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 (-0.757 kcal/mol/HA)
✓ Good fit quality (FQ -7.75)
✓ Good H-bonds (3 bonds)
✗ High strain energy (17.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.023
kcal/mol
LE
-0.757
kcal/mol/HA
Fit Quality
-7.75
FQ (Leeson)
HAC
37
heavy atoms
MW
485
Da
LogP
5.91
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 17.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 3
Clashes 3
Severe clashes 0
| Final rank | 4.034855583115575 | Score | -28.0234 |
|---|---|---|---|
| Inter norm | -0.804847 | Intra norm | 0.0474592 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 3 |
| Artifact reason | geometry warning; 16 clashes; 3 protein contact clashes; high strain Δ 21.0 | ||
| Residues | A:ARG29;A:ASN65;A:GLN36;A:GLU31;A:ILE61;A:ILE8;A:LEU23;A:LEU28;A:LEU68;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:SER60;A:TRP25;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 | 14 | Native recall | 0.67 |
| Jaccard | 0.56 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1923 | 4.034855583115575 | -0.804847 | -28.0234 | 3 | 18 | 14 | 0.67 | 0.20 | - | no | Current |
| 2680 | 5.621546834997885 | -0.570473 | -17.9944 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1920 | 5.846635229475261 | -0.712409 | -25.9779 | 2 | 19 | 14 | 0.67 | 0.00 | - | no | Open |
| 1922 | 6.3974437631832055 | -0.747862 | -28.249 | 4 | 20 | 18 | 0.86 | 0.00 | - | no | Open |
| 1921 | 6.816108271510244 | -0.75026 | -26.5763 | 2 | 17 | 13 | 0.62 | 0.20 | - | yes | Open |
| 2679 | 7.131239871172225 | -0.630148 | -21.3616 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2678 | 7.74156517903795 | -0.695417 | -21.2505 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2677 | 9.756317770605037 | -0.646196 | -22.1833 | 5 | 14 | 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
-28.023kcal/mol
Ligand efficiency (LE)
-0.7574kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.754
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
484.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.91
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
122.19kcal/mol
Minimised FF energy
104.45kcal/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.