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
17.7 kcal/mol
Protein clashes
2
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.68, H-bond role recall 0.25
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.161 kcal/mol/HA)
✓ Good fit quality (FQ -9.51)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (99% SASA buried)
✗ Moderate strain (17.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (7)
Score
-22.054
kcal/mol
LE
-1.161
kcal/mol/HA
Fit Quality
-9.51
FQ (Leeson)
HAC
19
heavy atoms
MW
298
Da
LogP
0.82
cLogP
Interaction summary
HB 7
HY 24
PI 2
CLASH 1
Interaction summary
HB 7
HY 24
PI 2
CLASH 1
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 | 0.004 | Score | -22.054 |
|---|---|---|---|
| Inter norm | -1.200 | Intra norm | 0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | geometry warning; 7 clashes; 2 protein contact clashes; 1 cofactor-context clash | ||
| Residues |
ALA34
ASP54
GLY161
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE58
PHE94
THR184
THR86
TYR166
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.25 |
| HB same residue | 2 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 274 | 0.004259456452601552 | -1.19998 | -22.0537 | 7 | 16 | 15 | 0.71 | 0.25 | - | no | Current |
| 297 | 1.499994412154343 | -1.10284 | -19.4731 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 2.0693543880229 | -1.44348 | -27.3657 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 325 | 2.7894550963165585 | -1.04816 | -18.5277 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 2.970470011926121 | -1.44374 | -27.3571 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 227 | 3.892181034674322 | -1.33338 | -23.5436 | 14 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 259 | 5.237778050113307 | -1.63455 | -29.0298 | 12 | 17 | 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
-22.054kcal/mol
Ligand efficiency (LE)
-1.1607kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.514
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
298.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.82
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-104.80kcal/mol
Minimised FF energy
-122.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
460.7Ų
Total solvent-accessible surface area of free ligand
BSA total
457.0Ų
Buried surface area upon binding
BSA apolar
265.6Ų
Hydrophobic contacts buried
BSA polar
191.4Ų
Polar contacts buried
Fraction buried
99.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
58.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1487.9Ų
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
590.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)