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 strong
SASA done
Strain ΔE
13.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.60, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.962 kcal/mol/HA)
✓ Good fit quality (FQ -8.86)
✓ Good H-bonds (4 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (13.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.002
kcal/mol
LE
-0.962
kcal/mol/HA
Fit Quality
-8.86
FQ (Leeson)
HAC
26
heavy atoms
MW
352
Da
LogP
0.38
cLogP
Interaction summary
HB 4
HY 23
PI 1
CLASH 3
Interaction summary
HB 4
HY 23
PI 1
CLASH 3
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 2.783 | Score | -25.002 |
|---|---|---|---|
| Inter norm | -1.028 | Intra norm | 0.066 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes | ||
| Residues |
ALA32
ARG48
ASP52
GLY157
ILE45
LEU94
MET53
NDP301
PHE55
PHE56
SER44
SER86
THR180
THR83
TRP47
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 15 | Native recall | 0.75 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 233 | 0.14653933344419917 | -1.03183 | -21.6106 | 3 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 280 | 2.78266335530566 | -1.02791 | -25.0018 | 4 | 20 | 15 | 0.75 | 0.20 | - | no | Current |
| 205 | 3.0538717605189416 | -1.08565 | -24.0703 | 8 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 256 | 3.583257971760246 | -0.793938 | -19.7364 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 285 | 4.433840347685919 | -0.758283 | -19.0409 | 8 | 8 | 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
-25.002kcal/mol
Ligand efficiency (LE)
-0.9616kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.860
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
352.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.67kcal/mol
Minimised FF energy
52.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
627.7Ų
Total solvent-accessible surface area of free ligand
BSA total
575.4Ų
Buried surface area upon binding
BSA apolar
481.0Ų
Hydrophobic contacts buried
BSA polar
94.4Ų
Polar contacts buried
Fraction buried
91.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1507.0Ų
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
820.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)