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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
18.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 1.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.722 kcal/mol/HA)
✓ Good fit quality (FQ -6.47)
✓ Strong H-bond network (7 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (18.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-17.336
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-6.47
FQ (Leeson)
HAC
24
heavy atoms
MW
409
Da
LogP
3.72
cLogP
Interaction summary
HB 7
HY 13
PI 1
CLASH 3
Interaction summary
HB 7
HY 13
PI 1
CLASH 3
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
| Final rank | 2.972 | Score | -17.336 |
|---|---|---|---|
| Inter norm | -0.815 | Intra norm | 0.093 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 7 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes | ||
| Residues |
ASN402
GLU466
GLU467
LEU399
LYS407
LYS410
PHE396
PRO398
SER464
THR397
THR463
| ||
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 | 0.46 | RMSD | - |
| HB strict | 1 | Strict recall | 0.50 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 437 | 1.0622373773057405 | -1.14598 | -24.2338 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 384 | 1.6543390194869305 | -1.30146 | -32.1781 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 1.8894308683503533 | -1.45598 | -31.2552 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 2.420917382962812 | -1.29827 | -28.0042 | 14 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 427 | 2.9718852536009854 | -0.815124 | -17.3361 | 7 | 11 | 6 | 0.75 | 1.00 | - | no | Current |
| 421 | 4.01819321477796 | -0.930807 | -22.6703 | 10 | 13 | 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
-17.336kcal/mol
Ligand efficiency (LE)
-0.7223kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.474
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
409.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.72
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.48kcal/mol
Minimised FF energy
82.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
615.0Ų
Total solvent-accessible surface area of free ligand
BSA total
356.5Ų
Buried surface area upon binding
BSA apolar
266.6Ų
Hydrophobic contacts buried
BSA polar
90.0Ų
Polar contacts buried
Fraction buried
58.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3032.5Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1517.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)