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
24.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.83, Jaccard 0.48
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.695 kcal/mol/HA)
✓ Good fit quality (FQ -7.12)
✓ Good H-bonds (4 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-25.719
kcal/mol
LE
-0.695
kcal/mol/HA
Fit Quality
-7.12
FQ (Leeson)
HAC
37
heavy atoms
MW
528
Da
LogP
7.49
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 3
Interaction summary
HB 4
HY 24
PI 2
CLASH 3
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
| Final rank | 2.625 | Score | -25.719 |
|---|---|---|---|
| Inter norm | -0.719 | Intra norm | 0.024 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 4 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 24.5 | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
ASN208
GLU82
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO187
PRO212
PRO213
SER76
TRP81
TYR210
VAL88
| ||
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 | 10 | Native recall | 0.83 |
| Jaccard | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 74 | 2.11350872350086 | -0.57715 | -24.9305 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 49 | 2.6250809586045385 | -0.719255 | -25.7194 | 4 | 19 | 10 | 0.83 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.719kcal/mol
Ligand efficiency (LE)
-0.6951kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.117
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
528.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.49
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.49kcal/mol
Minimised FF energy
26.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
816.8Ų
Total solvent-accessible surface area of free ligand
BSA total
587.3Ų
Buried surface area upon binding
BSA apolar
530.2Ų
Hydrophobic contacts buried
BSA polar
57.1Ų
Polar contacts buried
Fraction buried
71.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3296.3Ų
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
1517.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)