Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
47.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.40
Reason: strain 47.2 kcal/mol
strain ΔE 47.2 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.673 kcal/mol/HA)
✓ Good fit quality (FQ -6.20)
✓ Good H-bonds (3 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Extreme strain energy (47.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-17.501
kcal/mol
LE
-0.673
kcal/mol/HA
Fit Quality
-6.20
FQ (Leeson)
HAC
26
heavy atoms
MW
434
Da
LogP
3.90
cLogP
Final rank
2.0046
rank score
Inter norm
-0.965
normalised
Contacts
15
H-bonds 6
Interaction summary
HBD 3
HY 9
PI 1
CLASH 3
Interaction summary
HBD 3
HY 9
PI 1
CLASH 3
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
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.40 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 348 | 0.8740691109670798 | -0.941479 | -19.4368 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 399 | 1.1577229792848076 | -0.986813 | -19.3868 | 11 | 15 | 0 | 0.00 | - | - | no | Open |
| 362 | 1.8207036733733963 | -1.05976 | -19.1339 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 494 | 2.004621134921909 | -0.964958 | -17.5011 | 6 | 15 | 8 | 0.62 | - | - | no | Current |
| 367 | 3.0861066535632085 | -1.21974 | -29.9558 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 468 | 3.394597286173792 | -0.938909 | -18.0178 | 4 | 12 | 0 | 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
-17.501kcal/mol
Ligand efficiency (LE)
-0.6731kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.202
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
434.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.90
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
47.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
118.17kcal/mol
Minimised FF energy
70.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
645.4Ų
Total solvent-accessible surface area of free ligand
BSA total
498.8Ų
Buried surface area upon binding
BSA apolar
407.3Ų
Hydrophobic contacts buried
BSA polar
91.5Ų
Polar contacts buried
Fraction buried
77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2997.1Ų
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
1513.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)