Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
27.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.70, Jaccard 0.58, H-bond role recall 0.80
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.945 kcal/mol/HA)
✓ Good fit quality (FQ -8.71)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (27.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.566
kcal/mol
LE
-0.945
kcal/mol/HA
Fit Quality
-8.71
FQ (Leeson)
HAC
26
heavy atoms
MW
352
Da
LogP
0.38
cLogP
Interaction summary
HB 9
HY 22
PI 2
CLASH 2
Interaction summary
HB 9
HY 22
PI 2
CLASH 2
| Final rank | 1.830 | Score | -24.566 |
|---|---|---|---|
| Inter norm | -1.252 | Intra norm | 0.307 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; moderate strain Δ 27.0 | ||
| Residues |
ALA32
ARG48
ASP52
GLY157
ILE45
LEU94
MET53
NDP301
PHE56
SER86
THR83
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
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 | 14 | Native recall | 0.70 |
| Jaccard | 0.58 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 295 | 0.6848745770730704 | -0.992809 | -21.5063 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 236 | 1.380950836095837 | -1.01859 | -24.4746 | 3 | 21 | 1 | 0.05 | 0.00 | - | no | Open |
| 295 | 1.8295021937022387 | -1.25182 | -24.5663 | 9 | 18 | 14 | 0.70 | 0.80 | - | no | Current |
| 214 | 2.5703367368996966 | -1.33185 | -30.4746 | 8 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 291 | 4.193386414552068 | -0.751105 | -17.9194 | 9 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 268 | 5.7271341078999916 | -0.794776 | -19.5866 | 8 | 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
-24.566kcal/mol
Ligand efficiency (LE)
-0.9449kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.705
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
352.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
130.78kcal/mol
Minimised FF energy
103.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
595.8Ų
Total solvent-accessible surface area of free ligand
BSA total
549.1Ų
Buried surface area upon binding
BSA apolar
449.2Ų
Hydrophobic contacts buried
BSA polar
99.9Ų
Polar contacts buried
Fraction buried
92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1484.5Ų
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
812.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)