Molecular metrics status: queued
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Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: weak
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 13
Severe clashes 0
| Final rank | 6.002580860391582 | Score | -18.3346 |
|---|---|---|---|
| Inter norm | -0.878923 | Intra norm | 0.173668 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 11 clashes; 13 protein contact clashes; high strain Δ 22.4 | ||
| Residues | A:NDP301;B:ALA32;B:ARG48;B:ASP52;B:ILE45;B:MET53;B:PHE56;B:PRO50;B:PRO88;B:SER44;B:SER86;B:TRP47;B:VAL49 | ||
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:NDP301; B:ALA32; B:ARG97; B:ASP52; B:GLY157; B:ILE45; B:LEU94; B:LYS57; B:MET53; B:PHE55; B:PHE56; B:PHE91; B:PRO88; B:SER86; B:THR180; B:THR83; B:TYR162; B:VAL156; B:VAL30; B:VAL31; B:VAL87 | ||
| Current overlap | 8 | Native recall | 0.38 |
| Jaccard | 0.31 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 1 | Role recall | 0.17 |
| H-bond same residue | 1 | Residue recall | 0.17 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2556 | 2.56005718758619 | -0.892981 | -25.0544 | 1 | 19 | 19 | 0.90 | 0.17 | - | no | Open |
| 2299 | 2.631614367521299 | -1.06346 | -29.3292 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2554 | 2.7078098932547885 | -0.85633 | -21.7921 | 1 | 19 | 19 | 0.90 | 0.17 | - | no | Open |
| 2392 | 3.4007757905046723 | -0.89664 | -22.5064 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2860 | 3.459434025282788 | -0.586227 | -17.2719 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2297 | 3.864243300287797 | -1.0745 | -27.8525 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 3260 | 4.208806845415883 | -1.06066 | -27.9908 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 3264 | 4.23041207454424 | -1.0365 | -26.874 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2301 | 4.653312728446953 | -1.11181 | -27.0313 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2555 | 5.202364879127718 | -0.730112 | -18.8269 | 1 | 16 | 15 | 0.71 | 0.00 | - | no | Open |
| 2861 | 5.22955659252202 | -0.690301 | -13.1113 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2394 | 5.375966602034466 | -0.789683 | -21.5239 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2858 | 5.610705689186814 | -0.661211 | -16.1929 | 4 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2557 | 6.002580860391582 | -0.878923 | -18.3346 | 4 | 13 | 8 | 0.38 | 0.17 | - | no | Current |
| 3265 | 4.688739833711961 | -0.809414 | -18.7293 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3262 | 4.8431868433061736 | -0.946792 | -24.4373 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2859 | 5.814987639708491 | -0.668481 | -16.7205 | 2 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2395 | 5.956897104524552 | -0.856747 | -16.9129 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2393 | 5.972392960267089 | -0.988006 | -21.2129 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3263 | 8.058799273594556 | -0.797034 | -18.7622 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3261 | 9.365242317841728 | -0.879831 | -23.8497 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2302 | 10.056273785360728 | -1.34771 | -27.9477 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2298 | 10.706812236978191 | -1.34102 | -29.1209 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2300 | 14.113166681221848 | -1.25256 | -26.7006 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Molecular metrics have not been computed for this pose yet. This page now reads only cached values; use a background recompute when you want fresh metrics without slowing the UI.