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
31.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.502 kcal/mol/HA)
✓ Good fit quality (FQ -4.79)
✓ Good H-bonds (4 bonds)
✓ Good burial (57% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Very high strain energy (31.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-14.561
kcal/mol
LE
-0.502
kcal/mol/HA
Fit Quality
-4.79
FQ (Leeson)
HAC
29
heavy atoms
MW
406
Da
LogP
3.74
cLogP
Final rank
3.1279
rank score
Inter norm
-0.654
normalised
Contacts
9
H-bonds 5
Interaction summary
HBA 4
HY 4
PI 1
CLASH 1
Interaction summary
HBA 4
HY 4
PI 1
CLASH 1
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 | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 6 | Native recall | 0.75 |
| Jaccard | 0.55 | 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
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221 | ||
Receptor context
1 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 1
Excluded HETATM 0
Kept cofactors / ions
A: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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 127 | 3.127858519265289 | -0.653635 | -14.5608 | 5 | 9 | 6 | 0.75 | 0.00 | - | no | Current |
| 122 | 3.471987782665667 | -1.11657 | -28.4331 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 96 | 3.9466631181326814 | -1.13422 | -29.022 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 137 | 4.20025134010485 | -0.854363 | -22.8507 | 10 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 5.716832078836834 | -0.961696 | -23.7608 | 9 | 20 | 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
-14.561kcal/mol
Ligand efficiency (LE)
-0.5021kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.793
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
406.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.74
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
89.70kcal/mol
Minimised FF energy
58.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
660.3Ų
Total solvent-accessible surface area of free ligand
BSA total
374.1Ų
Buried surface area upon binding
BSA apolar
249.3Ų
Hydrophobic contacts buried
BSA polar
124.7Ų
Polar contacts buried
Fraction buried
56.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3077.6Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1503.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)