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 mixed
SASA done
Strain ΔE
15.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.29, Jaccard 0.23, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.979 kcal/mol/HA)
✓ Good fit quality (FQ -8.90)
✓ Good H-bonds (5 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (15.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-24.472
kcal/mol
LE
-0.979
kcal/mol/HA
Fit Quality
-8.90
FQ (Leeson)
HAC
25
heavy atoms
MW
348
Da
LogP
4.61
cLogP
Interaction summary
HB 5
HY 24
PI 1
CLASH 1
Interaction summary
HB 5
HY 24
PI 1
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 | 1.801 | Score | -24.472 |
|---|---|---|---|
| Inter norm | -1.057 | Intra norm | 0.078 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
NDP301
ARG48
ILE45
MET53
PRO50
PRO88
SER44
SER86
TRP47
VAL49
VAL87
| ||
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 | 6 | Native recall | 0.29 |
| Jaccard | 0.23 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 602 | 0.11430096132212113 | -1.27135 | -29.7382 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 0.8791360147483075 | -0.830152 | -18.6899 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 1.2194364801494049 | -1.02909 | -25.5113 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 612 | 1.5874584481341056 | -1.13378 | -28.2176 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 595 | 1.8006179207427564 | -1.05666 | -24.4722 | 5 | 11 | 6 | 0.29 | 0.00 | - | no | Current |
| 599 | 3.4431675101061257 | -0.887757 | -22.4323 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 4.478348342907414 | -1.13978 | -27.4314 | 7 | 9 | 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
-24.472kcal/mol
Ligand efficiency (LE)
-0.9789kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.899
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
348.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.50kcal/mol
Minimised FF energy
50.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
562.4Ų
Total solvent-accessible surface area of free ligand
BSA total
469.0Ų
Buried surface area upon binding
BSA apolar
352.3Ų
Hydrophobic contacts buried
BSA polar
116.6Ų
Polar contacts buried
Fraction buried
83.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3151.3Ų
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
1714.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)