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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
40.7 kcal/mol
Protein clashes
0
Internal clashes
19
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.60
Reason: 19 internal clashes
19 intramolecular clashes
72% of hydrophobic surface is solvent-exposed (23/32 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.506 kcal/mol/HA)
✓ Good fit quality (FQ -5.32)
✓ Strong H-bond network (11 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Extreme strain energy (40.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-20.738
kcal/mol
LE
-0.506
kcal/mol/HA
Fit Quality
-5.32
FQ (Leeson)
HAC
41
heavy atoms
MW
559
Da
LogP
5.24
cLogP
Final rank
4.6552
rank score
Inter norm
-0.706
normalised
Contacts
16
H-bonds 11
Interaction summary
HBD 1
HBA 10
HY 3
PI 5
CLASH 0
Interaction summary
HBD 1
HBA 10
HY 3
PI 5
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.
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: permissive.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 13 | Native recall | 0.81 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 6 | HB residue recall | 0.60 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
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:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 308 | 1.4719169858001477 | -0.645691 | -22.5301 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 189 | 4.655183948020784 | -0.706097 | -20.7375 | 11 | 16 | 13 | 0.81 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.738kcal/mol
Ligand efficiency (LE)
-0.5058kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.315
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
558.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.24
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
150.81kcal/mol
Minimised FF energy
110.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
857.0Ų
Total solvent-accessible surface area of free ligand
BSA total
533.3Ų
Buried surface area upon binding
BSA apolar
416.9Ų
Hydrophobic contacts buried
BSA polar
116.5Ų
Polar contacts buried
Fraction buried
62.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2373.6Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
807.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)