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 strong
SASA done
Strain ΔE
12.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.58, Jaccard 0.39
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.028 kcal/mol/HA)
✓ Good fit quality (FQ -9.21)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (12.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.677
kcal/mol
LE
-1.028
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
24
heavy atoms
MW
324
Da
LogP
3.45
cLogP
Interaction summary
HB 8
HY 12
PI 0
CLASH 4
Interaction summary
HB 8
HY 12
PI 0
CLASH 4
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 | 4.172 | Score | -24.677 |
|---|---|---|---|
| Inter norm | -0.992 | Intra norm | -0.036 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA209
ALA90
ARG74
ASN208
GLY214
GLY215
LYS211
LYS89
MET70
PRO212
PRO213
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.39 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 387 | 0.36051882321163314 | -1.34004 | -29.2797 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 417 | 1.8908796334170939 | -1.35793 | -33.9757 | 10 | 14 | 0 | 0.00 | - | - | no | Open |
| 435 | 1.9004749194382002 | -1.02058 | -25.9903 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 419 | 2.807878564222623 | -1.0264 | -24.6204 | 7 | 9 | 0 | 0.00 | - | - | no | Open |
| 403 | 3.0441745044344053 | -1.17278 | -25.3923 | 9 | 16 | 0 | 0.00 | - | - | no | Open |
| 401 | 3.272585015045708 | -1.014 | -21.3315 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 496 | 4.171712409869473 | -0.992234 | -24.6771 | 8 | 13 | 7 | 0.58 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.677kcal/mol
Ligand efficiency (LE)
-1.0282kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.215
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
324.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.45
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.80kcal/mol
Minimised FF energy
53.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
548.9Ų
Total solvent-accessible surface area of free ligand
BSA total
384.5Ų
Buried surface area upon binding
BSA apolar
295.6Ų
Hydrophobic contacts buried
BSA polar
88.9Ų
Polar contacts buried
Fraction buried
70.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3033.2Ų
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
1477.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)