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 mixed
SASA done
Strain ΔE
11.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.161 kcal/mol/HA)
✓ Good fit quality (FQ -10.41)
✓ Good H-bonds (4 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (11.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (6)
Score
-27.875
kcal/mol
LE
-1.161
kcal/mol/HA
Fit Quality
-10.41
FQ (Leeson)
HAC
24
heavy atoms
MW
354
Da
LogP
4.65
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
| Final rank | 0.249 | Score | -27.875 |
|---|---|---|---|
| Inter norm | -1.182 | Intra norm | 0.020 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 6 clashes; 4 protein contact clashes | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
ILE45
MET53
PHE56
SER44
THR180
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
| ||
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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 0.44 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 389 | -0.18784752275886354 | -1.01592 | -23.8653 | 1 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 480 | 0.044810234807672045 | -1.09043 | -25.2406 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 471 | 0.05669390183562073 | -1.09591 | -25.194 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 0.2488068813182308 | -1.18196 | -27.8753 | 4 | 15 | 11 | 0.52 | 0.00 | - | no | Current |
| 441 | 1.2946467321758754 | -1.18634 | -27.2383 | 3 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 383 | 2.0117884778778174 | -1.01577 | -22.8536 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 2.25182953308986 | -1.35937 | -32.3799 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 390 | 2.8542622317418695 | -1.17081 | -26.8659 | 9 | 15 | 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
-27.875kcal/mol
Ligand efficiency (LE)
-1.1615kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.409
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
354.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.65
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
15.48kcal/mol
Minimised FF energy
4.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
586.2Ų
Total solvent-accessible surface area of free ligand
BSA total
499.5Ų
Buried surface area upon binding
BSA apolar
337.1Ų
Hydrophobic contacts buried
BSA polar
162.4Ų
Polar contacts buried
Fraction buried
85.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3153.0Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1699.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)