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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
41.7 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.84, Jaccard 0.62, H-bond role recall 0.57
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.824 kcal/mol/HA)
✓ Good fit quality (FQ -8.25)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Extreme strain energy (41.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-28.025
kcal/mol
LE
-0.824
kcal/mol/HA
Fit Quality
-8.25
FQ (Leeson)
HAC
34
heavy atoms
MW
461
Da
LogP
3.08
cLogP
Final rank
4.6425
rank score
Inter norm
-0.949
normalised
Contacts
23
H-bonds 14
Interaction summary
HBD 1
HBA 7
PC 1
HY 5
PI 4
CLASH 6
Interaction summary
HBD 1
HBA 7
PC 1
HY 5
PI 4
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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 | 16 | Native recall | 0.84 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 379 | 1.7515119447063427 | -0.628624 | -16.1568 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 428 | 2.1508479025996894 | -0.801565 | -19.3286 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 3.090122770978229 | -0.741059 | -15.222 | 13 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 448 | 3.187813687353957 | -0.756461 | -24.6559 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 373 | 3.331493017527665 | -0.760459 | -20.8381 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 338 | 4.6424814593420125 | -0.949318 | -28.0247 | 14 | 23 | 16 | 0.84 | 0.57 | - | no | Current |
| 473 | 4.937071202872829 | -0.776684 | -21.8871 | 8 | 15 | 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
-28.025kcal/mol
Ligand efficiency (LE)
-0.8243kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.247
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
124.31kcal/mol
Minimised FF energy
82.63kcal/mol
SASA & burial
✓ computed
SASA (unbound)
792.0Ų
Total solvent-accessible surface area of free ligand
BSA total
661.4Ų
Buried surface area upon binding
BSA apolar
534.8Ų
Hydrophobic contacts buried
BSA polar
126.6Ų
Polar contacts buried
Fraction buried
83.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2725.5Ų
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
1376.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)