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 mixed
SASA done
Strain ΔE
16.0 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.50, Jaccard 0.32
Reason: 13 internal clashes
13 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.727 kcal/mol/HA)
✓ Good fit quality (FQ -6.93)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (16.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-21.070
kcal/mol
LE
-0.727
kcal/mol/HA
Fit Quality
-6.93
FQ (Leeson)
HAC
29
heavy atoms
MW
386
Da
LogP
5.42
cLogP
Interaction summary
HB 6
HY 22
PI 0
CLASH 0
Interaction summary
HB 6
HY 22
PI 0
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | 2.549 | Score | -21.070 |
|---|---|---|---|
| Inter norm | -0.798 | Intra norm | 0.072 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash | ||
| Residues |
ALA209
ALA90
ARG74
ASN208
ASN245
ASN91
GLY246
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
| ||
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 | 0.32 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 323 | 1.9880960137870662 | -1.21642 | -31.5302 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 420 | 2.548705262181661 | -0.798165 | -21.0698 | 6 | 13 | 6 | 0.50 | - | - | no | Current |
| 357 | 3.147742695757834 | -0.711274 | -16.5493 | 5 | 14 | 0 | 0.00 | - | - | no | Open |
| 340 | 3.304872371779209 | -0.822248 | -9.70627 | 7 | 17 | 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
-21.070kcal/mol
Ligand efficiency (LE)
-0.7265kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.935
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
386.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.42
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
80.87kcal/mol
Minimised FF energy
64.88kcal/mol
SASA & burial
✓ computed
SASA (unbound)
689.3Ų
Total solvent-accessible surface area of free ligand
BSA total
469.4Ų
Buried surface area upon binding
BSA apolar
400.7Ų
Hydrophobic contacts buried
BSA polar
68.7Ų
Polar contacts buried
Fraction buried
68.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3145.2Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1501.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)