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
18.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.30, Jaccard 0.26, 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 (-1.649 kcal/mol/HA)
✓ Good fit quality (FQ -13.22)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (18.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-29.690
kcal/mol
LE
-1.649
kcal/mol/HA
Fit Quality
-13.22
FQ (Leeson)
HAC
18
heavy atoms
MW
239
Da
LogP
2.01
cLogP
Interaction summary
HB 6
HY 11
PI 3
CLASH 2
Interaction summary
HB 6
HY 11
PI 3
CLASH 2
| Final rank | 1.558 | Score | -29.690 |
|---|---|---|---|
| Inter norm | -1.550 | Intra norm | -0.099 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 6 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ARG97
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
PHE91
PRO93
| ||
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
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 | 6 | Native recall | 0.30 |
| Jaccard | 0.26 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 25 | -0.40648109881247935 | -1.41095 | -25.4015 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 0.9108405699533281 | -1.61043 | -29.861 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 1.5550531976658688 | -1.57572 | -27.2292 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 95 | 1.5579141847049505 | -1.55021 | -29.6896 | 6 | 9 | 6 | 0.30 | 0.20 | - | no | Current |
| 68 | 2.22640486292557 | -1.74451 | -29.6736 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 2.259681596132118 | -1.5196 | -25.5447 | 10 | 15 | 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
-29.690kcal/mol
Ligand efficiency (LE)
-1.6494kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.219
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
239.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.01
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.49kcal/mol
Minimised FF energy
29.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
455.8Ų
Total solvent-accessible surface area of free ligand
BSA total
391.1Ų
Buried surface area upon binding
BSA apolar
314.2Ų
Hydrophobic contacts buried
BSA polar
76.9Ų
Polar contacts buried
Fraction buried
85.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1349.5Ų
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
850.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)