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
15.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.52, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.180 kcal/mol/HA)
✓ Good fit quality (FQ -11.01)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (15.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-31.871
kcal/mol
LE
-1.180
kcal/mol/HA
Fit Quality
-11.01
FQ (Leeson)
HAC
27
heavy atoms
MW
383
Da
LogP
4.21
cLogP
Final rank
1.8556
rank score
Inter norm
-1.174
normalised
Contacts
17
H-bonds 8
Interaction summary
HBD 2
HY 7
PI 2
CLASH 2
Interaction summary
HBD 2
HY 7
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 144 | 1.8555715740885987 | -1.17427 | -31.8707 | 8 | 17 | 13 | 0.62 | 0.50 | - | no | Current |
| 175 | 2.069423808981815 | -0.973654 | -25.8254 | 7 | 16 | 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
-31.871kcal/mol
Ligand efficiency (LE)
-1.1804kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.013
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
383.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.21
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.54kcal/mol
Minimised FF energy
63.72kcal/mol
SASA & burial
✓ computed
SASA (unbound)
603.0Ų
Total solvent-accessible surface area of free ligand
BSA total
525.8Ų
Buried surface area upon binding
BSA apolar
390.7Ų
Hydrophobic contacts buried
BSA polar
135.1Ų
Polar contacts buried
Fraction buried
87.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3219.5Ų
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
1673.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)