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 high
Native strong
SASA done
Strain ΔE
26.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.95, Jaccard 0.90, H-bond role recall 0.71
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.835 kcal/mol/HA)
✓ Good fit quality (FQ -8.06)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ High strain energy (26.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.063
kcal/mol
LE
-0.835
kcal/mol/HA
Fit Quality
-8.06
FQ (Leeson)
HAC
30
heavy atoms
MW
420
Da
LogP
2.51
cLogP
Interaction summary
HB 14
HY 4
PI 0
CLASH 1
Interaction summary
HB 14
HY 4
PI 0
CLASH 1
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 4.086 | Score | -25.063 |
|---|---|---|---|
| Inter norm | -0.930 | Intra norm | 0.095 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 14 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes; moderate strain Δ 26.2 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
HIS333
LYS69
PHE238
PRO275
SER200
TYR331
TYR389
| ||
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 | 18 | Native recall | 0.95 |
| Jaccard | 0.90 | RMSD | - |
| HB strict | 6 | Strict recall | 0.67 |
| HB same residue+role | 5 | HB role recall | 0.71 |
| HB same residue | 5 | HB residue recall | 0.71 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 271 | 1.9508639457546157 | -0.863085 | -22.4534 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 153 | 4.086391315056721 | -0.930383 | -25.0634 | 14 | 19 | 18 | 0.95 | 0.71 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.063kcal/mol
Ligand efficiency (LE)
-0.8354kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.059
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
419.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.51
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.30kcal/mol
Minimised FF energy
108.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
651.2Ų
Total solvent-accessible surface area of free ligand
BSA total
491.9Ų
Buried surface area upon binding
BSA apolar
357.6Ų
Hydrophobic contacts buried
BSA polar
134.3Ų
Polar contacts buried
Fraction buried
75.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2591.3Ų
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
1375.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)