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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
23.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.85, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
80% of hydrophobic surface is solvent-exposed (20/25 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 (-0.707 kcal/mol/HA)
✓ Good fit quality (FQ -7.02)
✓ Strong H-bond network (11 bonds)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (23.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-23.338
kcal/mol
LE
-0.707
kcal/mol/HA
Fit Quality
-7.02
FQ (Leeson)
HAC
33
heavy atoms
MW
475
Da
LogP
4.89
cLogP
Final rank
3.7492
rank score
Inter norm
-0.740
normalised
Contacts
20
H-bonds 12
Interaction summary
HBD 2
HBA 9
HY 3
PI 1
CLASH 3
Interaction summary
HBD 2
HBA 9
HY 3
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 8.
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 | 17 | Native recall | 1.00 |
| Jaccard | 0.85 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 8 | HB residue recall | 0.73 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 495 | 0.7636299668614087 | -0.944298 | -31.6224 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 547 | 1.3092080501017846 | -0.748973 | -24.4712 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 568 | 2.1136660153511535 | -0.774735 | -23.372 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 508 | 2.363635055852463 | -0.896611 | -27.6232 | 10 | 17 | 5 | 0.29 | 0.18 | - | no | Open |
| 506 | 2.512933131032401 | -0.972941 | -29.8517 | 9 | 26 | 0 | 0.00 | 0.00 | - | no | Open |
| 547 | 2.7275152541986074 | -0.63594 | -20.531 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 3.647484580817899 | -0.738297 | -22.9327 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 3.7491718068183464 | -0.73996 | -23.338 | 12 | 20 | 17 | 1.00 | 0.45 | - | no | Current |
| 555 | 4.578227095484919 | -0.730577 | -20.9774 | 4 | 14 | 0 | 0.00 | 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
-23.338kcal/mol
Ligand efficiency (LE)
-0.7072kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.017
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.67kcal/mol
Minimised FF energy
70.67kcal/mol
SASA & burial
✓ computed
SASA (unbound)
776.3Ų
Total solvent-accessible surface area of free ligand
BSA total
489.4Ų
Buried surface area upon binding
BSA apolar
354.4Ų
Hydrophobic contacts buried
BSA polar
135.0Ų
Polar contacts buried
Fraction buried
63.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2341.2Ų
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
685.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)