
0.02
0.09
-0.22
0.11
#> <PUBCHEM_SHAPE_SELFOVERLAP>
902.625
#> <PUBCHEM_SHAPE_VOLUME>
230.1
#> <PUBCHEM_COORDINATE_TYPE>
2
5
10
$$$$
And, what I got after converting the ligand with openbabel to .PDB is :
COMPND 6013
AUTHOR GENERATED BY OPEN BABEL 3.1.1
HETATM 1 O UNL 1 -5.169 1.064 0.361 1.00 0.00 O
HETATM 2 O UNL 1 5.593 -0.143 0.967 1.00 0.00 O
HETATM 3 C UNL 1 -1.999 -0.736 0.356 1.00 0.00 C
HETATM 4 C UNL 1 -2.781 0.550 0.027 1.00 0.00 C
HETATM 5 C UNL 1 -0.621 -0.777 -0.313 1.00 0.00 C
HETATM 6 C UNL 1 0.214 0.446 0.182 1.00 0.00 C
HETATM 7 C UNL 1 1.673 0.472 -0.417 1.00 0.00 C
HETATM 8 C UNL 1 -1.990 1.742 0.581 1.00 0.00 C
HETATM 9 C UNL 1 -0.560 1.783 0.014 1.00 0.00 C
HETATM 10 C UNL 1 -4.093 0.244 0.774 1.00 0.00 C
HETATM 11 C UNL 1 -3.002 -1.848 0.063 1.00 0.00 C
HETATM 12 C UNL 1 0.117 -2.083 0.007 1.00 0.00 C
HETATM 13 C UNL 1 -4.359 -1.244 0.468 1.00 0.00 C
HETATM 14 C UNL 1 2.327 -0.904 -0.237 1.00 0.00 C
HETATM 15 C UNL 1 1.499 -2.105 -0.632 1.00 0.00 C
HETATM 16 C UNL 1 -3.059 0.769 -1.482 1.00 0.00 C
HETATM 17 C UNL 1 2.494 1.554 0.343 1.00 0.00 C
HETATM 18 C UNL 1 1.673 0.812 -1.925 1.00 0.00 C
HETATM 19 C UNL 1 3.996 1.437 0.137 1.00 0.00 C
HETATM 20 C UNL 1 3.576 -1.089 0.221 1.00 0.00 C
HETATM 21 C UNL 1 4.470 0.057 0.507 1.00 0.00 C
HETATM 22 H UNL 1 -1.823 -0.766 1.445 1.00 0.00 H
HETATM 23 H UNL 1 -0.747 -0.725 -1.399 1.00 0.00 H
HETATM 24 H UNL 1 0.329 0.309 1.270 1.00 0.00 H
HETATM 25 H UNL 1 -1.929 1.677 1.675 1.00 0.00 H
HETATM 26 H UNL 1 -2.503 2.685 0.356 1.00 0.00 H
HETATM 27 H UNL 1 -0.604 2.066 -1.042 1.00 0.00 H
HETATM 28 H UNL 1 -0.025 2.591 0.526 1.00 0.00 H
HETATM 29 H UNL 1 -3.966 0.378 1.855 1.00 0.00 H
HETATM 30 H UNL 1 -2.786 -2.757 0.633 1.00 0.00 H
HETATM 31 H UNL 1 -3.006 -2.115 -1.000 1.00 0.00 H
HETATM 32 H UNL 1 -0.456 -2.941 -0.365 1.00 0.00 H
HETATM 33 H UNL 1 0.210 -2.210 1.093 1.00 0.00 H
HETATM 34 H UNL 1 -5.099 -1.385 -0.327 1.00 0.00 H
HETATM 35 H UNL 1 -4.754 -1.742 1.360 1.00 0.00 H
HETATM 36 H UNL 1 1.398 -2.123 -1.725 1.00 0.00 H
HETATM 37 H UNL 1 1.998 -3.042 -0.356 1.00 0.00 H
HETATM 38 H UNL 1 -3.668 -0.029 -1.917 1.00 0.00 H
HETATM 39 H UNL 1 -3.595 1.711 -1.644 1.00 0.00 H
HETATM 40 H UNL 1 -2.143 0.824 -2.076 1.00 0.00 H
HETATM 41 H UNL 1 2.293 1.475 1.421 1.00 0.00 H
HETATM 42 H UNL 1 2.181 2.561 0.043 1.00 0.00 H
HETATM 43 H UNL 1 0.998 0.167 -2.496 1.00 0.00 H
HETATM 44 H UNL 1 1.368 1.848 -2.105 1.00 0.00 H
HETATM 45 H UNL 1 2.671 0.693 -2.365 1.00 0.00 H
HETATM 46 H UNL 1 4.505 2.163 0.781 1.00 0.00 H
HETATM 47 H UNL 1 4.283 1.642 -0.899 1.00 0.00 H
HETATM 48 H UNL 1 4.000 -2.079 0.347 1.00 0.00 H
HETATM 49 H UNL 1 -5.448 0.793 -0.529 1.00 0.00 H
CONECT 1 10 49
CONECT 2 21 21
CONECT 3 4 5 11 22
CONECT 4 3 8 10 16
CONECT 5 3 6 12 23
CONECT 6 5 7 9 24
CONECT 7 6 14 17 18
CONECT 8 4 9 25 26
CONECT 9 6 8 27 28
CONECT 10 1 4 13 29
CONECT 11 3 13 30 31
CONECT 12 5 15 32 33
CONECT 13 10 11 34 35
CONECT 14 7 15 20 20
CONECT 15 12 14 36 37
CONECT 16 4 38 39 40
CONECT 17 7 19 41 42
CONECT 18 7 43 44 45
CONECT 19 17 21 46 47
CONECT 20 14 14 21 48
CONECT 21 2 2 19 20
CONECT 22 3
CONECT 23 5
CONECT 24 6
CONECT 25 8
CONECT 26 8
CONECT 27 9
CONECT 28 9
CONECT 29 10
CONECT 30 11
CONECT 31 11
CONECT 32 12
CONECT 33 12
CONECT 34 13
CONECT 35 13
CONECT 36 15
CONECT 37 15
CONECT 38 16
CONECT 39 16
CONECT 40 16
CONECT 41 17
CONECT 42 17
CONECT 43 18
CONECT 44 18
CONECT 45 18
CONECT 46 19
CONECT 47 19
CONECT 48 20
CONECT 49 1
MASTER 0 0 0 0 0 0 0 0 49 0 49 0
END
Could someone that knows what the ligand format should be for HADDOCK2.4 give me a hand here ? I would be really thankful !
