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
24.4 kcal/mol
Protein clashes
0
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.43
Reason: no major geometry red flags detected
4 intramolecular clashes
69% of hydrophobic surface is solvent-exposed (11/16 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.049 kcal/mol/HA)
✓ Good fit quality (FQ -9.66)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (24.4 kcal/mol)
✗ Geometry warnings
Score
-27.276
kcal/mol
LE
-1.049
kcal/mol/HA
Fit Quality
-9.66
FQ (Leeson)
HAC
26
heavy atoms
MW
385
Da
LogP
1.48
cLogP
Interaction summary
HB 13
HY 3
PI 2
CLASH 0
⚠ Exposure 68%
Interaction summary
HB 13
HY 3
PI 2
CLASH 0
⚠ Exposure 68%
Solvent-exposed hydrophobic surface — desolvation penalty likely
69% of hydrophobic surface is solvent-exposed (11/16 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 16
Buried (contacted) 5
Exposed 11
LogP 1.48
H-bonds 13
Exposed fragments:
aliphatic ring (3/5 atoms exposed)aliphatic ring (3/5 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 3.589 | Score | -27.276 |
|---|---|---|---|
| Inter norm | -1.171 | Intra norm | 0.122 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 13 |
| Artifact reason | geometry warning; 4 clashes; 3 protein clashes; moderate strain Δ 24.4 | ||
| Residues |
ALA67
ARG277
ASP332
ASP88
GLU274
GLY199
GLY236
GLY237
GLY276
HIS197
HIS333
LYS69
SER200
TYR389
| ||
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 | ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 3 | HB residue recall | 0.43 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 180 | 2.5227985153470405 | -1.26753 | -25.4795 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 129 | 3.5885931953399086 | -1.17115 | -27.2758 | 13 | 14 | 12 | 0.63 | 0.43 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.276kcal/mol
Ligand efficiency (LE)
-1.0491kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.665
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
384.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.48
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.23kcal/mol
Minimised FF energy
53.82kcal/mol
SASA & burial
✓ computed
SASA (unbound)
609.7Ų
Total solvent-accessible surface area of free ligand
BSA total
435.4Ų
Buried surface area upon binding
BSA apolar
356.9Ų
Hydrophobic contacts buried
BSA polar
78.6Ų
Polar contacts buried
Fraction buried
71.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2599.5Ų
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
1386.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)