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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
14.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.049 kcal/mol/HA)
✓ Good fit quality (FQ -9.40)
✓ Good H-bonds (3 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (14.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.180
kcal/mol
LE
-1.049
kcal/mol/HA
Fit Quality
-9.40
FQ (Leeson)
HAC
24
heavy atoms
MW
409
Da
LogP
3.72
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 4
Interaction summary
HB 3
HY 24
PI 2
CLASH 4
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.880 | Score | -25.180 |
|---|---|---|---|
| Inter norm | -0.991 | Intra norm | -0.082 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA34
ARG100
ARG59
ASP54
GLN56
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE58
PHE94
PRO91
VAL32
VAL33
| ||
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 391 | 0.21700719466234605 | -1.39302 | -32.2253 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 444 | 0.7062920106538152 | -0.950209 | -26.6197 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 1.2623877638131078 | -1.35339 | -29.6607 | 9 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 404 | 1.8802542420593948 | -0.990568 | -25.18 | 3 | 16 | 13 | 0.62 | 0.00 | - | no | Current |
| 447 | 3.109982217759302 | -1.12173 | -24.7218 | 9 | 12 | 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
-25.180kcal/mol
Ligand efficiency (LE)
-1.0492kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.403
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
409.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.72
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
110.92kcal/mol
Minimised FF energy
96.45kcal/mol
SASA & burial
✓ computed
SASA (unbound)
613.9Ų
Total solvent-accessible surface area of free ligand
BSA total
563.0Ų
Buried surface area upon binding
BSA apolar
437.6Ų
Hydrophobic contacts buried
BSA polar
125.3Ų
Polar contacts buried
Fraction buried
91.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1720.7Ų
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
572.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)