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
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
40.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (13/26 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 (-0.489 kcal/mol/HA)
✓ Good fit quality (FQ -4.85)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Extreme strain energy (40.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-16.137
kcal/mol
LE
-0.489
kcal/mol/HA
Fit Quality
-4.85
FQ (Leeson)
HAC
33
heavy atoms
MW
446
Da
LogP
4.87
cLogP
Final rank
3.8812
rank score
Inter norm
-0.759
normalised
Contacts
17
H-bonds 4
Interaction summary
HBD 1
HBA 2
HY 10
PI 1
CLASH 2
Interaction summary
HBD 1
HBA 2
HY 10
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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: permissive.
| 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 | 10 | Native recall | 0.77 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 3.8812476223088836 | -0.758815 | -16.1367 | 4 | 17 | 10 | 0.77 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-16.137kcal/mol
Ligand efficiency (LE)
-0.4890kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.852
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
445.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.87
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.12kcal/mol
Minimised FF energy
63.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
792.2Ų
Total solvent-accessible surface area of free ligand
BSA total
602.4Ų
Buried surface area upon binding
BSA apolar
555.8Ų
Hydrophobic contacts buried
BSA polar
46.6Ų
Polar contacts buried
Fraction buried
76.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3215.8Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1535.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)