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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
13.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.764 kcal/mol/HA)
✓ Good fit quality (FQ -7.52)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (13.5 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (12)
Score
-24.460
kcal/mol
LE
-0.764
kcal/mol/HA
Fit Quality
-7.52
FQ (Leeson)
HAC
32
heavy atoms
MW
457
Da
LogP
2.59
cLogP
Interaction summary
HB 1
HY 24
PI 1
CLASH 4
Interaction summary
HB 1
HY 24
PI 1
CLASH 4
| Final rank | 1.568 | Score | -24.460 |
|---|---|---|---|
| Inter norm | -0.803 | Intra norm | 0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | geometry warning; 12 clashes; 6 protein contact clashes | ||
| Residues |
ALA10
ASP22
GLU31
GLY21
ILE61
ILE8
LEU23
NAP201
PHE35
PRO26
PRO27
PRO62
SER60
THR137
THR57
TRP25
TYR122
VAL116
VAL9
| ||
Protein summary
200 residues
| Protein target | T01 | 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
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.67 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 501 | 0.8262027922765177 | -1.02666 | -32.9821 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 519 | 1.0018915608018395 | -1.00345 | -32.0672 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 1.5675777293950284 | -0.803251 | -24.4605 | 1 | 19 | 16 | 0.76 | 0.00 | - | no | Current |
| 551 | 1.9550632648671207 | -0.817321 | -24.5036 | 2 | 19 | 16 | 0.76 | 0.20 | - | no | Open |
| 532 | 2.4665076274441677 | -0.788684 | -22.8648 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 535 | 3.1900161179976054 | -0.768862 | -24.7614 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 513 | 3.7398750877612836 | -0.943214 | -29.7316 | 8 | 16 | 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
-24.460kcal/mol
Ligand efficiency (LE)
-0.7644kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.517
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
456.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.59
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
47.34kcal/mol
Minimised FF energy
33.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
723.1Ų
Total solvent-accessible surface area of free ligand
BSA total
639.4Ų
Buried surface area upon binding
BSA apolar
489.6Ų
Hydrophobic contacts buried
BSA polar
149.8Ų
Polar contacts buried
Fraction buried
88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1616.2Ų
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
621.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)