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
7.4 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.57, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (7.4 kcal/mol)
✓ Excellent LE (-1.107 kcal/mol/HA)
✓ Good fit quality (FQ -9.92)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-26.556
kcal/mol
LE
-1.107
kcal/mol/HA
Fit Quality
-9.92
FQ (Leeson)
HAC
24
heavy atoms
MW
330
Da
LogP
5.25
cLogP
Interaction summary
HB 2
HY 24
PI 1
CLASH 3
Interaction summary
HB 2
HY 24
PI 1
CLASH 3
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
| Final rank | 1.673 | Score | -26.556 |
|---|---|---|---|
| Inter norm | -1.174 | Intra norm | 0.068 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ALA10
GLU31
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
SER60
THR57
TRP25
TYR122
VAL116
VAL9
| ||
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.57 | 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 | 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 195 | 0.10528892999500275 | -1.38356 | -32.7669 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 233 | 0.45824176420557783 | -1.16971 | -23.6545 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 176 | 1.5356533775760015 | -1.24741 | -29.2047 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 1.67318136802326 | -1.17441 | -26.5562 | 2 | 15 | 13 | 0.62 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.556kcal/mol
Ligand efficiency (LE)
-1.1065kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.916
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
330.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.25
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.74kcal/mol
Minimised FF energy
57.35kcal/mol
SASA & burial
✓ computed
SASA (unbound)
567.8Ų
Total solvent-accessible surface area of free ligand
BSA total
526.9Ų
Buried surface area upon binding
BSA apolar
442.1Ų
Hydrophobic contacts buried
BSA polar
84.8Ų
Polar contacts buried
Fraction buried
92.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1527.2Ų
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
632.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)