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 high
Native strong
SASA done
Strain ΔE
23.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.47, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (10/26 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 (-0.520 kcal/mol/HA)
✓ Good fit quality (FQ -5.20)
✓ Good burial (59% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (23.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-17.667
kcal/mol
LE
-0.520
kcal/mol/HA
Fit Quality
-5.20
FQ (Leeson)
HAC
34
heavy atoms
MW
478
Da
LogP
5.21
cLogP
Interaction summary
HB 2
HY 17
PI 1
CLASH 2
⚠ Exposure 38%
Interaction summary
HB 2
HY 17
PI 1
CLASH 2
⚠ Exposure 38%
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
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (10/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 26
Buried (contacted) 16
Exposed 10
LogP 5.21
H-bonds 2
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 2.902 | Score | -17.667 |
|---|---|---|---|
| Inter norm | -0.567 | Intra norm | 0.047 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 2 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; moderate strain Δ 23.9 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
MET400
PHE396
PRO398
PRO462
SER395
SER464
SER470
THR397
THR463
| ||
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 | 0.47 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 389 | 2.901671907728243 | -0.566642 | -17.6668 | 2 | 14 | 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
-17.667kcal/mol
Ligand efficiency (LE)
-0.5196kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.199
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
478.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.21
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
198.20kcal/mol
Minimised FF energy
174.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
753.5Ų
Total solvent-accessible surface area of free ligand
BSA total
442.9Ų
Buried surface area upon binding
BSA apolar
398.8Ų
Hydrophobic contacts buried
BSA polar
44.1Ų
Polar contacts buried
Fraction buried
58.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3213.3Ų
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
1542.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)