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
28.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.73, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
41% of hydrophobic surface appears solvent-exposed (11/27 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 (-0.448 kcal/mol/HA)
✓ Good fit quality (FQ -4.58)
✓ Strong H-bond network (6 bonds)
✓ Good burial (47% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (28.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-16.569
kcal/mol
LE
-0.448
kcal/mol/HA
Fit Quality
-4.58
FQ (Leeson)
HAC
37
heavy atoms
MW
528
Da
LogP
3.52
cLogP
Interaction summary
HB 6
HY 9
PI 1
CLASH 3
⚠ Exposure 40%
Interaction summary
HB 6
HY 9
PI 1
CLASH 3
⚠ Exposure 40%
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (11/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 16
Exposed 11
LogP 3.52
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 5.615 | Score | -16.569 |
|---|---|---|---|
| Inter norm | -0.518 | Intra norm | 0.070 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 6 |
| Artifact reason | geometry warning; 15 clashes; 3 protein clashes; moderate strain Δ 28.4 | ||
| Residues |
ASN402
GLU467
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 | 8 | Native recall | 1.00 |
| Jaccard | 0.73 | 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 489 | 2.4081999083917935 | -0.718608 | -26.275 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 444 | 4.2265319089055575 | -0.846584 | -30.8759 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 451 | 5.615448471172846 | -0.518039 | -16.5688 | 6 | 11 | 8 | 1.00 | 0.00 | - | no | Current |
| 424 | 6.181503815847542 | -0.769821 | -26.7005 | 11 | 22 | 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
-16.569kcal/mol
Ligand efficiency (LE)
-0.4478kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.585
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
527.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.52
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-142.06kcal/mol
Minimised FF energy
-170.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
848.2Ų
Total solvent-accessible surface area of free ligand
BSA total
397.8Ų
Buried surface area upon binding
BSA apolar
288.5Ų
Hydrophobic contacts buried
BSA polar
109.3Ų
Polar contacts buried
Fraction buried
46.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3258.9Ų
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
1505.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)