Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
19.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.25
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.728 kcal/mol/HA)
✓ Good fit quality (FQ -6.87)
✓ Good H-bonds (5 bonds)
✓ Deep burial (65% SASA buried)
✗ Moderate strain (19.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-20.387
kcal/mol
LE
-0.728
kcal/mol/HA
Fit Quality
-6.87
FQ (Leeson)
HAC
28
heavy atoms
MW
419
Da
LogP
3.01
cLogP
Interaction summary
HB 5
HY 19
PI 0
CLASH 3
Interaction summary
HB 5
HY 19
PI 0
CLASH 3
| Final rank | 2.911 | Score | -20.387 |
|---|---|---|---|
| Inter norm | -0.879 | Intra norm | 0.151 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ALA90
ASN91
GLY214
GLY215
LYS211
LYS89
LYS93
PRO187
PRO212
PRO213
TRP92
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 | 5 | Native recall | 0.42 |
| Jaccard | 0.25 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 391 | 0.8112587710984578 | -0.883156 | -21.7804 | 4 | 19 | 0 | 0.00 | - | - | no | Open |
| 388 | 1.761457712336876 | -1.18388 | -28.0949 | 12 | 17 | 0 | 0.00 | - | - | no | Open |
| 484 | 2.388298171391906 | -0.868572 | -20.6754 | 5 | 12 | 5 | 0.42 | - | - | no | Open |
| 101 | 2.911216982679596 | -0.879119 | -20.3872 | 5 | 13 | 5 | 0.42 | - | - | no | Current |
| 95 | 2.970006987126121 | -1.08769 | -25.015 | 13 | 16 | 0 | 0.00 | - | - | no | Open |
| 379 | 3.450130273935065 | -0.998633 | -22.0405 | 14 | 15 | 0 | 0.00 | - | - | no | Open |
| 423 | 3.7405836219795368 | -1.00578 | -24.1953 | 10 | 15 | 0 | 0.00 | - | - | no | Open |
| 160 | 3.885655564123343 | -0.784425 | -18.1914 | 7 | 14 | 0 | 0.00 | - | - | no | Open |
| 100 | 4.225272845749715 | -1.07342 | -27.2468 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 73 | 5.143261743022093 | -1.07475 | -24.8662 | 12 | 15 | 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
-20.387kcal/mol
Ligand efficiency (LE)
-0.7281kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.874
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
419.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-22.34kcal/mol
Minimised FF energy
-42.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
667.5Ų
Total solvent-accessible surface area of free ligand
BSA total
436.4Ų
Buried surface area upon binding
BSA apolar
257.5Ų
Hydrophobic contacts buried
BSA polar
178.9Ų
Polar contacts buried
Fraction buried
65.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
59.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3067.9Ų
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
1473.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)