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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
21.4 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.55, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.702 kcal/mol/HA)
✓ Good fit quality (FQ -6.63)
✓ Good H-bonds (3 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (21.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (9)
Score
-19.659
kcal/mol
LE
-0.702
kcal/mol/HA
Fit Quality
-6.63
FQ (Leeson)
HAC
28
heavy atoms
MW
401
Da
LogP
3.56
cLogP
Final rank
0.5250
rank score
Inter norm
-0.850
normalised
Contacts
12
H-bonds 5
Interaction summary
HBD 3
HY 5
PI 4
CLASH 3
Interaction summary
HBD 3
HY 5
PI 4
CLASH 3
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
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 | 0.55 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.659kcal/mol
Ligand efficiency (LE)
-0.7021kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.628
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.56
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
8.37kcal/mol
Minimised FF energy
-13.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
667.7Ų
Total solvent-accessible surface area of free ligand
BSA total
501.5Ų
Buried surface area upon binding
BSA apolar
374.7Ų
Hydrophobic contacts buried
BSA polar
126.8Ų
Polar contacts buried
Fraction buried
75.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1663.7Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1011.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)