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 (-0.861 kcal/mol/HA)
✓ Good fit quality (FQ -8.31)
✓ Good H-bonds (5 bonds)
✗ High strain energy (15.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.841
kcal/mol
LE
-0.861
kcal/mol/HA
Fit Quality
-8.31
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 15.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 21
π–π 3
Clashes 8
Severe clashes 1
| Final rank | 55.51799674244559 | Score | -25.8415 |
|---|---|---|---|
| Inter norm | -0.814425 | Intra norm | -0.0469582 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 11 clashes; 1 protein clash; high strain Δ 20.9 | ||
| Residues | A:ALA10;A:ASN65;A:ASP22;A:GLU31;A:GLY21;A:ILE115;A:ILE61;A:ILE8;A:LEU23;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:SER60;A:THR57;A:TYR122;A:VAL116;A:VAL9 | ||
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 5 |
| IFP residues | A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9 | ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.70 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.60 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2068 | 1.662464669832739 | -0.787792 | -21.0846 | 3 | 18 | 17 | 0.81 | 0.00 | - | no | Open |
| 1076 | 3.3713557393494122 | -0.939642 | -26.2628 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2069 | 3.429425798449819 | -0.859805 | -26.3343 | 3 | 12 | 9 | 0.43 | 0.20 | - | no | Open |
| 832 | 3.6913987876806305 | -1.09336 | -28.971 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2098 | 4.124685217253968 | -0.870106 | -23.9953 | 5 | 17 | 16 | 0.76 | 0.00 | - | no | Open |
| 1180 | 6.129882628094019 | -0.763914 | -17.6165 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1077 | 5.414514005732158 | -0.93437 | -24.8321 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2099 | 55.51799674244559 | -0.814425 | -25.8415 | 5 | 18 | 16 | 0.76 | 0.60 | - | yes | Current |
| 1181 | 56.44278604343296 | -0.776336 | -19.1475 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 833 | 59.506899099693776 | -1.16463 | -31.7677 | 11 | 13 | 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
-25.841kcal/mol
Ligand efficiency (LE)
-0.8614kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.309
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.37kcal/mol
Minimised FF energy
41.42kcal/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.