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 (-0.506 kcal/mol/HA)
✓ Good fit quality (FQ -5.18)
✗ Very high strain energy (35.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-18.739
kcal/mol
LE
-0.506
kcal/mol/HA
Fit Quality
-5.18
FQ (Leeson)
HAC
37
heavy atoms
MW
502
Da
LogP
2.91
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 35.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 7
Severe clashes 1
| Final rank | 56.386666093425426 | Score | -18.7392 |
|---|---|---|---|
| Inter norm | -0.580608 | Intra norm | 0.0741434 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash | ||
| Residues | A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:PRO93;A:THR54;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 | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1307 | 5.6717749898289105 | -0.608688 | -20.363 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1312 | 6.0995281158912835 | -0.642754 | -21.6286 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1320 | 6.1580411939956505 | -0.67509 | -28.1125 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1310 | 6.338989872218614 | -0.640789 | -24.0675 | 1 | 14 | 10 | 0.50 | 0.00 | - | no | Open |
| 1317 | 7.396649576074735 | -0.596586 | -24.0544 | 1 | 16 | 15 | 0.75 | 0.00 | - | no | Open |
| 1315 | 7.452613869330801 | -0.669329 | -21.2143 | 1 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 1314 | 56.051396465208185 | -0.599773 | -18.7666 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1318 | 56.06274391409031 | -0.581805 | -16.8833 | 0 | 17 | 17 | 0.85 | 0.00 | - | no | Open |
| 1305 | 56.23555239464986 | -0.663881 | -19.0406 | 1 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 1313 | 56.42848850819141 | -0.612046 | -22.6957 | 1 | 14 | 12 | 0.60 | 0.00 | - | no | Open |
| 1319 | 56.440417781012115 | -0.708014 | -25.4563 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1311 | 56.58470072017249 | -0.702212 | -23.6807 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1308 | 56.877693005953326 | -0.681794 | -20.6617 | 1 | 12 | 10 | 0.50 | 0.00 | - | no | Open |
| 1309 | 56.07297167704862 | -0.611879 | -25.87 | 0 | 17 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1316 | 56.386666093425426 | -0.580608 | -18.7392 | 1 | 14 | 11 | 0.55 | 0.00 | - | yes | Current |
| 1306 | 58.35280729752718 | -0.640722 | -21.3406 | 1 | 21 | 17 | 0.85 | 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
-18.739kcal/mol
Ligand efficiency (LE)
-0.5065kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.185
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
501.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
180.50kcal/mol
Minimised FF energy
144.99kcal/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.