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 (-0.803 kcal/mol/HA)
✓ Good fit quality (FQ -7.67)
✗ High strain energy (15.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.301
kcal/mol
LE
-0.803
kcal/mol/HA
Fit Quality
-7.67
FQ (Leeson)
HAC
29
heavy atoms
MW
426
Da
LogP
5.37
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 15.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 2
Clashes 11
Severe clashes 0
| Final rank | 5.542241361549774 | Score | -23.3014 |
|---|---|---|---|
| Inter norm | -0.914506 | Intra norm | 0.111008 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 13 clashes; 11 protein contact clashes; moderate strain Δ 17.2 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER44;A:SER86;A:THR83;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1991 | 4.819490143075884 | -0.90653 | -20.8931 | 5 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 1475 | 4.962740542105822 | -0.773146 | -20.2159 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2899 | 5.299452533493081 | -0.876449 | -24.5843 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2834 | 5.542241361549774 | -0.914506 | -23.3014 | 2 | 19 | 15 | 0.75 | 0.20 | - | no | Current |
| 1476 | 5.561559224811429 | -0.838818 | -22.236 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1478 | 5.613641932231067 | -0.69062 | -16.7448 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1477 | 5.775010971811956 | -0.747567 | -19.1127 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2833 | 6.272852567478617 | -0.840999 | -19.4932 | 4 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2835 | 6.338854012321318 | -0.96341 | -25.2468 | 1 | 20 | 19 | 0.95 | 0.20 | - | yes | Open |
| 2832 | 6.385159074029015 | -0.900025 | -25.7287 | 3 | 16 | 16 | 0.80 | 0.20 | - | yes | Open |
| 2900 | 7.102127522241116 | -0.821543 | -23.5752 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2898 | 7.495613616474527 | -0.846231 | -19.0087 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1992 | 8.7860722877612 | -0.909917 | -24.0506 | 6 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1989 | 9.785917294222623 | -0.890102 | -20.8213 | 7 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2901 | 10.45431561116286 | -0.82708 | -23.7783 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1990 | 10.521905467957987 | -0.862785 | -18.6992 | 5 | 17 | 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
-23.301kcal/mol
Ligand efficiency (LE)
-0.8035kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.670
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
425.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.37
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.88kcal/mol
Minimised FF energy
52.87kcal/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.