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 mixed
SASA done
Strain ΔE
18.9 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.825 kcal/mol/HA)
✓ Good fit quality (FQ -7.79)
✓ Good H-bonds (4 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (18.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.092
kcal/mol
LE
-0.825
kcal/mol/HA
Fit Quality
-7.79
FQ (Leeson)
HAC
28
heavy atoms
MW
413
Da
LogP
3.65
cLogP
Final rank
3.0176
rank score
Inter norm
-0.904
normalised
Contacts
16
H-bonds 5
Interaction summary
HBA 4
HY 9
PI 3
CLASH 2
Interaction summary
HBA 4
HY 9
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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 | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 11 | Native recall | 0.52 |
| Jaccard | 0.42 | 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
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 663 | 0.2511577254753023 | -1.09851 | -30.8922 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 646 | 0.8020123366541132 | -0.883354 | -23.985 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 2.060226456342705 | -0.948105 | -29.2566 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.3297314190059755 | -1.12086 | -24.7821 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 2.7084623141150126 | -0.874177 | -26.6575 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 643 | 3.017585003862393 | -0.904163 | -23.0924 | 5 | 16 | 11 | 0.52 | 0.00 | - | no | Current |
| 668 | 3.3289291970169095 | -1.03104 | -25.9639 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 639 | 3.377817040032817 | -0.950565 | -28.199 | 7 | 13 | 8 | 0.38 | 0.00 | - | no | Open |
| 662 | 3.4574628969651684 | -0.923998 | -27.0934 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 655 | 5.144145577855445 | -1.05202 | -28.4978 | 16 | 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
-23.092kcal/mol
Ligand efficiency (LE)
-0.8247kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.786
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
412.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.65
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.71kcal/mol
Minimised FF energy
77.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
664.4Ų
Total solvent-accessible surface area of free ligand
BSA total
521.1Ų
Buried surface area upon binding
BSA apolar
353.5Ų
Hydrophobic contacts buried
BSA polar
167.7Ų
Polar contacts buried
Fraction buried
78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1502.9Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
654.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)