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
16.5 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 1.00
Reason: 12 internal clashes
12 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (13/24 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 (-0.565 kcal/mol/HA)
✓ Good fit quality (FQ -5.45)
✓ Strong H-bond network (7 bonds)
✓ Good burial (53% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (16.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-16.950
kcal/mol
LE
-0.565
kcal/mol/HA
Fit Quality
-5.45
FQ (Leeson)
HAC
30
heavy atoms
MW
412
Da
LogP
4.16
cLogP
Interaction summary
HB 7
HY 10
PI 1
CLASH 0
⚠ Exposure 54%
Interaction summary
HB 7
HY 10
PI 1
CLASH 0
⚠ Exposure 54%
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (13/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24
Buried (contacted) 11
Exposed 13
LogP 4.16
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 2.536 | Score | -16.950 |
|---|---|---|---|
| Inter norm | -0.622 | Intra norm | 0.057 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash | ||
| Residues |
ASN402
GLU466
GLU467
LEU399
LYS407
PHE396
PRO398
PRO462
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 | 6 | Native recall | 0.75 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 300 | 2.536358449038341 | -0.622233 | -16.9495 | 7 | 10 | 6 | 0.75 | 1.00 | - | no | Current |
| 281 | 4.132600369931899 | -0.882304 | -24.1478 | 9 | 14 | 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
-16.950kcal/mol
Ligand efficiency (LE)
-0.5650kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.450
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
411.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.16
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
23.40kcal/mol
Minimised FF energy
6.92kcal/mol
SASA & burial
✓ computed
SASA (unbound)
718.1Ų
Total solvent-accessible surface area of free ligand
BSA total
382.4Ų
Buried surface area upon binding
BSA apolar
312.5Ų
Hydrophobic contacts buried
BSA polar
70.0Ų
Polar contacts buried
Fraction buried
53.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3183.6Ų
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
1499.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)