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 high
Native strong
SASA done
Strain ΔE
18.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.50, Jaccard 0.40, H-bond role recall 0.80
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.441 kcal/mol/HA)
✓ Good fit quality (FQ -11.81)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (18.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-27.377
kcal/mol
LE
-1.441
kcal/mol/HA
Fit Quality
-11.81
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Interaction summary
HB 9
HY 19
PI 2
CLASH 2
Interaction summary
HB 9
HY 19
PI 2
CLASH 2
| Final rank | 3.534 | Score | -27.377 |
|---|---|---|---|
| Inter norm | -1.517 | Intra norm | 0.076 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA32
ARG48
ASP52
GLY157
ILE182
ILE45
MET53
NDP301
PHE56
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
| ||
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
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 | 10 | Native recall | 0.50 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 4 | Strict recall | 0.57 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 312 | -0.12698051497752788 | -1.4099 | -25.1999 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 409 | 1.5618486583435398 | -1.25392 | -19.5039 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 329 | 1.810958723850599 | -1.17778 | -21.5875 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 3.3656450884601203 | -1.63439 | -30.9104 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 265 | 3.3810319513898386 | -1.35166 | -24.7621 | 11 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 341 | 3.5339212025300557 | -1.51737 | -27.3765 | 9 | 15 | 10 | 0.50 | 0.80 | - | no | Current |
| 382 | 3.8196564752012465 | -1.26937 | -21.4516 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 4.003072569334565 | -1.34735 | -23.6626 | 10 | 17 | 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
-27.377kcal/mol
Ligand efficiency (LE)
-1.4409kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.810
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.02
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-121.34kcal/mol
Minimised FF energy
-139.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
482.9Ų
Total solvent-accessible surface area of free ligand
BSA total
428.0Ų
Buried surface area upon binding
BSA apolar
292.7Ų
Hydrophobic contacts buried
BSA polar
135.3Ų
Polar contacts buried
Fraction buried
88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1339.3Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
815.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)