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 mixed
SASA done
Strain ΔE
15.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.52, Jaccard 0.46, H-bond role recall 0.33
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 (-1.153 kcal/mol/HA)
✓ Good fit quality (FQ -9.84)
✓ Good H-bonds (4 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (15.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.220
kcal/mol
LE
-1.153
kcal/mol/HA
Fit Quality
-9.84
FQ (Leeson)
HAC
21
heavy atoms
MW
286
Da
LogP
2.28
cLogP
Final rank
2.8961
rank score
Inter norm
-1.214
normalised
Contacts
14
H-bonds 8
Interaction summary
HBD 3
HBA 1
HY 5
PI 2
CLASH 3
Interaction summary
HBD 3
HBA 1
HY 5
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: 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 | 11 | Native recall | 0.52 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.33 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 1.222860932044016 | -1.53558 | -29.3424 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 507 | 2.8658798137281876 | -1.3035 | -24.8475 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 2.896089366624946 | -1.21353 | -24.2204 | 8 | 14 | 11 | 0.52 | 0.33 | - | no | Current |
| 473 | 2.991356188843517 | -1.35257 | -28.5222 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 3.4604292682728732 | -1.15154 | -23.9773 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 446 | 3.547725783304717 | -1.35351 | -28.2583 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 3.728277754062 | -1.13114 | -23.4955 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 418 | 3.7308293894761544 | -1.61054 | -34.097 | 11 | 12 | 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
-24.220kcal/mol
Ligand efficiency (LE)
-1.1534kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.838
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
286.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.28
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.11kcal/mol
Minimised FF energy
59.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
475.9Ų
Total solvent-accessible surface area of free ligand
BSA total
453.0Ų
Buried surface area upon binding
BSA apolar
300.4Ų
Hydrophobic contacts buried
BSA polar
152.6Ų
Polar contacts buried
Fraction buried
95.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3079.7Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1672.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)