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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
18.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.54, Jaccard 0.37
Reason: no major geometry red flags detected
2 protein-contact clashes
42% of hydrophobic surface appears solvent-exposed (10/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.774 kcal/mol/HA)
✓ Good fit quality (FQ -7.39)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Moderate strain (18.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-22.456
kcal/mol
LE
-0.774
kcal/mol/HA
Fit Quality
-7.39
FQ (Leeson)
HAC
29
heavy atoms
MW
379
Da
LogP
3.97
cLogP
Final rank
3.6549
rank score
Inter norm
-0.829
normalised
Contacts
13
H-bonds 2
Interaction summary
HBD 1
HBA 1
HY 7
PI 1
CLASH 2
Interaction summary
HBD 1
HBA 1
HY 7
PI 1
CLASH 2
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
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.37 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 567 | 3.6548543690079307 | -0.829115 | -22.4557 | 2 | 13 | 7 | 0.54 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.456kcal/mol
Ligand efficiency (LE)
-0.7743kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.392
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
379.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.97
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-12.59kcal/mol
Minimised FF energy
-30.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
622.8Ų
Total solvent-accessible surface area of free ligand
BSA total
489.0Ų
Buried surface area upon binding
BSA apolar
442.6Ų
Hydrophobic contacts buried
BSA polar
46.4Ų
Polar contacts buried
Fraction buried
78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3010.4Ų
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
1535.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)