Molecular metrics status: done
Cached molecular metrics are available for this pose.
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.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.805 kcal/mol/HA)
✓ Good fit quality (FQ -7.91)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (21.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.746
kcal/mol
LE
-0.805
kcal/mol/HA
Fit Quality
-7.91
FQ (Leeson)
HAC
32
heavy atoms
MW
478
Da
LogP
3.61
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 21.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 18
π–π 0
Clashes 7
Severe clashes 2
| Final rank | 56.491681708803526 | Score | -25.7463 |
|---|---|---|---|
| Inter norm | -0.740201 | Intra norm | -0.0643695 |
| Top1000 | no | Excluded | yes |
| Contacts | 10 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 10 clashes; 2 protein clashes | ||
| Residues | A:ARG97;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:THR54;A:VAL87 | ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 9 | Native recall | 0.45 |
| Jaccard | 0.43 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 539 | 4.578051279948418 | -0.836441 | -23.7077 | 1 | 21 | 18 | 0.90 | 0.20 | - | no | Open |
| 531 | 4.873103504307923 | -0.755991 | -21.9113 | 1 | 21 | 18 | 0.90 | 0.20 | - | no | Open |
| 544 | 4.957947154718397 | -0.77194 | -27.5356 | 1 | 16 | 13 | 0.65 | 0.00 | - | no | Open |
| 424 | 4.9786679789210915 | -0.607541 | -14.4757 | 3 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 547 | 5.35220158640997 | -0.788979 | -23.0974 | 2 | 19 | 17 | 0.85 | 0.20 | - | no | Open |
| 418 | 5.503663179548383 | -0.591602 | -15.7788 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 5.592270017366477 | -0.760386 | -20.7067 | 1 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 421 | 6.130453196567059 | -0.634935 | -20.8308 | 3 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 416 | 55.392362047497045 | -0.680698 | -16.8839 | 5 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 422 | 56.08470595499364 | -0.652427 | -20.7805 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 5.351274929047857 | -0.708091 | -23.2492 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 428 | 54.92680923743816 | -0.612277 | -17.4971 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 542 | 54.93402315854781 | -0.805458 | -25.2612 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 543 | 55.11394031842511 | -0.719767 | -20.2266 | 1 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 538 | 55.320432949481805 | -0.847022 | -26.2041 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 554 | 55.44674008211802 | -0.826456 | -27.7497 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 425 | 55.634847078930164 | -0.69617 | -22.5042 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 426 | 55.978226159919124 | -0.653399 | -24.2595 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 419 | 56.099292180823014 | -0.726868 | -22.5368 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 550 | 56.15369218492761 | -0.823781 | -27.1051 | 2 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 417 | 56.17706705702731 | -0.608003 | -12.7259 | 4 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 549 | 56.491681708803526 | -0.740201 | -25.7463 | 3 | 10 | 9 | 0.45 | 0.20 | - | yes | Current |
| 541 | 56.59007578258512 | -0.764635 | -20.806 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 420 | 56.64458233008418 | -0.722115 | -24.8227 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 545 | 56.76538553890124 | -0.749641 | -23.9649 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 430 | 56.8614587127542 | -0.587938 | -18.1571 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 534 | 56.898701725433426 | -0.808824 | -25.7914 | 1 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 552 | 56.90385083398705 | -0.809357 | -17.8446 | 3 | 13 | 11 | 0.55 | 0.20 | - | yes | Open |
| 535 | 57.056440842723944 | -0.775288 | -21.1576 | 1 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 537 | 57.14621584789709 | -0.765841 | -16.9705 | 2 | 16 | 13 | 0.65 | 0.00 | - | yes | Open |
| 540 | 57.43980407676235 | -0.676081 | -18.3247 | 1 | 19 | 18 | 0.90 | 0.00 | - | yes | Open |
| 548 | 57.858147270023764 | -0.720473 | -17.1943 | 1 | 16 | 14 | 0.70 | 0.00 | - | yes | Open |
| 533 | 58.61620205238415 | -0.770822 | -25.5399 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 553 | 59.357423973642355 | -0.702808 | -22.5276 | 2 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 427 | 59.49085344586227 | -0.705055 | -24.2427 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 429 | 60.01765742426803 | -0.678756 | -20.4807 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 551 | 60.04628309910173 | -0.822051 | -24.2471 | 1 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 546 | 60.6066765495306 | -0.925317 | -25.6492 | 3 | 14 | 12 | 0.60 | 0.20 | - | yes | Open |
| 431 | 61.29124134893323 | -0.652682 | -23.0277 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 423 | 61.42540633024061 | -0.656692 | -19.582 | 4 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.746kcal/mol
Ligand efficiency (LE)
-0.8046kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.912
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
478.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.77kcal/mol
Minimised FF energy
36.20kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.