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 medium
Native strong
SASA done
Strain ΔE
32.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
43% of hydrophobic surface appears solvent-exposed (15/35 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 (-0.492 kcal/mol/HA)
✓ Good fit quality (FQ -5.17)
✓ Strong H-bond network (8 bonds)
✓ Lipophilic contacts well-matched (76%)
✗ Very high strain energy (32.4 kcal/mol)
✗ Poor burial (38% SASA buried)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.168
kcal/mol
LE
-0.492
kcal/mol/HA
Fit Quality
-5.17
FQ (Leeson)
HAC
41
heavy atoms
MW
565
Da
LogP
6.75
cLogP
Interaction summary
HB 8
HY 16
PI 0
CLASH 1
⚠ Exposure 42%
Interaction summary
HB 8
HY 16
PI 0
CLASH 1
⚠ Exposure 42%
Partial hydrophobic solvent exposure
43% of hydrophobic surface appears solvent-exposed (15/35 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 35
Buried (contacted) 20
Exposed 15
LogP 6.75
H-bonds 8
Exposed fragments:
cyclohexyl (2/5 atoms exposed)aliphatic chain/group (13 atoms exposed)
| Final rank | 4.234 | Score | -20.168 |
|---|---|---|---|
| Inter norm | -0.541 | Intra norm | 0.049 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes; high strain Δ 32.4 | ||
| Residues |
ASN402
GLU467
LEU399
MET393
MET471
PHE396
PRO398
SER394
SER395
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 | 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
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 20 | 4.233867626812268 | -0.541146 | -20.1675 | 8 | 10 | 7 | 0.88 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.168kcal/mol
Ligand efficiency (LE)
-0.4919kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.169
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
564.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.75
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
137.16kcal/mol
Minimised FF energy
104.75kcal/mol
SASA & burial
✓ computed
SASA (unbound)
810.0Ų
Total solvent-accessible surface area of free ligand
BSA total
310.3Ų
Buried surface area upon binding
BSA apolar
236.1Ų
Hydrophobic contacts buried
BSA polar
74.2Ų
Polar contacts buried
Fraction buried
38.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3276.5Ų
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
1505.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)