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
50.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.54, H-bond role recall 1.00
Reason: strain 50.6 kcal/mol
strain ΔE 50.6 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (14/28 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 (-0.456 kcal/mol/HA)
✓ Good fit quality (FQ -4.60)
✓ Good H-bonds (3 bonds)
✓ Good burial (59% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Extreme strain energy (50.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-15.963
kcal/mol
LE
-0.456
kcal/mol/HA
Fit Quality
-4.60
FQ (Leeson)
HAC
35
heavy atoms
MW
471
Da
LogP
4.43
cLogP
Interaction summary
HB 3
HY 15
PI 2
CLASH 3
⚠ Exposure 50%
Interaction summary
HB 3
HY 15
PI 2
CLASH 3
⚠ Exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (14/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 14
Exposed 14
LogP 4.43
H-bonds 3
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (8 atoms exposed)
| Final rank | 3.964 | Score | -15.963 |
|---|---|---|---|
| Inter norm | -0.541 | Intra norm | 0.085 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 3 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 50.5 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
MET400
PHE396
PRO398
SER464
SER470
THR397
THR463
| ||
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 | 0.54 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 581 | 0.5279466170560568 | -0.92298 | -21.7341 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 584 | 1.6032710136530173 | -0.671895 | -22.2796 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 580 | 2.233058305090961 | -0.978889 | -25.9835 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 619 | 2.798593001434877 | -0.91104 | -35.0462 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 3.5461906514861314 | -0.721784 | -23.941 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 3.9640623284702365 | -0.540965 | -15.9625 | 3 | 12 | 7 | 0.88 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.963kcal/mol
Ligand efficiency (LE)
-0.4561kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.600
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
470.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.43
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
50.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.18kcal/mol
Minimised FF energy
87.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
814.9Ų
Total solvent-accessible surface area of free ligand
BSA total
480.8Ų
Buried surface area upon binding
BSA apolar
446.3Ų
Hydrophobic contacts buried
BSA polar
34.5Ų
Polar contacts buried
Fraction buried
59.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3318.1Ų
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
1497.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)