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
35.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.31, H-bond role recall 1.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
71% of hydrophobic surface is solvent-exposed (17/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.572 kcal/mol/HA)
✓ Good fit quality (FQ -5.57)
✓ Good H-bonds (3 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (94%)
✗ Very high strain energy (35.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-17.717
kcal/mol
LE
-0.572
kcal/mol/HA
Fit Quality
-5.57
FQ (Leeson)
HAC
31
heavy atoms
MW
464
Da
LogP
3.89
cLogP
Interaction summary
HB 3
HY 7
PI 1
CLASH 3
⚠ Exposure 70%
Interaction summary
HB 3
HY 7
PI 1
CLASH 3
⚠ Exposure 70%
Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (17/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 24
Buried (contacted) 7
Exposed 17
LogP 3.89
H-bonds 3
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.600 | Score | -17.717 |
|---|---|---|---|
| Inter norm | -0.647 | Intra norm | 0.076 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; high strain Δ 35.6 | ||
| Residues |
CYS469
GLU466
GLU467
GLY459
HIS461
MET400
PHE396
PRO398
PRO462
SER394
SER464
SER470
THR463
| ||
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 | 5 | Native recall | 0.62 |
| Jaccard | 0.31 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 149 | 3.186636741914792 | -0.797165 | -23.7914 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 143 | 3.599525627754173 | -0.647312 | -17.7174 | 3 | 13 | 5 | 0.62 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.717kcal/mol
Ligand efficiency (LE)
-0.5715kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.568
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
464.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.33kcal/mol
Minimised FF energy
70.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
715.7Ų
Total solvent-accessible surface area of free ligand
BSA total
439.6Ų
Buried surface area upon binding
BSA apolar
412.3Ų
Hydrophobic contacts buried
BSA polar
27.3Ų
Polar contacts buried
Fraction buried
61.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3238.7Ų
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
1484.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)