Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
10.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.81, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.934 kcal/mol/HA)
✓ Good fit quality (FQ -8.92)
✓ Good H-bonds (3 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Moderate strain (10.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (8)
Score
-27.093
kcal/mol
LE
-0.934
kcal/mol/HA
Fit Quality
-8.92
FQ (Leeson)
HAC
29
heavy atoms
MW
529
Da
LogP
7.16
cLogP
Final rank
0.5690
rank score
Inter norm
-0.980
normalised
Contacts
17
H-bonds 3
Interaction summary
HBD 2
HBA 1
HY 9
PI 2
CLASH 2
Interaction summary
HBD 2
HBA 1
HY 9
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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: strict.
| 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 | 17 | Native recall | 0.81 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 667 | 0.5690369790417854 | -0.980307 | -27.0928 | 3 | 17 | 17 | 0.81 | 0.20 | - | no | Current |
| 666 | 1.6845879446949032 | -0.955644 | -24.0533 | 2 | 21 | 18 | 0.86 | 0.20 | - | no | Open |
| 677 | 1.7350019367006875 | -0.725009 | -18.0466 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 1.8545339706584674 | -0.92052 | -22.4775 | 3 | 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
-27.093kcal/mol
Ligand efficiency (LE)
-0.9342kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.918
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
529.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.16
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.30kcal/mol
Minimised FF energy
52.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
667.8Ų
Total solvent-accessible surface area of free ligand
BSA total
617.7Ų
Buried surface area upon binding
BSA apolar
559.9Ų
Hydrophobic contacts buried
BSA polar
57.8Ų
Polar contacts buried
Fraction buried
92.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1673.4Ų
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
614.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)