I tried to dock 708 ligand to FXR in order to obtain 3gd2 (https://www.rcsb.org/structure/3GD2).
According to this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3254253/table/t0005/?report=objectonly
i used the files below (only part of them is shown due to character limit).
active residues for FXR: activereslist = 265,269,270,273,284,287,288,290,291,294,325,328,329,331,333,335,336,340,342,348,352,357,361,362,365,366,369,447,450,451,454,461,469’,
active residues for ligand: activereslist = ‘1847,1849,1850,1852,1855,1856,1863,1864,1866,1873,1875’
I got results (cluster with minimum RMSD from the overall lowest-energy structure):
Cluster 3
HADDOCK score 7.3 +/- 1.4
Cluster size 7
RMSD from the overall lowest-energy structure 6.7 +/- 2.0
Van der Waals energy 0.0 +/- 0.0
Electrostatic energy 0.0 +/- 0.0
Desolvation energy 7.3 +/- 1.4
Restraints violation energy 0.3 +/- 0.19
Buried Surface Area -999999.0 +/- 0.0
Z-Score 1.2
The resulting structure is not docked. Shouldn’t i get a lower RMSD?
I also got no images graphics. Why?
708 ligand:
HETATM 1840 CL38 708 A 1 129.066 157.923 20.445 1.00 78.14 CL
HETATM 1841 C37 708 A 1 130.803 157.817 20.838 1.00 77.73 C
HETATM 1842 C25 708 A 1 131.639 156.778 20.420 1.00 78.14 C
HETATM 1843 C26 708 A 1 131.251 155.677 19.509 1.00 78.00 C
HETATM 1844 C27 708 A 1 130.106 155.695 18.836 1.00 80.26 C
HETATM 1845 C28 708 A 1 129.710 154.678 17.835 1.00 80.66 C
HETATM 1846 C33 708 A 1 128.518 154.924 17.160 1.00 81.06 C
HETATM 1847 C32 708 A 1 128.061 154.057 16.176 1.00 81.07 C
HETATM 1848 C34 708 A 1 126.767 154.361 15.485 1.00 81.28 C
HETATM 1849 O36 708 A 1 126.028 155.399 15.891 1.00 81.55 O
HETATM 1850 O35 708 A 1 126.397 153.691 14.528 1.00 82.93 O
HETATM 1851 C31 708 A 1 128.812 152.935 15.842 1.00 80.99 C
HETATM 1852 C30 708 A 1 130.019 152.694 16.501 1.00 81.25 C
HETATM 1853 C29 708 A 1 130.479 153.563 17.492 1.00 81.25 C
HETATM 1854 C24 708 A 1 132.981 156.817 20.792 1.00 77.90 C
HETATM 1855 C23 708 A 1 133.463 157.848 21.594 1.00 77.84 C
HETATM 1856 C39 708 A 1 131.281 158.842 21.638 1.00 77.46 C
HETATM 1857 C22 708 A 1 132.606 158.865 22.018 1.00 77.26 C
HETATM 1858 O21 708 A 1 133.012 159.897 22.802 1.00 76.55 O
HETATM 1859 C20 708 A 1 134.365 160.063 23.186 1.00 74.79 C
HETATM 1860 C19 708 A 1 134.454 161.233 24.123 1.00 73.89 C
HETATM 1861 C4 708 A 1 135.420 162.336 23.990 1.00 73.05 C
HETATM 1862 C2 708 A 1 136.517 162.647 23.047 1.00 72.72 C
HETATM 1863 C3 708 A 1 137.752 161.869 23.495 1.00 72.34 C
HETATM 1864 C1 708 A 1 136.787 164.149 22.955 1.00 72.82 C
HETATM 1865 C7 708 A 1 133.669 161.514 25.255 1.00 73.22 C
HETATM 1866 N6 708 A 1 134.080 162.674 25.825 1.00 72.97 N
HETATM 1867 O5 708 A 1 135.168 163.162 25.028 1.00 73.57 O
HETATM 1868 C8 708 A 1 132.554 160.667 25.810 1.00 73.31 C
HETATM 1869 S9 708 A 1 133.240 159.571 27.110 1.00 73.63 S
HETATM 1870 O10 708 A 1 131.844 158.772 27.892 1.00 74.87 O
HETATM 1871 C11 708 A 1 134.032 158.236 26.154 1.00 73.72 C
HETATM 1872 C17 708 A 1 133.294 157.273 25.474 1.00 73.65 C
HETATM 1873 CL18 708 A 1 131.504 157.278 25.471 1.00 73.61 CL
