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 medium
Native strong
SASA done
Strain ΔE
25.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.17
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.779 kcal/mol/HA)
✓ Good fit quality (FQ -7.58)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ High strain energy (25.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (13)
Score
-24.136
kcal/mol
LE
-0.779
kcal/mol/HA
Fit Quality
-7.58
FQ (Leeson)
HAC
31
heavy atoms
MW
479
Da
LogP
5.67
cLogP
Interaction summary
HB 2
HY 24
PI 4
CLASH 3
Interaction summary
HB 2
HY 24
PI 4
CLASH 3
| Final rank | 1.037 | Score | -24.136 |
|---|---|---|---|
| Inter norm | -0.828 | Intra norm | 0.049 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 13 clashes; 3 protein contact clashes; moderate strain Δ 25.1 | ||
| Residues |
NDP301
ALA32
ARG48
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
PHE56
PHE91
THR83
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
VAL87
| ||
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 404 | 1.0366803184650808 | -0.827652 | -24.1355 | 2 | 19 | 16 | 0.76 | 0.17 | - | no | Current |
| 389 | 3.994460711102173 | -1.22594 | -33.6324 | 10 | 23 | 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
-24.136kcal/mol
Ligand efficiency (LE)
-0.7786kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.585
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
479.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.67
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.85kcal/mol
Minimised FF energy
19.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
707.9Ų
Total solvent-accessible surface area of free ligand
BSA total
655.9Ų
Buried surface area upon binding
BSA apolar
571.8Ų
Hydrophobic contacts buried
BSA polar
84.1Ų
Polar contacts buried
Fraction buried
92.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3383.4Ų
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
1664.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)