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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
10.9 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.43, Jaccard 0.36, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
46% of hydrophobic surface appears solvent-exposed (6/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.220 kcal/mol/HA)
✓ Good fit quality (FQ -10.59)
✓ Good H-bonds (3 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (60%)
✗ Moderate strain (10.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-26.843
kcal/mol
LE
-1.220
kcal/mol/HA
Fit Quality
-10.59
FQ (Leeson)
HAC
22
heavy atoms
MW
347
Da
LogP
3.47
cLogP
Final rank
2.6126
rank score
Inter norm
-1.211
normalised
Contacts
13
H-bonds 4
Interaction summary
HBA 3
HY 7
PI 2
CLASH 2
Interaction summary
HBA 3
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 | 9 | Native recall | 0.43 |
| Jaccard | 0.36 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 503 | -0.412716455525595 | -1.4097 | -27.6491 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 1.74159394392578 | -1.15122 | -25.5295 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 2.6126169913137653 | -1.21113 | -26.8425 | 4 | 13 | 9 | 0.43 | 0.00 | - | no | Current |
| 520 | 3.4185448372354834 | -1.32408 | -28.697 | 12 | 13 | 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
-26.843kcal/mol
Ligand efficiency (LE)
-1.2201kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.593
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
346.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.47
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
9.60kcal/mol
Minimised FF energy
-1.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
524.4Ų
Total solvent-accessible surface area of free ligand
BSA total
447.1Ų
Buried surface area upon binding
BSA apolar
268.8Ų
Hydrophobic contacts buried
BSA polar
178.3Ų
Polar contacts buried
Fraction buried
85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3033.1Ų
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
1739.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)