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
22.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.54, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Good LE (-0.385 kcal/mol/HA)
✓ Good fit quality (FQ -3.50)
✓ Good H-bonds (5 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ High strain energy (22.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-9.615
kcal/mol
LE
-0.385
kcal/mol/HA
Fit Quality
-3.50
FQ (Leeson)
HAC
25
heavy atoms
MW
336
Da
LogP
2.07
cLogP
Interaction summary
HB 5
HY 16
PI 1
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 5
HY 16
PI 1
CLASH 2
⚠ Exposure 35%
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
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 13
Exposed 7
LogP 2.07
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.111 | Score | -9.615 |
|---|---|---|---|
| Inter norm | -0.783 | Intra norm | 0.398 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 22.6 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
MET400
PHE396
PRO398
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 | 0.54 | 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 |
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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-9.615kcal/mol
Ligand efficiency (LE)
-0.3846kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.496
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
336.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.07
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
38.90kcal/mol
Minimised FF energy
16.32kcal/mol
SASA & burial
✓ computed
SASA (unbound)
629.6Ų
Total solvent-accessible surface area of free ligand
BSA total
419.5Ų
Buried surface area upon binding
BSA apolar
368.7Ų
Hydrophobic contacts buried
BSA polar
50.8Ų
Polar contacts buried
Fraction buried
66.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3109.6Ų
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
1513.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)