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 (-0.835 kcal/mol/HA)
✓ Good fit quality (FQ -7.70)
✗ Very high strain energy (24.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.721
kcal/mol
LE
-0.835
kcal/mol/HA
Fit Quality
-7.70
FQ (Leeson)
HAC
26
heavy atoms
MW
369
Da
LogP
2.84
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 24.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 3
Clashes 8
Severe clashes 0
| Final rank | 4.899918197049692 | Score | -21.721 |
|---|---|---|---|
| Inter norm | -0.931164 | Intra norm | 0.0957388 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 2 |
| Artifact reason | geometry warning; 12 clashes; 8 protein contact clashes; high strain Δ 24.6 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.80 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1194 | 3.3330933994231584 | -0.775569 | -19.1656 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2066 | 3.746020292766851 | -0.688109 | -21.0053 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1196 | 4.080938656014805 | -0.804298 | -19.9796 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1193 | 4.225282388448564 | -0.767966 | -18.7252 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1816 | 4.403569138286684 | -0.745802 | -21.369 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1195 | 4.815807510469393 | -0.904031 | -24.7577 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2663 | 4.899918197049692 | -0.931164 | -21.721 | 2 | 16 | 16 | 0.80 | 0.20 | - | no | Current |
| 1819 | 5.587276140508173 | -0.583483 | -15.0875 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1593 | 5.632498254449315 | -0.814464 | -19.6799 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1243 | 6.596835662525375 | -0.916955 | -21.2025 | 3 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 2068 | 6.253660736156609 | -0.672619 | -20.433 | 6 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2069 | 6.284650086704847 | -0.660892 | -16.0336 | 6 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2070 | 6.98568342562347 | -0.672115 | -14.0837 | 7 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1592 | 7.182700776310237 | -0.813693 | -23.6292 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1817 | 7.525975222622855 | -0.718907 | -18.6129 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2661 | 7.551928228801605 | -0.785766 | -19.2447 | 2 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1242 | 7.63896418141783 | -0.913808 | -22.9851 | 3 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1245 | 8.791171282926179 | -0.729578 | -18.3048 | 6 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2067 | 8.9829338433256 | -0.649697 | -11.3924 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1818 | 9.198691320721796 | -0.824987 | -18.7544 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2660 | 9.3396848045856 | -1.06417 | -19.044 | 3 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2662 | 9.370883843603515 | -0.920609 | -20.4658 | 3 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1244 | 9.933492211023694 | -0.753887 | -19.6855 | 5 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1591 | 10.198157148767574 | -0.847332 | -20.3988 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1590 | 11.88924984012254 | -0.933543 | -22.4803 | 6 | 15 | 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
-21.721kcal/mol
Ligand efficiency (LE)
-0.8354kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.697
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
369.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.20kcal/mol
Minimised FF energy
31.22kcal/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.