Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
39.6 kcal/mol
Protein clashes
0
Internal clashes
23
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 0.00
Reason: 23 internal clashes
23 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.520 kcal/mol/HA)
✓ Good fit quality (FQ -5.28)
✓ Good H-bonds (4 bonds)
✓ Good burial (51% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Very high strain energy (39.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (23)
Score
-18.716
kcal/mol
LE
-0.520
kcal/mol/HA
Fit Quality
-5.28
FQ (Leeson)
HAC
36
heavy atoms
MW
486
Da
LogP
3.07
cLogP
Interaction summary
HB 4
HY 17
PI 2
CLASH 0
Interaction summary
HB 4
HY 17
PI 2
CLASH 0
| Final rank | 4.879 | Score | -18.716 |
|---|---|---|---|
| Inter norm | -0.551 | Intra norm | 0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 23 clashes; 2 protein clashes; high strain Δ 39.5 | ||
| Residues |
ASN402
GLU467
LEU399
LYS410
MET393
MET471
PHE396
PRO398
SER394
SER395
THR397
| ||
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 7 | Native recall | 0.88 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 430 | 3.6219031466768117 | -0.759357 | -22.6077 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 409 | 4.87924638482997 | -0.551435 | -18.7157 | 4 | 11 | 7 | 0.88 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.716kcal/mol
Ligand efficiency (LE)
-0.5199kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.284
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
485.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.07
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
170.60kcal/mol
Minimised FF energy
131.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
800.4Ų
Total solvent-accessible surface area of free ligand
BSA total
405.9Ų
Buried surface area upon binding
BSA apolar
357.5Ų
Hydrophobic contacts buried
BSA polar
48.4Ų
Polar contacts buried
Fraction buried
50.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3209.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1539.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)