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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
34.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.64
Reason: no major geometry red flags detected
2 protein-contact clashes
73% of hydrophobic surface is solvent-exposed (19/26 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.760 kcal/mol/HA)
✓ Good fit quality (FQ -7.61)
✓ Strong H-bond network (7 bonds)
✓ Good burial (59% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (34.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-25.848
kcal/mol
LE
-0.760
kcal/mol/HA
Fit Quality
-7.61
FQ (Leeson)
HAC
34
heavy atoms
MW
488
Da
LogP
4.11
cLogP
Final rank
5.1564
rank score
Inter norm
-0.772
normalised
Contacts
17
H-bonds 11
Interaction summary
HBA 7
HY 2
PI 2
CLASH 2
Interaction summary
HBA 7
HY 2
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 16 | Native recall | 0.94 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 7 | HB role recall | 0.64 |
| HB same residue | 7 | HB residue recall | 0.64 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 279 | 2.951164842988615 | -0.668499 | -22.8232 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 183 | 5.156400225908865 | -0.771667 | -25.848 | 11 | 17 | 16 | 0.94 | 0.64 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.848kcal/mol
Ligand efficiency (LE)
-0.7602kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.607
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
487.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.11
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.70kcal/mol
Minimised FF energy
71.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
789.1Ų
Total solvent-accessible surface area of free ligand
BSA total
463.2Ų
Buried surface area upon binding
BSA apolar
376.3Ų
Hydrophobic contacts buried
BSA polar
86.9Ų
Polar contacts buried
Fraction buried
58.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2420.2Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
686.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)