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 medium
Native strong
SASA done
Strain ΔE
8.3 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.76, Jaccard 0.76, H-bond role recall 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.349 kcal/mol/HA)
✓ Good fit quality (FQ -10.27)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (99% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (8.3 kcal/mol)
✗ Geometry warnings
Score
-21.583
kcal/mol
LE
-1.349
kcal/mol/HA
Fit Quality
-10.27
FQ (Leeson)
HAC
16
heavy atoms
MW
222
Da
LogP
-0.19
cLogP
Interaction summary
HB 7
HY 10
PI 2
CLASH 5
Interaction summary
HB 7
HY 10
PI 2
CLASH 5
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
| Final rank | 2.208 | Score | -21.583 |
|---|---|---|---|
| Inter norm | -1.422 | Intra norm | 0.073 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | geometry warning; 3 clashes; 2 protein clashes; 2 cofactor-context clashes | ||
| Residues |
ALA34
ASP54
HIS182
ILE160
ILE47
LEU97
MET55
NDP301
PHE233
PHE58
THR184
THR86
TYR166
TYR57
VAL32
VAL33
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 8RHT | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA34
ASP54
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE233
PHE58
PHE94
PRO91
SER89
THR184
THR86
TRP49
TYR166
TYR57
VAL32
VAL33
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.76 | RMSD | - |
| HB strict | 2 | Strict recall | 0.40 |
| HB same residue+role | 2 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.75 |
Protein summary
223 residues
| Protein target | T06 | Atoms | 3452 |
|---|---|---|---|
| Residues | 223 | Chains | 1 |
| Residue summary | ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 240 | -0.9575213856046881 | -1.92853 | -27.7645 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 1.3353371102338811 | -1.26392 | -19.2163 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 219 | 1.8619677573339846 | -1.71071 | -27.1737 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 224 | 2.208227771750752 | -1.42154 | -21.5833 | 7 | 16 | 16 | 0.76 | 0.50 | - | no | Current |
| 217 | 2.539177750072255 | -1.51499 | -21.7052 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 208 | 2.9554619952564956 | -2.11338 | -31.6674 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 164 | 3.5204397139105086 | -1.77214 | -26.8263 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 361 | 3.5327696926214855 | -1.50218 | -21.5641 | 7 | 12 | 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
-21.583kcal/mol
Ligand efficiency (LE)
-1.3490kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.268
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
16HA
Physicochemical properties
Molecular weight
222.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.19
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.02kcal/mol
Minimised FF energy
24.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
435.3Ų
Total solvent-accessible surface area of free ligand
BSA total
429.1Ų
Buried surface area upon binding
BSA apolar
321.4Ų
Hydrophobic contacts buried
BSA polar
107.6Ų
Polar contacts buried
Fraction buried
98.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1538.9Ų
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
1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
597.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)