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
19.6 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.55, Jaccard 0.50, H-bond role recall 0.20
Reason: no major geometry red flags detected
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.976 kcal/mol/HA)
✓ Good fit quality (FQ -8.99)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (19.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-25.376
kcal/mol
LE
-0.976
kcal/mol/HA
Fit Quality
-8.99
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
2.92
cLogP
Interaction summary
HB 6
HY 20
PI 3
CLASH 0
Interaction summary
HB 6
HY 20
PI 3
CLASH 0
| Final rank | 1.571 | Score | -25.376 |
|---|---|---|---|
| Inter norm | -1.064 | Intra norm | 0.088 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 5 clashes; 1 protein clash | ||
| Residues |
ARG97
ILE45
LEU94
LYS57
LYS95
MET53
PHE56
PHE91
PRO88
PRO93
SER86
THR83
VAL87
| ||
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 | 11 | Native recall | 0.55 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 253 | 0.19807840433788065 | -0.837071 | -18.4969 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 231 | 0.5272779714366282 | -0.937238 | -23.9222 | 2 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 237 | 0.6354838805780988 | -1.25219 | -31.6245 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 284 | 0.7823962866555599 | -1.09244 | -27.8173 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 202 | 0.8808999213169224 | -1.09214 | -28.6167 | 6 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 241 | 1.4294098967066227 | -1.27784 | -31.7113 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 278 | 1.5706253236876964 | -1.06354 | -25.3758 | 6 | 13 | 11 | 0.55 | 0.20 | - | no | Current |
| 169 | 2.374618991612418 | -0.91184 | -21.2224 | 16 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 2.703325505043773 | -0.877203 | -22.0583 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 282 | 2.7306916933281316 | -0.8242 | -20.8388 | 8 | 11 | 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
-25.376kcal/mol
Ligand efficiency (LE)
-0.9760kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.992
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.92
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
38.72kcal/mol
Minimised FF energy
19.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
631.7Ų
Total solvent-accessible surface area of free ligand
BSA total
531.4Ų
Buried surface area upon binding
BSA apolar
421.3Ų
Hydrophobic contacts buried
BSA polar
110.1Ų
Polar contacts buried
Fraction buried
84.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1518.5Ų
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
820.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)