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
33.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.29
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 (-0.791 kcal/mol/HA)
✓ Good fit quality (FQ -7.38)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (33.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-21.370
kcal/mol
LE
-0.791
kcal/mol/HA
Fit Quality
-7.38
FQ (Leeson)
HAC
27
heavy atoms
MW
378
Da
LogP
2.27
cLogP
Final rank
2.4341
rank score
Inter norm
-1.061
normalised
Contacts
16
H-bonds 8
Interaction summary
HBD 4
HBA 1
HY 3
PI 5
CLASH 4
Interaction summary
HBD 4
HBA 1
HY 3
PI 5
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 | 0.59 | RMSD | - |
| HB strict | 2 | Strict recall | 0.22 |
| HB same residue+role | 2 | HB role recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 83 | 0.2926960968942545 | -1.21859 | -25.5241 | 5 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 105 | 0.7752453917590536 | -0.897078 | -15.3685 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 63 | 2.434070692638824 | -1.0614 | -21.37 | 8 | 16 | 13 | 0.68 | 0.29 | - | no | Current |
| 74 | 2.711650149851395 | -1.07125 | -23.2545 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 116 | 4.331959399363628 | -0.71141 | -15.4524 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.370kcal/mol
Ligand efficiency (LE)
-0.7915kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.384
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
378.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.27
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.22kcal/mol
Minimised FF energy
10.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
652.1Ų
Total solvent-accessible surface area of free ligand
BSA total
509.4Ų
Buried surface area upon binding
BSA apolar
420.2Ų
Hydrophobic contacts buried
BSA polar
89.2Ų
Polar contacts buried
Fraction buried
78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2597.4Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1410.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)