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
9.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.90, Jaccard 0.86, H-bond role recall 0.17
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.731 kcal/mol/HA)
✓ Good fit quality (FQ -7.12)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ Moderate strain (9.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-22.653
kcal/mol
LE
-0.731
kcal/mol/HA
Fit Quality
-7.12
FQ (Leeson)
HAC
31
heavy atoms
MW
538
Da
LogP
6.38
cLogP
Final rank
2.7470
rank score
Inter norm
-0.905
normalised
Contacts
20
H-bonds 2
Interaction summary
HBD 2
HY 9
PI 2
CLASH 1
Interaction summary
HBD 2
HY 9
PI 2
CLASH 1
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.86 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 667 | 0.21288028751871968 | -1.04117 | -31.6316 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 1.829106599470338 | -0.901066 | -22.6062 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.4436102006853537 | -0.743977 | -20.1815 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 2.7469642685769946 | -0.904768 | -22.6527 | 2 | 20 | 19 | 0.90 | 0.17 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.653kcal/mol
Ligand efficiency (LE)
-0.7307kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.119
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
538.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.59kcal/mol
Minimised FF energy
45.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
757.2Ų
Total solvent-accessible surface area of free ligand
BSA total
656.9Ų
Buried surface area upon binding
BSA apolar
644.0Ų
Hydrophobic contacts buried
BSA polar
12.9Ų
Polar contacts buried
Fraction buried
86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3491.6Ų
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
1681.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)