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
15.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.52, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.028 kcal/mol/HA)
✓ Good fit quality (FQ -9.22)
✓ Deep burial (96% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (15.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.680
kcal/mol
LE
-1.028
kcal/mol/HA
Fit Quality
-9.22
FQ (Leeson)
HAC
24
heavy atoms
MW
356
Da
LogP
3.86
cLogP
Final rank
1.4671
rank score
Inter norm
-1.059
normalised
Contacts
17
H-bonds 1
Interaction summary
HBD 1
HY 8
PI 3
CLASH 2
Interaction summary
HBD 1
HY 8
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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: permissive.
| 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 | 13 | Native recall | 0.62 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 434 | -0.4668083215898139 | -1.31204 | -30.9004 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 452 | -0.37662489320663173 | -1.17752 | -26.7718 | 0 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 435 | 1.4671220138259826 | -1.05881 | -24.6798 | 1 | 17 | 13 | 0.62 | 0.00 | - | no | Current |
| 421 | 2.0801239860173624 | -1.19225 | -27.6069 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 2.792260057719946 | -1.18388 | -25.1263 | 5 | 14 | 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
-24.680kcal/mol
Ligand efficiency (LE)
-1.0283kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.216
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
355.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.92kcal/mol
Minimised FF energy
41.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
580.0Ų
Total solvent-accessible surface area of free ligand
BSA total
556.9Ų
Buried surface area upon binding
BSA apolar
479.7Ų
Hydrophobic contacts buried
BSA polar
77.1Ų
Polar contacts buried
Fraction buried
96.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1728.3Ų
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
583.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)