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 (-0.745 kcal/mol/HA)
✓ Good fit quality (FQ -7.39)
✗ Very high strain energy (21.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.592
kcal/mol
LE
-0.745
kcal/mol/HA
Fit Quality
-7.39
FQ (Leeson)
HAC
33
heavy atoms
MW
448
Da
LogP
1.80
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 21.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 9
Severe clashes 0
| Final rank | 55.27166827387172 | Score | -24.5924 |
|---|---|---|---|
| Inter norm | -0.722275 | Intra norm | -0.0229497 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | geometry warning; 16 clashes; 9 protein contact clashes | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;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 | 14 | Native recall | 0.70 |
| Jaccard | 0.58 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1161 | 3.948337522565226 | -0.698773 | -20.5161 | 0 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 1159 | 3.988460996319415 | -0.58319 | -18.5155 | 0 | 16 | 16 | 0.80 | 0.00 | - | no | Open |
| 1160 | 5.231694147560967 | -0.65838 | -17.8591 | 0 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 1167 | 5.313383335619879 | -0.589913 | -18.7042 | 0 | 16 | 16 | 0.80 | 0.00 | - | no | Open |
| 1172 | 6.785674728234417 | -0.699496 | -24.8133 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1170 | 7.173303122797061 | -0.697002 | -20.4603 | 0 | 16 | 12 | 0.60 | 0.00 | - | no | Open |
| 1157 | 54.84402317720628 | -0.671848 | -22.0822 | 1 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1162 | 54.893565489220194 | -0.707083 | -23.1132 | 0 | 16 | 13 | 0.65 | 0.00 | - | no | Open |
| 1158 | 55.27166827387172 | -0.722275 | -24.5924 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Current |
| 1168 | 57.148456020128535 | -0.72006 | -22.3168 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1166 | 55.50472937125539 | -0.715134 | -22.644 | 0 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1164 | 56.60132096244247 | -0.679079 | -24.6809 | 0 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1165 | 56.9682291355801 | -0.658516 | -21.4696 | 1 | 14 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1169 | 57.802881614178645 | -0.596696 | -17.3389 | 0 | 16 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1171 | 57.87321100162594 | -0.791324 | -24.4577 | 0 | 21 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1163 | 58.17970061634287 | -0.758886 | -24.0237 | 1 | 21 | 18 | 0.90 | 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
-24.592kcal/mol
Ligand efficiency (LE)
-0.7452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.394
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
447.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.80
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
116.13kcal/mol
Minimised FF energy
94.47kcal/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.