HETATM 1874 C16 708 A 1 133.940 156.275 24.759 1.00 73.76 C
HETATM 1875 C15 708 A 1 135.327 156.236 24.725 1.00 73.81 C
HETATM 1876 C14 708 A 1 136.068 157.193 25.402 1.00 73.65 C
HETATM 1877 C12 708 A 1 135.415 158.185 26.118 1.00 73.64 C
HETATM 1878 CL13 708 A 1 136.366 159.418 26.998 1.00 74.03 CL
END
FXR
ATOM 1 N GLY A 244 100.456 143.509 29.625 1.00104.95 N
ATOM 2 CA GLY A 244 100.013 143.891 28.252 1.00105.00 C
ATOM 3 C GLY A 244 100.129 145.404 28.034 1.00105.09 C
ATOM 4 O GLY A 244 99.760 146.198 28.904 1.00105.15 O
ATOM 5 N SER A 245 100.638 145.785 26.863 1.00105.13 N
ATOM 6 CA SER A 245 100.842 147.190 26.502 1.00104.99 C
ATOM 7 C SER A 245 99.597 147.764 25.824 1.00104.85 C
ATOM 8 O SER A 245 98.955 147.083 25.022 1.00104.89 O
ATOM 9 CB SER A 245 102.038 147.303 25.551 1.00105.11 C
ATOM 10 N THR A 246 99.271 149.018 26.129 1.00104.63 N
ATOM 11 CA THR A 246 98.099 149.674 25.539 1.00104.58 C
ATOM 12 C THR A 246 98.414 150.111 24.100 1.00104.58 C
ATOM 13 O THR A 246 99.584 150.193 23.720 1.00104.51 O
ATOM 14 CB THR A 246 97.636 150.902 26.371 1.00104.45 C
ATOM 15 CG2 THR A 246 97.661 150.599 27.867 1.00104.21 C
ATOM 16 OG1 THR A 246 98.469 152.033 26.087 1.00104.42 O
ATOM 17 N PRO A 247 97.374 150.373 23.284 1.00104.63 N
ATOM 18 CA PRO A 247 97.639 150.891 21.937 1.00104.58 C
ATOM 19 C PRO A 247 98.184 152.320 21.951 1.00104.50 C
ATOM 20 O PRO A 247 98.890 152.726 21.025 1.00104.50 O
ATOM 21 CB PRO A 247 96.263 150.840 21.259 1.00104.60 C
ATOM 22 CG PRO A 247 95.287 150.899 22.368 1.00104.72 C
ATOM 23 CD PRO A 247 95.930 150.197 23.530 1.00104.69 C
ATOM 24 N ASP A 248 97.858 153.069 22.997 1.00104.40 N
ATOM 25 CA ASP A 248 98.339 154.434 23.131 1.00104.34 C
ATOM 26 C ASP A 248 99.784 154.449 23.636 1.00104.27 C
ATOM 27 O ASP A 248 100.522 155.405 23.403 1.00104.28 O
ATOM 28 CB ASP A 248 97.428 155.228 24.068 1.00104.32 C
ATOM 29 CG ASP A 248 97.436 156.703 23.766 1.00104.24 C
ATOM 30 OD1 ASP A 248 97.657 157.067 22.594 1.00104.01 O
ATOM 31 OD2 ASP A 248 97.215 157.501 24.699 1.00104.60 O1-
ATOM 32 N GLN A 249 100.175 153.393 24.342 1.00104.13 N
ATOM 33 CA GLN A 249 101.579 153.175 24.671 1.00104.07 C
ATOM 34 C GLN A 249 102.307 152.595 23.459 1.00104.14 C
ATOM 35 O GLN A 249 103.445 152.967 23.183 1.00104.22 O
ATOM 36 CB GLN A 249 101.726 152.224 25.863 1.00103.99 C
ATOM 37 CG GLN A 249 101.441 152.858 27.216 1.00103.83 C
ATOM 38 CD GLN A 249 101.468 151.850 28.359 1.00103.83 C
ATOM 39 NE2 GLN A 249 101.719 152.335 29.569 1.00103.61 N
ATOM 40 OE1 GLN A 249 101.262 150.653 28.157 1.00103.60 O
ATOM 41 N GLN A 250 101.643 151.685 22.741 1.00104.10 N
ATOM 42 CA GLN A 250 102.245 150.982 21.596 1.00103.94 C
ATOM 43 C GLN A 250 102.729 151.935 20.507 1.00103.77 C
ATOM 44 O GLN A 250 103.772 151.708 19.896 1.00103.60 O
ATOM 45 CB GLN A 250 101.257 149.975 21.008 1.00103.97 C
ATOM 46 N THR A 251 101.958 152.991 20.266 1.00103.70 N
ATOM 47 CA THR A 251 102.355 154.035 19.318 1.00103.67 C
ATOM 48 C THR A 251 103.660 154.728 19.742 1.00103.59 C
ATOM 49 O THR A 251 104.476 155.097 18.893 1.00103.63 O