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
27.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.78, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.735 kcal/mol/HA)
✓ Good fit quality (FQ -7.22)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (100%)
✗ High strain energy (27.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (9)
Score
-23.509
kcal/mol
LE
-0.735
kcal/mol/HA
Fit Quality
-7.22
FQ (Leeson)
HAC
32
heavy atoms
MW
434
Da
LogP
2.28
cLogP
Final rank
0.8275
rank score
Inter norm
-0.826
normalised
Contacts
20
H-bonds 1
Interaction summary
HBD 1
HY 11
PI 1
CLASH 2
Interaction summary
HBD 1
HY 11
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| 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 | 18 | Native recall | 0.86 |
| Jaccard | 0.78 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 153 | 0.827470533273789 | -0.825993 | -23.5085 | 1 | 20 | 18 | 0.86 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.509kcal/mol
Ligand efficiency (LE)
-0.7346kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.224
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
433.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.28
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
161.72kcal/mol
Minimised FF energy
133.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
763.3Ų
Total solvent-accessible surface area of free ligand
BSA total
675.5Ų
Buried surface area upon binding
BSA apolar
672.3Ų
Hydrophobic contacts buried
BSA polar
3.2Ų
Polar contacts buried
Fraction buried
88.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
99.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3529.5Ų
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
1659.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)