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
15.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.69, Jaccard 0.69
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 (-0.554 kcal/mol/HA)
✓ Good fit quality (FQ -5.34)
✓ Good H-bonds (3 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (15.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (8)
Score
-16.612
kcal/mol
LE
-0.554
kcal/mol/HA
Fit Quality
-5.34
FQ (Leeson)
HAC
30
heavy atoms
MW
543
Da
LogP
6.80
cLogP
Interaction summary
HB 3
HY 24
PI 4
CLASH 3
Interaction summary
HB 3
HY 24
PI 4
CLASH 3
| Final rank | 0.811 | Score | -16.612 |
|---|---|---|---|
| Inter norm | -0.697 | Intra norm | 0.143 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 3 |
| Artifact reason | geometry warning; 8 clashes; 4 protein contact clashes | ||
| Residues |
ASP116
GLU18
GLY112
LEU17
MET113
SER109
THR117
TRP21
TYR110
| ||
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| 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 | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 9 | Native recall | 0.69 |
| Jaccard | 0.69 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 672 | 0.514679985666019 | -0.894442 | -23.4063 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 678 | 0.8105169412196023 | -0.697208 | -16.6119 | 3 | 9 | 9 | 0.69 | - | - | no | Current |
| 674 | 2.040126377083499 | -0.900631 | -24.1106 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 676 | 2.2112625099320904 | -0.894359 | -20.4876 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 672 | 2.23237953245765 | -0.881443 | -23.9855 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 674 | 2.7366679178174302 | -0.777686 | -22.0152 | 2 | 16 | 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
-16.612kcal/mol
Ligand efficiency (LE)
-0.5537kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.341
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
543.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.32kcal/mol
Minimised FF energy
27.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
681.0Ų
Total solvent-accessible surface area of free ligand
BSA total
423.2Ų
Buried surface area upon binding
BSA apolar
354.7Ų
Hydrophobic contacts buried
BSA polar
68.5Ų
Polar contacts buried
Fraction buried
62.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3083.1Ų
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
1583.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)