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
54.6 kcal/mol
Protein clashes
11
Internal clashes
13
Native overlap
contact recall 0.75, Jaccard 0.35, H-bond role recall 0.00
Reason: 2 severe internal clashes, 11 protein-contact clashes, 13 internal clashes, strain 54.6 kcal/mol
strain ΔE 54.6 kcal/mol
2 severe internal clashes
11 protein-contact clashes
13 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (10/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.539 kcal/mol/HA)
✓ Good fit quality (FQ -5.48)
✓ Good H-bonds (3 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Extreme strain energy (54.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-19.417
kcal/mol
LE
-0.539
kcal/mol/HA
Fit Quality
-5.48
FQ (Leeson)
HAC
36
heavy atoms
MW
509
Da
LogP
4.66
cLogP
Final rank
6.1283
rank score
Inter norm
-0.619
normalised
Contacts
23
H-bonds 7
Interaction summary
HBD 1
HBA 2
HY 8
PI 3
CLASH 13
Severe 2
Interaction summary
HBD 1
HBA 2
HY 8
PI 3
CLASH 13
Severe 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 9 | Native recall | 0.75 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 441 | 6.128290478896019 | -0.619313 | -19.4167 | 7 | 23 | 9 | 0.75 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.417kcal/mol
Ligand efficiency (LE)
-0.5394kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.482
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
508.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.66
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
54.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
136.32kcal/mol
Minimised FF energy
81.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
807.6Ų
Total solvent-accessible surface area of free ligand
BSA total
660.0Ų
Buried surface area upon binding
BSA apolar
518.5Ų
Hydrophobic contacts buried
BSA polar
141.6Ų
Polar contacts buried
Fraction buried
81.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6640.9Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2065.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)