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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
72.4 kcal/mol
Protein clashes
2
Internal clashes
15
Native overlap
contact recall 0.75, Jaccard 0.43
Reason: 15 internal clashes, strain 72.4 kcal/mol
strain ΔE 72.4 kcal/mol
2 protein-contact clashes
15 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.728 kcal/mol/HA)
✓ Good fit quality (FQ -7.60)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Extreme strain energy (72.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (15)
Score
-29.118
kcal/mol
LE
-0.728
kcal/mol/HA
Fit Quality
-7.60
FQ (Leeson)
HAC
40
heavy atoms
MW
600
Da
LogP
5.35
cLogP
Final rank
1.4225
rank score
Inter norm
-0.721
normalised
Contacts
18
H-bonds 4
Interaction summary
HBA 2
HY 9
PI 1
CLASH 0
Interaction summary
HBA 2
HY 9
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.43 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 637 | 1.422454228843464 | -0.721445 | -29.1179 | 4 | 18 | 9 | 0.75 | - | - | no | Current |
| 638 | 1.6131283764588384 | -0.666796 | -30.8424 | 5 | 20 | 0 | 0.00 | - | - | no | Open |
| 659 | 3.108477076869559 | -0.580916 | -17.9506 | 7 | 20 | 0 | 0.00 | - | - | no | Open |
| 650 | 3.7068637616931417 | -0.681046 | -27.753 | 12 | 18 | 0 | 0.00 | - | - | no | Open |
| 660 | 4.678675419925 | -0.693709 | -22.2586 | 11 | 21 | 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
-29.118kcal/mol
Ligand efficiency (LE)
-0.7279kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.603
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
600.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.35
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
72.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.21kcal/mol
Minimised FF energy
25.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
901.9Ų
Total solvent-accessible surface area of free ligand
BSA total
672.8Ų
Buried surface area upon binding
BSA apolar
552.6Ų
Hydrophobic contacts buried
BSA polar
120.2Ų
Polar contacts buried
Fraction buried
74.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3299.7Ų
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
1470.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)