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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
57.6 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.88, Jaccard 0.70, H-bond role recall 0.00
Reason: 12 internal clashes, strain 57.6 kcal/mol
strain ΔE 57.6 kcal/mol
12 intramolecular clashes
45% of hydrophobic surface appears solvent-exposed (10/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.480 kcal/mol/HA)
✓ Good fit quality (FQ -4.77)
✓ Good H-bonds (3 bonds)
✓ Good burial (48% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Extreme strain energy (57.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-15.854
kcal/mol
LE
-0.480
kcal/mol/HA
Fit Quality
-4.77
FQ (Leeson)
HAC
33
heavy atoms
MW
489
Da
LogP
4.46
cLogP
Final rank
3.1052
rank score
Inter norm
-0.582
normalised
Contacts
9
H-bonds 4
Interaction summary
HBD 1
HBA 2
HY 3
PI 1
CLASH 0
Interaction summary
HBD 1
HBA 2
HY 3
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 0.70 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 577 | 1.5790230036333115 | -0.959463 | -27.8254 | 5 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 586 | 3.105226486580899 | -0.581932 | -15.8538 | 4 | 9 | 7 | 0.88 | 0.00 | - | no | Current |
| 590 | 4.72161139180752 | -0.854819 | -23.3658 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 4.995951227667286 | -0.966543 | -31.2537 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.854kcal/mol
Ligand efficiency (LE)
-0.4804kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.767
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
488.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.46
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
57.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.68kcal/mol
Minimised FF energy
25.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
703.6Ų
Total solvent-accessible surface area of free ligand
BSA total
334.9Ų
Buried surface area upon binding
BSA apolar
256.3Ų
Hydrophobic contacts buried
BSA polar
78.5Ų
Polar contacts buried
Fraction buried
47.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3050.2Ų
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
1539.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)