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 mixed
SASA done
Strain ΔE
19.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.25, Jaccard 0.21, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.196 kcal/mol/HA)
✓ Good fit quality (FQ -10.38)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (19.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-26.313
kcal/mol
LE
-1.196
kcal/mol/HA
Fit Quality
-10.38
FQ (Leeson)
HAC
22
heavy atoms
MW
298
Da
LogP
1.43
cLogP
Final rank
3.7652
rank score
Inter norm
-1.340
normalised
Contacts
9
H-bonds 10
Interaction summary
HBD 3
HBA 4
HY 3
PI 2
CLASH 2
Interaction summary
HBD 3
HBA 4
HY 3
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
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 | 20 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 5 | Native recall | 0.25 |
| Jaccard | 0.21 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 348 | 0.42852216441102114 | -1.51718 | -31.4288 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 333 | 1.339614803622845 | -1.35118 | -28.1684 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 413 | 3.765212929298701 | -1.33975 | -26.3127 | 10 | 9 | 5 | 0.25 | 0.20 | - | no | Current |
| 433 | 4.545002909003321 | -1.05952 | -24.126 | 7 | 11 | 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
-26.313kcal/mol
Ligand efficiency (LE)
-1.1960kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.384
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
298.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.43
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.37kcal/mol
Minimised FF energy
79.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
486.1Ų
Total solvent-accessible surface area of free ligand
BSA total
396.1Ų
Buried surface area upon binding
BSA apolar
256.8Ų
Hydrophobic contacts buried
BSA polar
139.3Ų
Polar contacts buried
Fraction buried
81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1329.1Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
822.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)