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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
30.4 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.50, Jaccard 0.29, H-bond role recall 1.00
Reason: 11 internal clashes
11 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.708 kcal/mol/HA)
✓ Good fit quality (FQ -6.90)
✓ Good H-bonds (4 bonds)
✓ Good burial (53% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Very high strain energy (30.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.947
kcal/mol
LE
-0.708
kcal/mol/HA
Fit Quality
-6.90
FQ (Leeson)
HAC
31
heavy atoms
MW
460
Da
LogP
2.49
cLogP
Interaction summary
HB 4
HY 11
PI 2
CLASH 0
⚠ Exposure 38%
Interaction summary
HB 4
HY 11
PI 2
CLASH 0
⚠ Exposure 38%
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 13
Exposed 8
LogP 2.49
H-bonds 4
Exposed fragments:
phenyl (5/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.344 | Score | -21.947 |
|---|---|---|---|
| Inter norm | -0.675 | Intra norm | -0.033 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 4 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; high strain Δ 30.3 | ||
| Residues |
CYS469
GLU466
GLU467
GLY459
HIS461
PHE396
SER394
SER395
SER470
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 | 4 | Native recall | 0.50 |
| Jaccard | 0.29 | 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 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 517 | 0.8033075431695811 | -0.824519 | -27.514 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 1.1073605408917213 | -0.835412 | -27.7086 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 486 | 2.3443851257078063 | -0.674504 | -21.9468 | 4 | 10 | 4 | 0.50 | 1.00 | - | no | Current |
| 518 | 2.663920897533413 | -0.857198 | -27.5751 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 3.9319423886939506 | -0.715958 | -22.623 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 4.82598670924582 | -0.976122 | -30.1806 | 9 | 23 | 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
-21.947kcal/mol
Ligand efficiency (LE)
-0.7080kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.897
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
459.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-123.09kcal/mol
Minimised FF energy
-153.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
724.4Ų
Total solvent-accessible surface area of free ligand
BSA total
381.0Ų
Buried surface area upon binding
BSA apolar
294.9Ų
Hydrophobic contacts buried
BSA polar
86.2Ų
Polar contacts buried
Fraction buried
52.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3110.1Ų
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
1476.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)