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
13.6 kcal/mol
Protein clashes
5
Internal clashes
12
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.00
Reason: 12 internal clashes
5 protein-contact clashes
12 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (11/22 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 (-0.568 kcal/mol/HA)
✓ Good fit quality (FQ -5.48)
✓ Strong H-bond network (7 bonds)
✓ Good burial (47% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (13.6 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (12)
Score
-17.040
kcal/mol
LE
-0.568
kcal/mol/HA
Fit Quality
-5.48
FQ (Leeson)
HAC
30
heavy atoms
MW
429
Da
LogP
4.30
cLogP
Interaction summary
HB 7
HY 11
PI 2
CLASH 0
⚠ Exposure 50%
Interaction summary
HB 7
HY 11
PI 2
CLASH 0
⚠ Exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (11/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 11
Exposed 11
LogP 4.3
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.525 | Score | -17.040 |
|---|---|---|---|
| Inter norm | -0.662 | Intra norm | 0.094 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 5 protein contact clashes | ||
| Residues |
ASN402
LEU399
MET393
MET471
PHE396
PRO398
SER394
SER395
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 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 280 | 1.52539503686563 | -0.662194 | -17.04 | 7 | 10 | 7 | 0.88 | 0.00 | - | no | Current |
| 229 | 1.6445127772881427 | -0.831216 | -20.0129 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 304 | 2.4289558876805577 | -0.883414 | -27.2825 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 200 | 2.7943043630904865 | -0.991983 | -29.0382 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 338 | 2.9426194963746157 | -0.805084 | -22.5863 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 276 | 3.0164538929855427 | -1.03597 | -29.4518 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 255 | 5.08809010873305 | -1.00429 | -26.0374 | 10 | 16 | 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
-17.040kcal/mol
Ligand efficiency (LE)
-0.5680kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.479
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
428.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.30
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
83.75kcal/mol
Minimised FF energy
70.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
676.9Ų
Total solvent-accessible surface area of free ligand
BSA total
319.4Ų
Buried surface area upon binding
BSA apolar
210.3Ų
Hydrophobic contacts buried
BSA polar
109.1Ų
Polar contacts buried
Fraction buried
47.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3081.3Ų
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
1513.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)