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 (-0.975 kcal/mol/HA)
✓ Good fit quality (FQ -9.50)
✗ High strain energy (19.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.223
kcal/mol
LE
-0.975
kcal/mol/HA
Fit Quality
-9.50
FQ (Leeson)
HAC
31
heavy atoms
MW
500
Da
LogP
5.50
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 19.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 2
Clashes 5
Severe clashes 0
| Final rank | 4.072703977033648 | Score | -30.2227 |
|---|---|---|---|
| Inter norm | -0.910836 | Intra norm | -0.0640893 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 2 |
| Artifact reason | geometry warning; 13 clashes; 5 protein contact clashes; high strain Δ 24.8 | ||
| Residues | A:ALA10;A:ARG29;A:ASN65;A:GLN36;A:GLU31;A:ILE61;A:ILE8;A:LEU23;A:LEU68;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:PRO62;A:THR137;A:THR57;A:TYR122;A:TYR34;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 | 17 | Native recall | 0.81 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.40 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2300 | 2.975199293457856 | -0.795059 | -28.9903 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 3042 | 4.072703977033648 | -0.910836 | -30.2227 | 2 | 20 | 17 | 0.81 | 0.40 | - | no | Current |
| 3044 | 4.167622120393544 | -0.823917 | -25.3697 | 1 | 18 | 16 | 0.76 | 0.20 | - | no | Open |
| 2403 | 4.357679872175534 | -0.685104 | -21.0742 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 3710 | 4.430265866663566 | -0.727157 | -21.84 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2187 | 4.616422523988748 | -0.750283 | -26.2709 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2549 | 4.825437208171437 | -0.642671 | -23.6962 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2018 | 4.939329756217788 | -1.04522 | -37.461 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3043 | 4.977027617950462 | -0.770072 | -27.1949 | 1 | 20 | 16 | 0.76 | 0.20 | - | no | Open |
| 2401 | 5.406678525852967 | -0.689693 | -24.6956 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1846 | 5.656921740362672 | -0.936859 | -32.4435 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1845 | 7.140819470640418 | -0.992852 | -33.9409 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2302 | 5.3690098490596245 | -0.741315 | -23.5675 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3709 | 5.54423829292957 | -0.754262 | -27.3292 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2188 | 6.363719603077262 | -0.739161 | -25.0271 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2550 | 6.476803507875923 | -0.607289 | -22.283 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2017 | 6.5810355141227594 | -1.10765 | -37.5989 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3711 | 7.839426744555876 | -0.62985 | -20.2381 | 1 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2551 | 8.096988315137459 | -0.638837 | -21.1506 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2019 | 8.320791027619784 | -0.838933 | -26.3305 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2301 | 8.420651808228492 | -0.7417 | -26.2675 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2402 | 8.43645946478735 | -0.580544 | -21.5996 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1847 | 8.500167348157591 | -0.898004 | -27.8574 | 11 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2186 | 9.508457596523543 | -0.894636 | -26.6402 | 9 | 16 | 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
-30.223kcal/mol
Ligand efficiency (LE)
-0.9749kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.498
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
500.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.50
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
46.88kcal/mol
Minimised FF energy
27.20kcal/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.