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 high
Native strong
SASA done
Strain ΔE
19.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.71, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.104 kcal/mol/HA)
✓ Good fit quality (FQ -9.74)
✓ Good H-bonds (5 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (19.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-25.396
kcal/mol
LE
-1.104
kcal/mol/HA
Fit Quality
-9.74
FQ (Leeson)
HAC
23
heavy atoms
MW
311
Da
LogP
1.70
cLogP
Interaction summary
HB 5
HY 17
PI 2
CLASH 2
Interaction summary
HB 5
HY 17
PI 2
CLASH 2
| Final rank | 1.889 | Score | -25.396 |
|---|---|---|---|
| Inter norm | -1.125 | Intra norm | 0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ALA10
GLU31
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
SER60
THR57
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.71 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 647 | 1.5369423264640099 | -1.51564 | -34.221 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 631 | 1.7438540370937325 | -1.46157 | -32.5334 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 628 | 1.8888772517239385 | -1.12492 | -25.3959 | 5 | 15 | 15 | 0.71 | 0.00 | - | no | Current |
| 639 | 2.0651593307692404 | -1.20531 | -24.0791 | 7 | 8 | 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
-25.396kcal/mol
Ligand efficiency (LE)
-1.1042kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.745
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
311.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.70
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.88kcal/mol
Minimised FF energy
85.50kcal/mol
SASA & burial
✓ computed
SASA (unbound)
514.2Ų
Total solvent-accessible surface area of free ligand
BSA total
482.7Ų
Buried surface area upon binding
BSA apolar
366.5Ų
Hydrophobic contacts buried
BSA polar
116.2Ų
Polar contacts buried
Fraction buried
93.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1452.6Ų
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
612.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)