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
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
15.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.74, H-bond role recall 0.17
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.910 kcal/mol/HA)
✓ Good fit quality (FQ -8.87)
✓ Good H-bonds (3 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Moderate strain (15.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (14)
Score
-28.214
kcal/mol
LE
-0.910
kcal/mol/HA
Fit Quality
-8.87
FQ (Leeson)
HAC
31
heavy atoms
MW
413
Da
LogP
3.60
cLogP
Final rank
1.1079
rank score
Inter norm
-0.922
normalised
Contacts
19
H-bonds 4
Interaction summary
HBD 3
HY 10
PI 2
CLASH 1
Interaction summary
HBD 3
HY 10
PI 2
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.74 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 218 | 0.9379658438872591 | -0.943162 | -27.6313 | 5 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 157 | 1.1079134596156153 | -0.921748 | -28.2136 | 4 | 19 | 17 | 0.81 | 0.17 | - | no | Current |
| 234 | 2.12699497934314 | -0.885557 | -26.2468 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 2.4771180272731397 | -0.754589 | -22.2052 | 2 | 14 | 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
-28.214kcal/mol
Ligand efficiency (LE)
-0.9101kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.867
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
412.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.60
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.50kcal/mol
Minimised FF energy
88.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
707.5Ų
Total solvent-accessible surface area of free ligand
BSA total
620.7Ų
Buried surface area upon binding
BSA apolar
603.5Ų
Hydrophobic contacts buried
BSA polar
17.2Ų
Polar contacts buried
Fraction buried
87.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3448.2Ų
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
1670.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)