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 mixed
SASA done
Strain ΔE
24.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.50, Jaccard 0.27
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 (-0.756 kcal/mol/HA)
✓ Good fit quality (FQ -7.44)
✓ Good H-bonds (4 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ High strain energy (24.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.207
kcal/mol
LE
-0.756
kcal/mol/HA
Fit Quality
-7.44
FQ (Leeson)
HAC
32
heavy atoms
MW
467
Da
LogP
4.70
cLogP
Interaction summary
HB 4
HY 24
PI 0
CLASH 3
Interaction summary
HB 4
HY 24
PI 0
CLASH 3
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
| Final rank | 2.742 | Score | -24.207 |
|---|---|---|---|
| Inter norm | -0.710 | Intra norm | -0.047 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; moderate strain Δ 24.9 | ||
| Residues |
ALA209
ALA90
ASN208
ASN91
GLY214
GLY215
LYS211
LYS89
LYS93
MET70
PRO187
PRO212
PRO213
TRP92
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 | 6 | Native recall | 0.50 |
| Jaccard | 0.27 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 481 | 0.833260595904217 | -0.99353 | -31.3183 | 8 | 13 | 0 | 0.00 | - | - | no | Open |
| 488 | 0.9430789113896668 | -0.763464 | -24.1793 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 469 | 2.5792744908747576 | -0.930947 | -30.9076 | 7 | 15 | 0 | 0.00 | - | - | no | Open |
| 482 | 2.61080621143186 | -0.91774 | -24.0255 | 12 | 19 | 1 | 0.08 | - | - | no | Open |
| 503 | 2.6537518010083168 | -0.872065 | -27.8131 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 537 | 2.741837643516047 | -0.70956 | -24.207 | 4 | 16 | 6 | 0.50 | - | - | no | Current |
| 476 | 2.8526863726121 | -0.830155 | -26.7459 | 15 | 14 | 0 | 0.00 | - | - | no | Open |
| 495 | 3.187958920184594 | -0.765818 | -26.7542 | 11 | 14 | 0 | 0.00 | - | - | no | Open |
| 516 | 3.9807987113699346 | -0.690298 | -20.9193 | 5 | 14 | 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
-24.207kcal/mol
Ligand efficiency (LE)
-0.7565kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.439
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.70
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.90kcal/mol
Minimised FF energy
28.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
720.0Ų
Total solvent-accessible surface area of free ligand
BSA total
473.1Ų
Buried surface area upon binding
BSA apolar
298.8Ų
Hydrophobic contacts buried
BSA polar
174.3Ų
Polar contacts buried
Fraction buried
65.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3102.3Ų
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
1498.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)