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 high
Native strong
SASA done
Strain ΔE
22.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.57, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.594 kcal/mol/HA)
✓ Good fit quality (FQ -5.89)
✓ Strong H-bond network (8 bonds)
✓ Good burial (53% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (22.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-19.603
kcal/mol
LE
-0.594
kcal/mol/HA
Fit Quality
-5.89
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
4.67
cLogP
Interaction summary
HB 8
HY 14
PI 1
CLASH 2
Interaction summary
HB 8
HY 14
PI 1
CLASH 2
| Final rank | 4.668 | Score | -19.603 |
|---|---|---|---|
| Inter norm | -0.612 | Intra norm | 0.014 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 3 protein clashes; moderate strain Δ 22.6 | ||
| Residues |
ARG472
ASN402
GLU467
LEU399
MET393
MET471
PHE396
PRO398
SER394
SER395
SER470
THR397
THR473
TYR455
| ||
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
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 | 0.57 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 268 | 0.974102900606285 | -0.753355 | -22.1827 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 2.048310136114584 | -0.934394 | -26.071 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 315 | 3.3238944949654337 | -0.72587 | -20.4346 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 291 | 3.5287369862351285 | -0.96868 | -26.5329 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 314 | 3.6667135220935343 | -0.697525 | -18.9353 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 211 | 4.016080999071254 | -0.860195 | -23.0569 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 218 | 4.624022710023361 | -0.952362 | -25.0393 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 4.667651235211368 | -0.611785 | -19.6032 | 8 | 14 | 8 | 1.00 | 0.00 | - | no | Current |
| 341 | 4.781422519779941 | -0.793315 | -20.1332 | 4 | 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
-19.603kcal/mol
Ligand efficiency (LE)
-0.5940kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.894
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
38.93kcal/mol
Minimised FF energy
16.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
773.7Ų
Total solvent-accessible surface area of free ligand
BSA total
406.9Ų
Buried surface area upon binding
BSA apolar
321.5Ų
Hydrophobic contacts buried
BSA polar
85.4Ų
Polar contacts buried
Fraction buried
52.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3202.9Ų
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
1518.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)