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
32.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.57
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
55% of hydrophobic surface appears solvent-exposed (6/11 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 (-1.032 kcal/mol/HA)
✓ Good fit quality (FQ -8.81)
✓ Strong H-bond network (10 bonds)
✓ Good burial (63% SASA buried)
✗ Very high strain energy (32.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-21.682
kcal/mol
LE
-1.032
kcal/mol/HA
Fit Quality
-8.81
FQ (Leeson)
HAC
21
heavy atoms
MW
327
Da
LogP
0.87
cLogP
Interaction summary
HB 10
HY 7
PI 0
CLASH 3
⚠ Exposure 54%
Interaction summary
HB 10
HY 7
PI 0
CLASH 3
⚠ Exposure 54%
Partial hydrophobic solvent exposure
55% of hydrophobic surface appears solvent-exposed (6/11 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 11
Buried (contacted) 5
Exposed 6
LogP 0.87
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 4.175 | Score | -21.682 |
|---|---|---|---|
| Inter norm | -1.086 | Intra norm | 0.053 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes; high strain Δ 32.7 | ||
| Residues |
ALA90
GLY85
LYS89
PRO187
PRO212
PRO213
SER86
SER87
TYR210
VAL88
| ||
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | 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:276; 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 | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 8 | Native recall | 0.67 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 291 | 1.0967612246539307 | -1.34511 | -30.2038 | 9 | 11 | 0 | 0.00 | - | - | no | Open |
| 322 | 1.293053659419753 | -1.2063 | -25.6189 | 8 | 19 | 0 | 0.00 | - | - | no | Open |
| 270 | 1.7191106795656168 | -1.17853 | -22.541 | 16 | 12 | 0 | 0.00 | - | - | no | Open |
| 390 | 2.3538397766138504 | -1.22354 | -25.7047 | 7 | 15 | 0 | 0.00 | - | - | no | Open |
| 373 | 2.4588288780248044 | -1.25312 | -26.3897 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 336 | 2.886003700201454 | -1.17246 | -25.6474 | 10 | 17 | 0 | 0.00 | - | - | no | Open |
| 317 | 2.9899836999992475 | -1.31975 | -28.8678 | 11 | 16 | 0 | 0.00 | - | - | no | Open |
| 408 | 4.174722979043151 | -1.08565 | -21.6821 | 10 | 10 | 8 | 0.67 | - | - | no | Current |
| 439 | 4.345171388067734 | -1.19467 | -26.3824 | 10 | 12 | 0 | 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
-21.682kcal/mol
Ligand efficiency (LE)
-1.0325kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.807
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
327.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.87
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-36.41kcal/mol
Minimised FF energy
-69.13kcal/mol
SASA & burial
✓ computed
SASA (unbound)
522.9Ų
Total solvent-accessible surface area of free ligand
BSA total
327.9Ų
Buried surface area upon binding
BSA apolar
188.6Ų
Hydrophobic contacts buried
BSA polar
139.3Ų
Polar contacts buried
Fraction buried
62.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
57.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2971.1Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1469.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)