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
18.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.50
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.786 kcal/mol/HA)
✓ Good fit quality (FQ -7.14)
✓ Deep burial (96% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (18.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-19.646
kcal/mol
LE
-0.786
kcal/mol/HA
Fit Quality
-7.14
FQ (Leeson)
HAC
25
heavy atoms
MW
377
Da
LogP
3.88
cLogP
Final rank
2.5383
rank score
Inter norm
-0.933
normalised
Contacts
18
H-bonds 2
Interaction summary
HBD 1
HY 9
PI 3
CLASH 4
Interaction summary
HBD 1
HY 9
PI 3
CLASH 4
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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 8RHT | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA34
ASP54
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE233
PHE58
PHE94
PRO91
SER89
THR184
THR86
TRP49
TYR166
TYR57
VAL32
VAL33
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 2 | Strict recall | 0.40 |
| HB same residue+role | 2 | HB role recall | 0.50 |
| HB same residue | 2 | HB residue recall | 0.50 |
Protein summary
223 residues
| Protein target | T06 | Atoms | 3452 |
|---|---|---|---|
| Residues | 223 | Chains | 1 |
| Residue summary | ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74 | ||
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:NDP301
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.646kcal/mol
Ligand efficiency (LE)
-0.7858kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
376.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.88
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.28kcal/mol
Minimised FF energy
78.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
626.6Ų
Total solvent-accessible surface area of free ligand
BSA total
599.9Ų
Buried surface area upon binding
BSA apolar
493.9Ų
Hydrophobic contacts buried
BSA polar
105.9Ų
Polar contacts buried
Fraction buried
95.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1747.0Ų
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
1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
582.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)