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
39.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.400 kcal/mol/HA)
✓ Good fit quality (FQ -3.73)
✓ Good H-bonds (5 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Very high strain energy (39.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-10.809
kcal/mol
LE
-0.400
kcal/mol/HA
Fit Quality
-3.73
FQ (Leeson)
HAC
27
heavy atoms
MW
408
Da
LogP
2.56
cLogP
Interaction summary
HB 5
HY 16
PI 2
CLASH 3
Interaction summary
HB 5
HY 16
PI 2
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 | 3.286 | Score | -10.809 |
|---|---|---|---|
| Inter norm | -0.724 | Intra norm | 0.323 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes; high strain Δ 39.7 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
MET400
PHE396
PRO398
PRO462
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 | 0.43 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 387 | 3.285700678836707 | -0.723755 | -10.8095 | 5 | 12 | 6 | 0.75 | 0.00 | - | no | Current |
| 364 | 3.6972539831852793 | -1.16852 | -27.4379 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 390 | 4.168243620208268 | -0.929845 | -20.354 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 4.504355784231469 | -1.05457 | -17.1995 | 12 | 18 | 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
-10.809kcal/mol
Ligand efficiency (LE)
-0.4004kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.735
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
407.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.56
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.52kcal/mol
Minimised FF energy
32.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
667.4Ų
Total solvent-accessible surface area of free ligand
BSA total
397.0Ų
Buried surface area upon binding
BSA apolar
268.1Ų
Hydrophobic contacts buried
BSA polar
129.0Ų
Polar contacts buried
Fraction buried
59.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3090.9Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1504.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)