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 medium
Native strong
SASA done
Strain ΔE
38.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.68, Jaccard 0.52, H-bond role recall 0.57
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.058 kcal/mol/HA)
✓ Good fit quality (FQ -9.33)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Very high strain energy (38.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.326
kcal/mol
LE
-1.058
kcal/mol/HA
Fit Quality
-9.33
FQ (Leeson)
HAC
23
heavy atoms
MW
337
Da
LogP
0.83
cLogP
Final rank
3.9313
rank score
Inter norm
-1.247
normalised
Contacts
19
H-bonds 13
Interaction summary
HBD 3
HBA 7
HY 2
PI 3
CLASH 5
Interaction summary
HBD 3
HBA 7
HY 2
PI 3
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.
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 | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| HB same residue+role | 4 | HB role recall | 0.57 |
| HB same residue | 4 | HB residue recall | 0.57 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.326kcal/mol
Ligand efficiency (LE)
-1.0576kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.334
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.83
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-17.03kcal/mol
Minimised FF energy
-55.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
542.0Ų
Total solvent-accessible surface area of free ligand
BSA total
469.7Ų
Buried surface area upon binding
BSA apolar
320.7Ų
Hydrophobic contacts buried
BSA polar
149.0Ų
Polar contacts buried
Fraction buried
86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2452.7Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1380.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)