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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.70, Jaccard 0.61, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.085 kcal/mol/HA)
✓ Good fit quality (FQ -10.12)
✓ Good H-bonds (5 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (17.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-29.293
kcal/mol
LE
-1.085
kcal/mol/HA
Fit Quality
-10.12
FQ (Leeson)
HAC
27
heavy atoms
MW
430
Da
LogP
2.31
cLogP
Interaction summary
HB 5
HY 24
PI 1
CLASH 2
Interaction summary
HB 5
HY 24
PI 1
CLASH 2
| Final rank | 1.690 | Score | -29.293 |
|---|---|---|---|
| Inter norm | -1.046 | Intra norm | -0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA32
ARG48
ASP52
ILE45
MET53
NDP301
PHE56
PRO88
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 | 0.61 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 48 | -0.030515709128067177 | -1.19877 | -34.747 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 44 | 1.6895562317880846 | -1.04603 | -29.2926 | 5 | 17 | 14 | 0.70 | 0.20 | - | no | Current |
| 40 | 1.9507185505028426 | -0.979011 | -26.2128 | 4 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 55 | 2.0459669774127516 | -1.02625 | -26.334 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 47 | 2.5025793028420766 | -0.832971 | -22.4124 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 3.027762445054875 | -0.971648 | -24.2602 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 3.5528368927609004 | -0.893906 | -24.8711 | 12 | 17 | 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
-29.293kcal/mol
Ligand efficiency (LE)
-1.0849kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.122
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
430.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.31
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
127.83kcal/mol
Minimised FF energy
110.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
597.9Ų
Total solvent-accessible surface area of free ligand
BSA total
538.0Ų
Buried surface area upon binding
BSA apolar
430.9Ų
Hydrophobic contacts buried
BSA polar
107.1Ų
Polar contacts buried
Fraction buried
90.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1445.4Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
861.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)