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
20.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 0.73, H-bond role recall 1.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.703 kcal/mol/HA)
✓ Good fit quality (FQ -6.85)
✓ Strong H-bond network (6 bonds)
✓ Good burial (54% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (20.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.786
kcal/mol
LE
-0.703
kcal/mol/HA
Fit Quality
-6.85
FQ (Leeson)
HAC
31
heavy atoms
MW
456
Da
LogP
3.78
cLogP
Interaction summary
HB 6
HY 9
PI 1
CLASH 4
Interaction summary
HB 6
HY 9
PI 1
CLASH 4
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 | 3.503 | Score | -21.786 |
|---|---|---|---|
| Inter norm | -0.630 | Intra norm | -0.072 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 20.3 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
LYS407
PHE396
PRO398
SER394
SER470
THR397
| ||
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 | 8 | Native recall | 1.00 |
| Jaccard | 0.73 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 244 | 1.4466031914952318 | -0.669174 | -20.9036 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 2.84930993815511 | -0.802404 | -21.6259 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 272 | 3.503185721960202 | -0.630392 | -21.7857 | 6 | 11 | 8 | 1.00 | 1.00 | - | no | Current |
| 201 | 4.415259639265987 | -1.09695 | -33.4999 | 7 | 22 | 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
-21.786kcal/mol
Ligand efficiency (LE)
-0.7028kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.847
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
455.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.78
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
16.30kcal/mol
Minimised FF energy
-4.01kcal/mol
SASA & burial
✓ computed
SASA (unbound)
713.9Ų
Total solvent-accessible surface area of free ligand
BSA total
388.6Ų
Buried surface area upon binding
BSA apolar
325.7Ų
Hydrophobic contacts buried
BSA polar
62.9Ų
Polar contacts buried
Fraction buried
54.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3090.6Ų
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
1516.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)