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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
17.4 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.17
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.638 kcal/mol/HA)
✓ Good fit quality (FQ -6.66)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (17.4 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (18)
Score
-25.503
kcal/mol
LE
-0.638
kcal/mol/HA
Fit Quality
-6.66
FQ (Leeson)
HAC
40
heavy atoms
MW
540
Da
LogP
5.07
cLogP
Interaction summary
HB 5
HY 24
PI 3
CLASH 3
Interaction summary
HB 5
HY 24
PI 3
CLASH 3
| Final rank | 2.170 | Score | -25.503 |
|---|---|---|---|
| Inter norm | -0.675 | Intra norm | 0.038 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 5 |
| Artifact reason | geometry warning; 18 clashes; 5 protein contact clashes; 1 cofactor-context clash | ||
| Residues |
NDP301
ALA32
ARG97
ILE45
LEU94
LYS57
LYS95
MET53
PHE56
PHE91
PRO50
PRO88
PRO93
THR54
THR83
TYR162
VAL156
VAL31
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 2.085904116821016 | -0.689121 | -27.2607 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 23 | 2.1701300817805826 | -0.675101 | -25.5028 | 5 | 19 | 15 | 0.71 | 0.17 | - | no | Current |
| 22 | 3.4612009219277655 | -0.699987 | -23.8891 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 3.8141245244208646 | -0.630551 | -23.742 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 11 | 3.842246669612219 | -0.815955 | -30.8126 | 11 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 23 | 4.243877337445351 | -0.580358 | -22.9581 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 11 | 4.9090251791855755 | -0.835688 | -32.1088 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 5.00112541062026 | -0.513565 | -18.5786 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 5.122166298635419 | -0.789091 | -27.5249 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 24 | 5.182612819385439 | -0.664602 | -23.5725 | 6 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 25 | 5.220830016407855 | -0.703529 | -25.5734 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 5.522584583539993 | -0.672093 | -28.6314 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 28 | 5.779053666691942 | -0.677449 | -23.7205 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 10 | 6.104412655989357 | -0.702536 | -24.6488 | 9 | 24 | 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
-25.503kcal/mol
Ligand efficiency (LE)
-0.6376kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.659
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
540.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.07
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
141.09kcal/mol
Minimised FF energy
123.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
797.5Ų
Total solvent-accessible surface area of free ligand
BSA total
636.5Ų
Buried surface area upon binding
BSA apolar
463.2Ų
Hydrophobic contacts buried
BSA polar
173.3Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3320.2Ų
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
1673.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)