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
13.0 kcal/mol
Protein clashes
0
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.520 kcal/mol/HA)
✓ Good fit quality (FQ -11.88)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (13.0 kcal/mol)
✗ Geometry warnings
Score
-25.837
kcal/mol
LE
-1.520
kcal/mol/HA
Fit Quality
-11.88
FQ (Leeson)
HAC
17
heavy atoms
MW
263
Da
LogP
2.52
cLogP
Final rank
-0.7429
rank score
Inter norm
-1.534
normalised
Contacts
11
H-bonds 1
Interaction summary
HBA 1
HY 4
PI 4
CLASH 0
Interaction summary
HBA 1
HY 4
PI 4
CLASH 0
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
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 11 | Native recall | 0.58 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 488 | -0.7428771606203456 | -1.53449 | -25.837 | 1 | 11 | 11 | 0.58 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.837kcal/mol
Ligand efficiency (LE)
-1.5198kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.885
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
17HA
Physicochemical properties
Molecular weight
263.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.52
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-10.34kcal/mol
Minimised FF energy
-23.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
464.8Ų
Total solvent-accessible surface area of free ligand
BSA total
410.7Ų
Buried surface area upon binding
BSA apolar
279.5Ų
Hydrophobic contacts buried
BSA polar
131.3Ų
Polar contacts buried
Fraction buried
88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1463.1Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1014.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)