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
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
37.8 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.40, Jaccard 0.32, H-bond role recall 0.20
Reason: 15 internal clashes
15 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (15/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.804 kcal/mol/HA)
✓ Good fit quality (FQ -8.23)
✓ Good H-bonds (3 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (37.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-29.732
kcal/mol
LE
-0.804
kcal/mol/HA
Fit Quality
-8.23
FQ (Leeson)
HAC
37
heavy atoms
MW
495
Da
LogP
2.80
cLogP
Final rank
3.4875
rank score
Inter norm
-0.778
normalised
Contacts
13
H-bonds 3
Interaction summary
HBA 3
HY 6
PI 2
CLASH 0
Interaction summary
HBA 3
HY 6
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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: permissive.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 8 | Native recall | 0.40 |
| Jaccard | 0.32 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 274 | 1.5343558782166318 | -0.707796 | -25.4668 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 2.2264712251249796 | -0.812406 | -26.9547 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 182 | 2.4926765076912942 | -0.683388 | -47.3376 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 232 | 3.4874898592347314 | -0.778194 | -29.7321 | 3 | 13 | 8 | 0.40 | 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
-29.732kcal/mol
Ligand efficiency (LE)
-0.8036kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.227
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
494.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.80
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
112.02kcal/mol
Minimised FF energy
74.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
830.5Ų
Total solvent-accessible surface area of free ligand
BSA total
590.2Ų
Buried surface area upon binding
BSA apolar
471.8Ų
Hydrophobic contacts buried
BSA polar
118.4Ų
Polar contacts buried
Fraction buried
71.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1651.7Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
847.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)