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 (-0.737 kcal/mol/HA)
✓ Good fit quality (FQ -7.55)
✗ High strain energy (12.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.274
kcal/mol
LE
-0.737
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
37
heavy atoms
MW
495
Da
LogP
4.43
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 12.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 4
Clashes 11
Severe clashes 2
| Final rank | 8.603768764228624 | Score | -27.2741 |
|---|---|---|---|
| Inter norm | -0.683635 | Intra norm | -0.053503 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 16 clashes; 2 protein clashes; moderate strain Δ 16.1 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR180;A:THR54;A:TRP47;A:VAL156;A:VAL30;A:VAL31;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 | 18 | Native recall | 0.90 |
| Jaccard | 0.78 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 394 | 4.824031120225275 | -0.559793 | -17.9593 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 4.8342966363052895 | -0.874586 | -28.7263 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 5.544913036571565 | -0.837917 | -25.4211 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 5.71545161130506 | -0.531814 | -22.122 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 523 | 5.853583757572163 | -0.475833 | -14.4118 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 400 | 5.991578804880139 | -0.6343 | -23.2541 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 6.016219807250548 | -0.503386 | -16.6918 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 6.271765321214856 | -0.532132 | -26.5306 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 717 | 6.359048231967443 | -0.366984 | -12.9882 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 720 | 6.454657660615654 | -0.439902 | -16.8067 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 538 | 6.461885054046319 | -0.485127 | -22.026 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 588 | 6.469183471884971 | -0.642205 | -21.2297 | 1 | 18 | 17 | 0.85 | 0.20 | - | no | Open |
| 582 | 6.557615301449495 | -0.660037 | -17.1485 | 0 | 19 | 18 | 0.90 | 0.00 | - | no | Open |
| 712 | 6.820650888681524 | -0.391361 | -14.3591 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 527 | 7.163080623390221 | -0.625227 | -23.7366 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 7.391532983625233 | -0.715721 | -21.8731 | 1 | 17 | 15 | 0.75 | 0.20 | - | no | Open |
| 537 | 7.6183813565571885 | -0.587778 | -19.2357 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 713 | 7.769950286759409 | -0.481214 | -15.2582 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 8.260915333543338 | -0.552057 | -24.578 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 718 | 8.686843616583896 | -0.450704 | -19.2841 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 6.732147949674597 | -0.704644 | -25.0006 | 0 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 531 | 7.074134258414574 | -0.475045 | -19.5657 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 529 | 7.461715263826837 | -0.463645 | -17.571 | 0 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 528 | 7.486579424380058 | -0.511433 | -21.3373 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 587 | 7.531982670403918 | -0.586933 | -20.6302 | 0 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 397 | 7.780685289612809 | -0.639316 | -26.3868 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 534 | 7.870906154971624 | -0.549002 | -23.6055 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 398 | 7.953263128225099 | -0.8172 | -28.1181 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 719 | 8.062327028852009 | -0.470867 | -13.935 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 396 | 8.068583176739661 | -0.769401 | -19.7046 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 711 | 8.236743801116575 | -0.579801 | -22.5862 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 579 | 8.261263508834592 | -0.708317 | -21.9743 | 1 | 19 | 17 | 0.85 | 0.00 | - | yes | Open |
| 585 | 8.383207669517338 | -0.707315 | -24.7732 | 0 | 19 | 18 | 0.90 | 0.00 | - | yes | Open |
| 716 | 8.552341082283359 | -0.374775 | -12.8459 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 581 | 8.603768764228624 | -0.683635 | -27.2741 | 1 | 21 | 18 | 0.90 | 0.00 | - | yes | Current |
| 526 | 8.830135839323713 | -0.478375 | -19.3293 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 540 | 9.305664535969818 | -0.553463 | -23.5298 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 402 | 9.672259340185855 | -0.599865 | -14.2895 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 580 | 10.447446779426922 | -0.645172 | -24.8712 | 3 | 10 | 7 | 0.35 | 0.20 | - | yes | Open |
| 584 | 10.720186707206247 | -0.783426 | -21.1736 | 1 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 399 | 56.65304746631722 | -0.56375 | -17.945 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 532 | 57.0975813531502 | -0.584451 | -23.4639 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 539 | 57.32768770998607 | -0.461476 | -15.804 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 715 | 57.421555140899216 | -0.539862 | -20.0272 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 714 | 57.73022582961767 | -0.443412 | -16.8325 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 525 | 58.73819404495769 | -0.410954 | -18.5926 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 586 | 59.099750611742564 | -0.791936 | -27.0296 | 1 | 20 | 17 | 0.85 | 0.20 | - | yes | Open |
| 535 | 59.36500216101931 | -0.535377 | -21.3038 | 3 | 14 | 0 | 0.00 | 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
-27.274kcal/mol
Ligand efficiency (LE)
-0.7371kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.547
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.43
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
121.69kcal/mol
Minimised FF energy
109.42kcal/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.