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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
38.1 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.57, Jaccard 0.50, H-bond role recall 0.00
Reason: 15 internal clashes
15 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.890 kcal/mol/HA)
✓ Good fit quality (FQ -8.40)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Very high strain energy (38.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-24.913
kcal/mol
LE
-0.890
kcal/mol/HA
Fit Quality
-8.40
FQ (Leeson)
HAC
28
heavy atoms
MW
398
Da
LogP
3.12
cLogP
Final rank
2.1077
rank score
Inter norm
-0.929
normalised
Contacts
15
H-bonds 3
Interaction summary
HBA 2
HY 6
PI 2
CLASH 0
Interaction summary
HBA 2
HY 6
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 12 | Native recall | 0.57 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 541 | 1.1756627018338413 | -1.07597 | -27.1024 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 549 | 2.1077041195670354 | -0.929171 | -24.9126 | 3 | 15 | 12 | 0.57 | 0.00 | - | no | Current |
| 577 | 2.689294324477287 | -0.751854 | -19.032 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 576 | 3.045521506689257 | -0.880563 | -22.2631 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 571 | 3.7610343430078648 | -1.06427 | -28.8526 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 572 | 4.364803537312127 | -0.889484 | -23.7896 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 563 | 4.520953703473275 | -0.951393 | -24.1315 | 3 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 544 | 5.1376893518949105 | -0.987943 | -22.5162 | 16 | 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
-24.913kcal/mol
Ligand efficiency (LE)
-0.8897kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.399
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.12
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.18kcal/mol
Minimised FF energy
26.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
610.5Ų
Total solvent-accessible surface area of free ligand
BSA total
527.3Ų
Buried surface area upon binding
BSA apolar
349.9Ų
Hydrophobic contacts buried
BSA polar
177.4Ų
Polar contacts buried
Fraction buried
86.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3137.2Ų
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
1672.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)