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
68.7 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.85, Jaccard 0.52
Reason: 15 internal clashes, strain 68.7 kcal/mol
strain ΔE 68.7 kcal/mol
15 intramolecular clashes
48% of hydrophobic surface appears solvent-exposed (14/29 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 (-0.633 kcal/mol/HA)
✓ Good fit quality (FQ -6.61)
✓ Good H-bonds (3 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Extreme strain energy (68.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-25.318
kcal/mol
LE
-0.633
kcal/mol/HA
Fit Quality
-6.61
FQ (Leeson)
HAC
40
heavy atoms
MW
545
Da
LogP
2.83
cLogP
Final rank
3.5546
rank score
Inter norm
-0.615
normalised
Contacts
19
H-bonds 5
Interaction summary
HBD 2
HBA 1
HY 10
PI 1
CLASH 0
Interaction summary
HBD 2
HBA 1
HY 10
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
| Name | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 11 | Native recall | 0.85 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | 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:204 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 339 | 3.5545811982670665 | -0.614897 | -25.3178 | 5 | 19 | 11 | 0.85 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.318kcal/mol
Ligand efficiency (LE)
-0.6329kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.610
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
544.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.83
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
68.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.00kcal/mol
Minimised FF energy
45.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
950.9Ų
Total solvent-accessible surface area of free ligand
BSA total
705.2Ų
Buried surface area upon binding
BSA apolar
610.2Ų
Hydrophobic contacts buried
BSA polar
95.0Ų
Polar contacts buried
Fraction buried
74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3300.3Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1526.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)