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 strong
SASA done
Strain ΔE
14.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.75
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.147 kcal/mol/HA)
✓ Good fit quality (FQ -9.96)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (99% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Moderate strain (14.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.230
kcal/mol
LE
-1.147
kcal/mol/HA
Fit Quality
-9.96
FQ (Leeson)
HAC
22
heavy atoms
MW
335
Da
LogP
3.13
cLogP
Interaction summary
HB 6
HY 24
PI 3
CLASH 2
Interaction summary
HB 6
HY 24
PI 3
CLASH 2
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 | 2.518 | Score | -25.230 |
|---|---|---|---|
| Inter norm | -1.306 | Intra norm | 0.159 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 6 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA34
ASP54
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE233
PHE58
PHE94
PRO91
SER89
THR184
THR86
TRP49
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 | 21 | Native recall | 1.00 |
| Jaccard | 1.00 | RMSD | - |
| HB strict | 4 | Strict recall | 0.80 |
| HB same residue+role | 3 | HB role recall | 0.75 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 78 | -0.20912994509114985 | -1.75118 | -36.1308 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 84 | 0.5438443585937882 | -1.2573 | -27.98 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 0.6506929664465294 | -1.24509 | -27.1953 | 5 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 68 | 0.7497043112738141 | -1.73014 | -35.9228 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 75 | 1.5541187281168434 | -1.03619 | -21.9615 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 77 | 1.9234445748383517 | -1.24712 | -26.67 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 60 | 2.0098157272063952 | -1.10131 | -20.5867 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 62 | 2.071239823785125 | -1.01983 | -22.2505 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 67 | 2.518150442780698 | -1.30567 | -25.2304 | 6 | 21 | 21 | 1.00 | 0.75 | - | no | Current |
| 73 | 3.396519251747581 | -0.9275 | -16.5183 | 6 | 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
-25.230kcal/mol
Ligand efficiency (LE)
-1.1468kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.957
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
335.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.13
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
2.34kcal/mol
Minimised FF energy
-12.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
553.3Ų
Total solvent-accessible surface area of free ligand
BSA total
545.6Ų
Buried surface area upon binding
BSA apolar
496.8Ų
Hydrophobic contacts buried
BSA polar
48.9Ų
Polar contacts buried
Fraction buried
98.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1719.6Ų
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
593.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)