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
18.5 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.63, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.321 kcal/mol/HA)
✓ Good fit quality (FQ -11.06)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (18.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
Score
-26.430
kcal/mol
LE
-1.321
kcal/mol/HA
Fit Quality
-11.06
FQ (Leeson)
HAC
20
heavy atoms
MW
295
Da
LogP
1.74
cLogP
Interaction summary
HB 2
HY 15
PI 4
CLASH 0
Interaction summary
HB 2
HY 15
PI 4
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | -0.449 | Score | -26.430 |
|---|---|---|---|
| Inter norm | -1.357 | Intra norm | 0.036 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 2 |
| Artifact reason | geometry warning; 4 clashes; 2 protein contact clashes; 1 severe cofactor-context clash | ||
| Residues |
GLY225
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
SER227
TYR194
ARG287
| ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.63 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 300 | -0.44910725466171075 | -1.35736 | -26.4299 | 2 | 12 | 12 | 0.63 | 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
-26.430kcal/mol
Ligand efficiency (LE)
-1.3215kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.059
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
295.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.74
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-18.02kcal/mol
Minimised FF energy
-36.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
525.0Ų
Total solvent-accessible surface area of free ligand
BSA total
433.4Ų
Buried surface area upon binding
BSA apolar
287.0Ų
Hydrophobic contacts buried
BSA polar
146.4Ų
Polar contacts buried
Fraction buried
82.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1532.1Ų
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
1015.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)