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
31.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.43, H-bond role recall 0.14
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.908 kcal/mol/HA)
✓ Good fit quality (FQ -8.47)
✓ Good H-bonds (5 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-24.518
kcal/mol
LE
-0.908
kcal/mol/HA
Fit Quality
-8.47
FQ (Leeson)
HAC
27
heavy atoms
MW
365
Da
LogP
3.52
cLogP
Final rank
3.7512
rank score
Inter norm
-1.033
normalised
Contacts
21
H-bonds 7
Interaction summary
HBD 2
HBA 3
HY 3
PI 2
CLASH 4
Interaction summary
HBD 2
HBA 3
HY 3
PI 2
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
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 | 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 | 12 | Native recall | 0.63 |
| Jaccard | 0.43 | RMSD | - |
| HB strict | 1 | Strict recall | 0.11 |
| HB same residue+role | 1 | HB role recall | 0.14 |
| HB same residue | 2 | HB residue recall | 0.29 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 43 | 3.751197311733678 | -1.03293 | -24.518 | 7 | 21 | 12 | 0.63 | 0.14 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.518kcal/mol
Ligand efficiency (LE)
-0.9081kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.472
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
365.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.52
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.89kcal/mol
Minimised FF energy
70.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
631.9Ų
Total solvent-accessible surface area of free ligand
BSA total
527.7Ų
Buried surface area upon binding
BSA apolar
428.2Ų
Hydrophobic contacts buried
BSA polar
99.5Ų
Polar contacts buried
Fraction buried
83.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2604.8Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1378.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)