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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
24.5 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.74, Jaccard 0.52, H-bond role recall 0.57
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes
10 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.722 kcal/mol/HA)
✓ Good fit quality (FQ -7.16)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-23.810
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-7.16
FQ (Leeson)
HAC
33
heavy atoms
MW
467
Da
LogP
2.53
cLogP
Final rank
6.7609
rank score
Inter norm
-0.871
normalised
Contacts
22
H-bonds 11
Interaction summary
HBD 2
HBA 8
HY 5
PI 2
CLASH 10
Interaction summary
HBD 2
HBA 8
HY 5
PI 2
CLASH 10
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 6 | Strict recall | 0.67 |
| 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
-23.810kcal/mol
Ligand efficiency (LE)
-0.7215kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.159
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
466.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.53
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
2.77kcal/mol
Minimised FF energy
-21.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
763.0Ų
Total solvent-accessible surface area of free ligand
BSA total
601.4Ų
Buried surface area upon binding
BSA apolar
511.0Ų
Hydrophobic contacts buried
BSA polar
90.4Ų
Polar contacts buried
Fraction buried
78.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2705.1Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1407.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)