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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.657 kcal/mol/HA)
✓ Good fit quality (FQ -6.52)
✗ Very high strain energy (33.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.674
kcal/mol
LE
-0.657
kcal/mol/HA
Fit Quality
-6.52
FQ (Leeson)
HAC
33
heavy atoms
MW
477
Da
LogP
1.81
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 33.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 3
Clashes 11
Severe clashes 0
| Final rank | 6.346638730015562 | Score | -21.6745 |
|---|---|---|---|
| Inter norm | -0.717074 | Intra norm | 0.0602708 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 11 protein contact clashes; high strain Δ 35.4 | ||
| 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:THR54;A:THR83;A:TYR162;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 | 19 | Native recall | 0.95 |
| Jaccard | 0.95 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 3.8840715490426887 | -0.722711 | -21.7454 | 2 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 446 | 4.35769441122194 | -0.911223 | -30.6016 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 5.067846025116949 | -0.957055 | -28.4693 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 452 | 5.1291715272872 | -0.775075 | -23.3235 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 5.247009396814082 | -0.571614 | -17.3009 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 6.008765931258514 | -0.650242 | -20.613 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 6.082926958825837 | -0.857518 | -27.9425 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 490 | 6.346638730015562 | -0.717074 | -21.6745 | 2 | 19 | 19 | 0.95 | 0.20 | - | no | Current |
| 367 | 6.384760529767993 | -0.649129 | -19.5902 | 2 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 368 | 7.290869591443741 | -0.603964 | -16.7595 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 429 | 5.522913112731401 | -0.72625 | -25.2614 | 2 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 483 | 6.396892644125071 | -0.7221 | -24.9222 | 2 | 16 | 12 | 0.60 | 0.00 | - | yes | Open |
| 361 | 6.575864139783592 | -0.59434 | -21.4473 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 451 | 6.688316365817855 | -0.952365 | -30.6657 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 448 | 6.729709980923917 | -0.888053 | -26.4026 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 487 | 6.806346688093569 | -0.731947 | -21.4574 | 3 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 362 | 6.839393997640773 | -0.615709 | -17.2499 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 434 | 6.873496918519347 | -0.522811 | -16.967 | 4 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 436 | 7.10053059660853 | -0.772552 | -22.9248 | 4 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 430 | 7.431076745847866 | -0.535033 | -16.9844 | 4 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 489 | 7.659385448545859 | -0.751505 | -23.7205 | 3 | 21 | 19 | 0.95 | 0.20 | - | yes | Open |
| 365 | 7.881357062750198 | -0.650064 | -21.2651 | 5 | 11 | 1 | 0.05 | 0.00 | - | yes | Open |
| 485 | 8.870862631968425 | -0.681485 | -18.7582 | 1 | 21 | 19 | 0.95 | 0.20 | - | yes | Open |
| 486 | 9.219719130430658 | -0.712182 | -19.3634 | 2 | 19 | 17 | 0.85 | 0.00 | - | yes | Open |
| 366 | 9.940726351765546 | -0.615714 | -20.8153 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 433 | 10.243289061210085 | -0.739347 | -22.6327 | 2 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 363 | 11.419125882890718 | -0.832714 | -26.2276 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 365 | 11.46264684441211 | -0.656114 | -20.0149 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 369 | 14.18280842945374 | -0.776682 | -22.8437 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 370 | 14.576079944322883 | -0.71461 | -21.5368 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 363 | 56.328610250795435 | -0.628498 | -20.8925 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 449 | 56.36327849321316 | -0.800246 | -25.344 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 445 | 56.75262840181659 | -0.841435 | -28.3143 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 431 | 56.8321064935309 | -0.711287 | -22.8056 | 5 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 488 | 57.71905130971411 | -0.649561 | -20.7203 | 3 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 484 | 59.44256791162809 | -0.633698 | -21.4301 | 2 | 15 | 10 | 0.50 | 0.20 | - | yes | Open |
| 435 | 59.9598923432017 | -0.838175 | -25.9773 | 5 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 368 | 60.39291892413463 | -0.592914 | -17.4802 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 367 | 63.8296401791971 | -0.659495 | -20.2432 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 364 | 64.20129428770224 | -0.655235 | -19.5358 | 8 | 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.
Scoring & efficiency
Docking score
-21.674kcal/mol
Ligand efficiency (LE)
-0.6568kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.517
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
476.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
34.09kcal/mol
Minimised FF energy
0.23kcal/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.