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
33.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.27
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.269 kcal/mol/HA)
✓ Good fit quality (FQ -11.02)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (33.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-27.913
kcal/mol
LE
-1.269
kcal/mol/HA
Fit Quality
-11.02
FQ (Leeson)
HAC
22
heavy atoms
MW
341
Da
LogP
1.09
cLogP
Final rank
4.2547
rank score
Inter norm
-1.170
normalised
Contacts
13
H-bonds 13
Interaction summary
HBD 1
HBA 5
HY 1
PI 1
CLASH 3
Interaction summary
HBD 1
HBA 5
HY 1
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 1.626499043761604 | -1.37094 | -30.1527 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 1.6518041180779013 | -1.37003 | -30.346 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 300 | 2.0875862514939527 | -1.29433 | -28.7606 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 2.3075074574600802 | -1.36833 | -30.0855 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 2.606219346550542 | -1.13545 | -26.0457 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 2.8599754316936856 | -1.28494 | -28.9186 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 3.0559467618395817 | -1.44185 | -31.3269 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 282 | 4.254727390078342 | -1.16966 | -27.913 | 13 | 13 | 12 | 0.71 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.913kcal/mol
Ligand efficiency (LE)
-1.2688kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.015
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-68.27kcal/mol
Minimised FF energy
-101.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
558.6Ų
Total solvent-accessible surface area of free ligand
BSA total
368.9Ų
Buried surface area upon binding
BSA apolar
259.3Ų
Hydrophobic contacts buried
BSA polar
109.6Ų
Polar contacts buried
Fraction buried
66.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2153.8Ų
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
653.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)