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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
47.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 1.00
Reason: strain 47.0 kcal/mol
strain ΔE 47.0 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.676 kcal/mol/HA)
✓ Good fit quality (FQ -6.31)
✓ Good H-bonds (5 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Extreme strain energy (47.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-18.252
kcal/mol
LE
-0.676
kcal/mol/HA
Fit Quality
-6.31
FQ (Leeson)
HAC
27
heavy atoms
MW
405
Da
LogP
2.13
cLogP
Interaction summary
HB 5
HY 8
PI 1
CLASH 3
⚠ Exposure 42%
Interaction summary
HB 5
HY 8
PI 1
CLASH 3
⚠ Exposure 42%
Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 11
Exposed 8
LogP 2.13
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.482 | Score | -18.252 |
|---|---|---|---|
| Inter norm | -0.744 | Intra norm | 0.068 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; high strain Δ 47.0 | ||
| Residues |
GLU466
GLU467
GLY459
LEU399
MET471
PHE396
PRO398
SER394
SER470
THR397
| ||
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 | 7 | Native recall | 0.88 |
| Jaccard | 0.64 | 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 252 | 1.8924839980752985 | -1.19706 | -31.6537 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 261 | 2.4818963539636436 | -0.744241 | -18.2519 | 5 | 10 | 7 | 0.88 | 1.00 | - | no | Current |
| 348 | 3.7006308152014857 | -0.865004 | -22.5456 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 325 | 5.348360805395551 | -0.901166 | -28.302 | 4 | 11 | 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
-18.252kcal/mol
Ligand efficiency (LE)
-0.6760kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.307
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
404.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
47.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
22.03kcal/mol
Minimised FF energy
-25.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
660.6Ų
Total solvent-accessible surface area of free ligand
BSA total
397.8Ų
Buried surface area upon binding
BSA apolar
352.2Ų
Hydrophobic contacts buried
BSA polar
45.6Ų
Polar contacts buried
Fraction buried
60.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3158.2Ų
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
1488.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)