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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
28.2 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.86, Jaccard 0.72, H-bond role recall 0.75
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes
9 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.462 kcal/mol/HA)
✓ Good fit quality (FQ -4.66)
✓ Good H-bonds (3 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (28.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-16.154
kcal/mol
LE
-0.462
kcal/mol/HA
Fit Quality
-4.66
FQ (Leeson)
HAC
35
heavy atoms
MW
480
Da
LogP
1.45
cLogP
Final rank
4.1343
rank score
Inter norm
-0.713
normalised
Contacts
22
H-bonds 6
Interaction summary
HBD 3
HY 10
PI 3
CLASH 9
Interaction summary
HBD 3
HY 10
PI 3
CLASH 9
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 | 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 | 18 | Native recall | 0.86 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 3 | Strict recall | 0.60 |
| HB same residue+role | 3 | HB role recall | 0.75 |
| HB same residue | 3 | HB residue recall | 0.75 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 20 | 2.1939628179865047 | -1.02133 | -33.7229 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 17 | 2.3265272319011476 | -1.05255 | -36.6414 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 14 | 4.134283078679938 | -0.713349 | -16.1542 | 6 | 22 | 18 | 0.86 | 0.75 | - | no | Current |
| 14 | 4.649433580819565 | -0.794446 | -29.5766 | 6 | 22 | 1 | 0.05 | 0.00 | - | no | Open |
| 14 | 4.955806310701608 | -0.67906 | -20.1759 | 5 | 21 | 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
-16.154kcal/mol
Ligand efficiency (LE)
-0.4615kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.655
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
479.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.45
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
31.18kcal/mol
Minimised FF energy
2.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
782.5Ų
Total solvent-accessible surface area of free ligand
BSA total
720.0Ų
Buried surface area upon binding
BSA apolar
570.4Ų
Hydrophobic contacts buried
BSA polar
149.6Ų
Polar contacts buried
Fraction buried
92.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1862.1Ų
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
578.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)