Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
34.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.62, Jaccard 0.45, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
68% of hydrophobic surface is solvent-exposed (15/22 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 (-0.464 kcal/mol/HA)
✓ Good fit quality (FQ -4.52)
✓ Good H-bonds (5 bonds)
✓ Good burial (53% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (34.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-14.388
kcal/mol
LE
-0.464
kcal/mol/HA
Fit Quality
-4.52
FQ (Leeson)
HAC
31
heavy atoms
MW
456
Da
LogP
4.12
cLogP
Interaction summary
HB 5
HY 10
PI 1
CLASH 5
⚠ Exposure 68%
Interaction summary
HB 5
HY 10
PI 1
CLASH 5
⚠ Exposure 68%
Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (15/22 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 22
Buried (contacted) 7
Exposed 15
LogP 4.12
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.895 | Score | -14.388 |
|---|---|---|---|
| Inter norm | -0.603 | Intra norm | 0.139 |
| Top1000 | no | Excluded | no |
| Contacts | 8 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; high strain Δ 34.4 | ||
| Residues |
ASN402
LEU399
LYS407
LYS410
PHE396
PRO398
SER395
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 | 5 | Native recall | 0.62 |
| Jaccard | 0.45 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 559 | 1.0652672842289361 | -0.786115 | -21.2543 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 158 | 1.1523854723589628 | -1.03453 | -27.1701 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 123 | 1.2084656822000692 | -1.00211 | -25.0502 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 526 | 2.0214467499040696 | -1.01684 | -25.2689 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 125 | 2.164020308450243 | -0.764539 | -21.2514 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 553 | 2.8947686097992844 | -0.602994 | -14.3882 | 5 | 8 | 5 | 0.62 | 0.00 | - | no | Current |
| 81 | 3.7691860107617496 | -0.826819 | -16.7461 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 537 | 3.771237611358482 | -0.82715 | -16.8709 | 8 | 15 | 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
-14.388kcal/mol
Ligand efficiency (LE)
-0.4641kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.522
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
455.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.12
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.09kcal/mol
Minimised FF energy
59.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
713.9Ų
Total solvent-accessible surface area of free ligand
BSA total
377.8Ų
Buried surface area upon binding
BSA apolar
306.0Ų
Hydrophobic contacts buried
BSA polar
71.8Ų
Polar contacts buried
Fraction buried
52.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3111.2Ų
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
1530.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)