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 high
Native strong
SASA done
Strain ΔE
20.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.92, Jaccard 0.65
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.747 kcal/mol/HA)
✓ Good fit quality (FQ -7.13)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Moderate strain (20.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-21.651
kcal/mol
LE
-0.747
kcal/mol/HA
Fit Quality
-7.13
FQ (Leeson)
HAC
29
heavy atoms
MW
530
Da
LogP
6.13
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 1
Interaction summary
HB 3
HY 24
PI 1
CLASH 1
| Final rank | 2.965 | Score | -21.651 |
|---|---|---|---|
| Inter norm | -0.899 | Intra norm | 0.153 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
ASP71
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO212
PRO213
SER86
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 | 11 | Native recall | 0.92 |
| Jaccard | 0.65 | 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
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 673 | 0.7497194082801134 | -0.82269 | -17.2529 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 669 | 1.232737016346297 | -0.788014 | -20.274 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 674 | 1.4914675157547654 | -0.918953 | -25.5943 | 3 | 19 | 1 | 0.08 | - | - | no | Open |
| 670 | 1.6936239314371768 | -0.843158 | -22.4207 | 2 | 16 | 0 | 0.00 | - | - | no | Open |
| 667 | 2.9645212209224328 | -0.899472 | -21.6515 | 3 | 16 | 11 | 0.92 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.651kcal/mol
Ligand efficiency (LE)
-0.7466kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.127
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
530.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.67kcal/mol
Minimised FF energy
34.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
658.7Ų
Total solvent-accessible surface area of free ligand
BSA total
503.9Ų
Buried surface area upon binding
BSA apolar
461.7Ų
Hydrophobic contacts buried
BSA polar
42.1Ų
Polar contacts buried
Fraction buried
76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3186.4Ų
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
1497.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)