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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
37.4 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.75, Jaccard 0.47
Reason: 13 internal clashes
13 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.698 kcal/mol/HA)
✓ Good fit quality (FQ -6.86)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (37.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-22.325
kcal/mol
LE
-0.698
kcal/mol/HA
Fit Quality
-6.86
FQ (Leeson)
HAC
32
heavy atoms
MW
472
Da
LogP
3.33
cLogP
Final rank
3.0126
rank score
Inter norm
-0.713
normalised
Contacts
16
H-bonds 7
Interaction summary
HBD 4
HBA 2
HY 6
PI 0
CLASH 0
Interaction summary
HBD 4
HBA 2
HY 6
PI 0
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 306 | 1.0399415523302338 | -0.766429 | -19.6042 | 2 | 20 | 0 | 0.00 | - | - | no | Open |
| 325 | 1.7622918572042872 | -0.72501 | -21.6638 | 5 | 16 | 0 | 0.00 | - | - | no | Open |
| 339 | 1.8756034248014986 | -0.623323 | -14.0022 | 6 | 12 | 0 | 0.00 | - | - | no | Open |
| 288 | 1.941314636855978 | -1.0223 | -32.8605 | 10 | 15 | 0 | 0.00 | - | - | no | Open |
| 287 | 2.3052789623162595 | -0.860388 | -25.3677 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 391 | 3.0126089501724107 | -0.713197 | -22.3245 | 7 | 16 | 9 | 0.75 | - | - | no | Current |
| 376 | 3.3532299697325993 | -0.830769 | -26.6969 | 7 | 19 | 0 | 0.00 | - | - | no | Open |
| 306 | 3.4749873966025415 | -0.769904 | -23.8063 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 254 | 3.797851917357343 | -0.767932 | -25.5546 | 10 | 21 | 0 | 0.00 | - | - | no | Open |
| 267 | 4.770866832306279 | -0.910892 | -28.0567 | 7 | 21 | 1 | 0.08 | - | - | no | Open |
| 266 | 4.987550321084067 | -1.00253 | -26.5548 | 11 | 18 | 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
-22.325kcal/mol
Ligand efficiency (LE)
-0.6976kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.861
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
471.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.33
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-59.79kcal/mol
Minimised FF energy
-97.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
772.5Ų
Total solvent-accessible surface area of free ligand
BSA total
528.6Ų
Buried surface area upon binding
BSA apolar
424.2Ų
Hydrophobic contacts buried
BSA polar
104.3Ų
Polar contacts buried
Fraction buried
68.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3205.1Ų
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
1459.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)