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 mixed
SASA done
Strain ΔE
34.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.35, Jaccard 0.32, H-bond role recall 0.20
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.955 kcal/mol/HA)
✓ Good fit quality (FQ -9.21)
✓ Good H-bonds (5 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (34.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-28.640
kcal/mol
LE
-0.955
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
4.39
cLogP
Interaction summary
HB 5
HY 22
PI 2
CLASH 5
Interaction summary
HB 5
HY 22
PI 2
CLASH 5
| Final rank | 3.475 | Score | -28.640 |
|---|---|---|---|
| Inter norm | -0.916 | Intra norm | -0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 5 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes; high strain Δ 30.1 | ||
| Residues |
ARG97
LEU94
LYS57
LYS95
MET53
PHE56
PHE91
PRO50
THR54
| ||
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 | 7 | Native recall | 0.35 |
| Jaccard | 0.32 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 638 | 0.34325018158882725 | -0.807998 | -21.4581 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 0.39759002964385937 | -0.907597 | -28.7047 | 4 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 626 | 1.1227923024226714 | -1.1074 | -32.2501 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 1.1240171034297752 | -0.831029 | -27.0616 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 1.7563715265578972 | -0.846368 | -25.076 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 646 | 2.8590489487856874 | -0.784314 | -23.0842 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 639 | 3.474974056717497 | -0.915663 | -28.6397 | 5 | 9 | 7 | 0.35 | 0.20 | - | no | Current |
| 649 | 3.8018158212879913 | -0.815353 | -24.1731 | 5 | 14 | 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
-28.640kcal/mol
Ligand efficiency (LE)
-0.9547kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.209
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.39
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-4.53kcal/mol
Minimised FF energy
-38.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
659.2Ų
Total solvent-accessible surface area of free ligand
BSA total
490.1Ų
Buried surface area upon binding
BSA apolar
341.9Ų
Hydrophobic contacts buried
BSA polar
148.2Ų
Polar contacts buried
Fraction buried
74.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1458.8Ų
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
837.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)