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 mixed
SASA done
Strain ΔE
19.7 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Reason: no major geometry red flags detected
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.702 kcal/mol/HA)
✓ Good fit quality (FQ -12.17)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (19.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-23.821
kcal/mol
LE
-1.702
kcal/mol/HA
Fit Quality
-12.17
FQ (Leeson)
HAC
14
heavy atoms
MW
217
Da
LogP
1.20
cLogP
Final rank
1.5597
rank score
Inter norm
-1.750
normalised
Contacts
10
H-bonds 2
Interaction summary
HBA 2
HY 2
PI 2
CLASH 0
Interaction summary
HBA 2
HY 2
PI 2
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 172 | 1.5447833934380724 | -1.75543 | -23.7816 | 2 | 10 | 10 | 0.53 | 0.20 | - | no | Open |
| 143 | 1.5597429191723426 | -1.75025 | -23.8207 | 2 | 10 | 10 | 0.53 | 0.20 | - | no | Current |
| 185 | 2.559403422284915 | -2.00536 | -22.0181 | 5 | 11 | 8 | 0.42 | 0.20 | - | no | Open |
| 160 | 2.559421931348862 | -2.0061 | -22.0636 | 5 | 11 | 8 | 0.42 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.821kcal/mol
Ligand efficiency (LE)
-1.7015kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.166
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
14HA
Physicochemical properties
Molecular weight
216.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.20
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
47.23kcal/mol
Minimised FF energy
27.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
409.3Ų
Total solvent-accessible surface area of free ligand
BSA total
369.9Ų
Buried surface area upon binding
BSA apolar
284.0Ų
Hydrophobic contacts buried
BSA polar
85.9Ų
Polar contacts buried
Fraction buried
90.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1475.2Ų
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
1024.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)