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
Promising
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
11.8 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.58, Jaccard 0.35
Reason: 7 internal clashes
7 protein-contact clashes
7 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.728 kcal/mol/HA)
✓ Good fit quality (FQ -7.02)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Moderate strain (11.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-21.836
kcal/mol
LE
-0.728
kcal/mol/HA
Fit Quality
-7.02
FQ (Leeson)
HAC
30
heavy atoms
MW
527
Da
LogP
6.33
cLogP
Interaction summary
HB 6
HY 24
PI 1
CLASH 7
Interaction summary
HB 6
HY 24
PI 1
CLASH 7
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 | 3.323 | Score | -21.836 |
|---|---|---|---|
| Inter norm | -0.817 | Intra norm | 0.089 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ALA209
ALA67
ALA90
GLY214
GLY215
GLY66
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
TYR69
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 | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 670 | 0.525452057697768 | -0.801607 | -21.9446 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 671 | 1.2452403104088678 | -0.91337 | -24.4708 | 6 | 21 | 0 | 0.00 | - | - | no | Open |
| 671 | 1.654222623131364 | -0.918624 | -25.248 | 2 | 20 | 0 | 0.00 | - | - | no | Open |
| 676 | 1.6805072898158524 | -0.957408 | -25.1533 | 5 | 20 | 1 | 0.08 | - | - | no | Open |
| 673 | 1.9779781356169357 | -0.870975 | -24.7896 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 673 | 3.3230474842728452 | -0.81709 | -21.836 | 6 | 15 | 7 | 0.58 | - | - | no | Current |
| 675 | 3.6470904213179978 | -0.838203 | -23.206 | 6 | 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
-21.836kcal/mol
Ligand efficiency (LE)
-0.7279kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.021
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
527.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.33
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.27kcal/mol
Minimised FF energy
36.44kcal/mol
SASA & burial
✓ computed
SASA (unbound)
699.5Ų
Total solvent-accessible surface area of free ligand
BSA total
506.9Ų
Buried surface area upon binding
BSA apolar
448.6Ų
Hydrophobic contacts buried
BSA polar
58.3Ų
Polar contacts buried
Fraction buried
72.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3148.0Ų
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
1562.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)