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 high
Native strong
SASA done
Strain ΔE
23.8 kcal/mol
Protein clashes
3
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
41% of hydrophobic surface appears solvent-exposed (9/22 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 (-0.838 kcal/mol/HA)
✓ Good fit quality (FQ -8.08)
✓ Good H-bonds (3 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (23.8 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (9)
Score
-25.140
kcal/mol
LE
-0.838
kcal/mol/HA
Fit Quality
-8.08
FQ (Leeson)
HAC
30
heavy atoms
MW
470
Da
LogP
0.42
cLogP
Final rank
0.6965
rank score
Inter norm
-0.899
normalised
Contacts
18
H-bonds 3
Interaction summary
HBD 3
HY 9
PI 1
CLASH 1
Interaction summary
HBD 3
HY 9
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 15 | Native recall | 0.71 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 50 | 0.30070945429934953 | -1.17685 | -33.079 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 41 | 0.6964582031660637 | -0.899163 | -25.14 | 3 | 18 | 15 | 0.71 | 0.00 | - | no | Current |
| 38 | 0.874672363861708 | -0.793444 | -22.095 | 3 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 47 | 3.285066974059781 | -0.861542 | -23.7118 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.140kcal/mol
Ligand efficiency (LE)
-0.8380kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.084
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
470.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.42
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
286.34kcal/mol
Minimised FF energy
262.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
635.1Ų
Total solvent-accessible surface area of free ligand
BSA total
567.5Ų
Buried surface area upon binding
BSA apolar
510.5Ų
Hydrophobic contacts buried
BSA polar
56.9Ų
Polar contacts buried
Fraction buried
89.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3303.3Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1700.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)