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
17.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.65, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.837 kcal/mol/HA)
✓ Good fit quality (FQ -7.71)
✓ Good H-bonds (3 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (17.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (9)
Score
-21.765
kcal/mol
LE
-0.837
kcal/mol/HA
Fit Quality
-7.71
FQ (Leeson)
HAC
26
heavy atoms
MW
387
Da
LogP
4.27
cLogP
Interaction summary
HB 3
HY 24
PI 3
CLASH 4
Interaction summary
HB 3
HY 24
PI 3
CLASH 4
| Final rank | 0.841 | Score | -21.765 |
|---|---|---|---|
| Inter norm | -0.931 | Intra norm | 0.094 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 4 protein contact clashes | ||
| Residues |
ALA34
ARG100
ARG59
ASP54
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE58
PHE94
PRO91
TYR166
TYR57
VAL32
VAL33
| ||
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
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 | 0.65 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 576 | 0.42784014967993933 | -1.15565 | -27.3377 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 589 | 0.517102839641185 | -1.19254 | -28.2173 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 581 | 0.8411607055745534 | -0.930872 | -21.7648 | 3 | 17 | 15 | 0.71 | 0.00 | - | no | Current |
| 605 | 1.0384437838432372 | -0.912944 | -23.7431 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 3.8781591269490674 | -1.20911 | -29.1116 | 10 | 20 | 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
-21.765kcal/mol
Ligand efficiency (LE)
-0.8371kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.713
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
386.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.27
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
53.02kcal/mol
Minimised FF energy
35.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
593.4Ų
Total solvent-accessible surface area of free ligand
BSA total
576.1Ų
Buried surface area upon binding
BSA apolar
476.3Ų
Hydrophobic contacts buried
BSA polar
99.8Ų
Polar contacts buried
Fraction buried
97.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1712.0Ų
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
590.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)