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 (-0.623 kcal/mol/HA)
✓ Good fit quality (FQ -5.81)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (21.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-16.826
kcal/mol
LE
-0.623
kcal/mol/HA
Fit Quality
-5.81
FQ (Leeson)
HAC
27
heavy atoms
MW
368
Da
LogP
3.37
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 21.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 17
π–π 1
Clashes 8
Severe clashes 3
| Final rank | 57.57073127203884 | Score | -16.8255 |
|---|---|---|---|
| Inter norm | -0.694403 | Intra norm | 0.0712347 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 10 clashes; 3 protein clashes | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS90;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:VAL156 | ||
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 | 11 | Native recall | 0.55 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2608 | 3.698278565307773 | -0.94739 | -24.9655 | 5 | 17 | 15 | 0.75 | 0.60 | - | no | Open |
| 2612 | 3.70057410392316 | -0.726303 | -17.5994 | 2 | 16 | 11 | 0.55 | 0.40 | - | no | Open |
| 1182 | 4.362055859919374 | -0.884136 | -19.6065 | 2 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 2604 | 4.419994708340056 | -0.756398 | -17.5123 | 4 | 12 | 11 | 0.55 | 0.40 | - | no | Open |
| 2605 | 5.008733444313428 | -1.0097 | -24.4552 | 6 | 16 | 15 | 0.75 | 0.80 | - | no | Open |
| 2609 | 5.410862809071742 | -0.81119 | -14.6132 | 4 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 2601 | 5.436304521940765 | -0.846938 | -21.9185 | 4 | 18 | 13 | 0.65 | 0.20 | - | no | Open |
| 1191 | 5.365938897605203 | -0.810506 | -20.692 | 3 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1186 | 5.479093802955195 | -0.752228 | -17.993 | 3 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1188 | 5.537619678184513 | -0.838075 | -11.4512 | 2 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1193 | 5.80687590716687 | -0.872121 | -23.5192 | 2 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1181 | 6.097609180236347 | -0.97482 | -18.2139 | 3 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1184 | 6.359659961901646 | -0.680177 | -18.9206 | 4 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2603 | 6.5570386699385015 | -0.844485 | -25.0836 | 4 | 17 | 16 | 0.80 | 0.40 | - | yes | Open |
| 1192 | 6.812379661133425 | -0.82684 | -19.3107 | 4 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2614 | 6.962520459224539 | -0.791448 | -23.0718 | 2 | 19 | 18 | 0.90 | 0.20 | - | yes | Open |
| 2613 | 7.157504635431177 | -0.725153 | -21.9182 | 5 | 16 | 12 | 0.60 | 0.20 | - | yes | Open |
| 2602 | 7.341619388530795 | -0.848996 | -18.6678 | 4 | 20 | 17 | 0.85 | 0.40 | - | yes | Open |
| 1183 | 8.492270677751259 | -0.760172 | -19.3597 | 2 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1189 | 55.23594419180738 | -0.940873 | -10.675 | 1 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2610 | 56.06968259624646 | -0.867828 | -22.4346 | 3 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2606 | 56.54156088939767 | -0.789539 | -17.657 | 3 | 17 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1185 | 57.03122331557638 | -0.816234 | -17.0131 | 3 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2600 | 57.167598560916105 | -0.76276 | -14.091 | 6 | 16 | 15 | 0.75 | 0.40 | - | yes | Open |
| 1194 | 57.173033596652324 | -0.678613 | -16.6003 | 5 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2611 | 57.57073127203884 | -0.694403 | -16.8255 | 3 | 13 | 11 | 0.55 | 0.20 | - | yes | Current |
| 1190 | 58.96388150318519 | -0.763762 | -11.9454 | 1 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1180 | 60.5179075520816 | -0.678169 | -6.22749 | 6 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2607 | 60.64472946672734 | -0.749019 | -18.5811 | 5 | 11 | 8 | 0.40 | 0.20 | - | yes | Open |
| 1187 | 63.88677328233778 | -0.660785 | -6.17783 | 5 | 16 | 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
-16.826kcal/mol
Ligand efficiency (LE)
-0.6232kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.814
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
368.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.37
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
69.81kcal/mol
Minimised FF energy
48.21kcal/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.