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
19.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.50, Jaccard 0.42, H-bond role recall 0.80
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.401 kcal/mol/HA)
✓ Good fit quality (FQ -11.49)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (61%)
✗ Moderate strain (19.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-26.629
kcal/mol
LE
-1.401
kcal/mol/HA
Fit Quality
-11.49
FQ (Leeson)
HAC
19
heavy atoms
MW
282
Da
LogP
-0.14
cLogP
Interaction summary
HB 10
HY 18
PI 2
CLASH 1
Interaction summary
HB 10
HY 18
PI 2
CLASH 1
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 | 3.566 | Score | -26.629 |
|---|---|---|---|
| Inter norm | -1.447 | Intra norm | 0.046 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA32
ARG48
ASP52
GLY157
ILE45
MET53
NDP301
PHE56
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
| ||
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 | 0.42 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 289 | -0.40236088474816856 | -1.41075 | -24.2398 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 332 | 3.566210191296415 | -1.44745 | -26.6287 | 10 | 14 | 10 | 0.50 | 0.80 | - | no | Current |
| 345 | 3.858845350060888 | -1.39675 | -24.8616 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 319 | 4.2834356851988105 | -1.2485 | -24.388 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 240 | 4.295306117068615 | -1.44832 | -25.4888 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 226 | 4.722098174019196 | -1.39318 | -26.0715 | 11 | 13 | 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
-26.629kcal/mol
Ligand efficiency (LE)
-1.4015kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.488
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
282.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.14
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-42.17kcal/mol
Minimised FF energy
-61.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
470.6Ų
Total solvent-accessible surface area of free ligand
BSA total
418.9Ų
Buried surface area upon binding
BSA apolar
254.9Ų
Hydrophobic contacts buried
BSA polar
164.0Ų
Polar contacts buried
Fraction buried
89.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1298.5Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
817.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)