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
16.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.20
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 (-0.737 kcal/mol/HA)
✓ Good fit quality (FQ -7.49)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Moderate strain (16.4 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (17)
Score
-26.535
kcal/mol
LE
-0.737
kcal/mol/HA
Fit Quality
-7.49
FQ (Leeson)
HAC
36
heavy atoms
MW
497
Da
LogP
5.77
cLogP
Interaction summary
HB 2
HY 24
PI 3
CLASH 4
Interaction summary
HB 2
HY 24
PI 3
CLASH 4
| Final rank | 1.915 | Score | -26.535 |
|---|---|---|---|
| Inter norm | -0.731 | Intra norm | -0.006 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 2 |
| Artifact reason | geometry warning; 17 clashes; 5 protein contact clashes | ||
| Residues |
ALA10
ARG29
ASN65
GLU31
ILE61
ILE8
LEU28
LEU68
LYS64
PHE32
PHE35
PRO27
PRO62
THR137
TYR34
VAL116
VAL9
| ||
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
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 | 12 | Native recall | 0.57 |
| Jaccard | 0.46 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 17 | 1.7072284370268758 | -0.727521 | -19.1925 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 1.9145000543311115 | -0.730596 | -26.5346 | 2 | 17 | 12 | 0.57 | 0.20 | - | no | Current |
| 29 | 3.020862307535669 | -0.646601 | -19.2049 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 3.099639412616397 | -0.651628 | -20.9225 | 5 | 14 | 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
-26.535kcal/mol
Ligand efficiency (LE)
-0.7371kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.491
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
497.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.77
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
29.22kcal/mol
Minimised FF energy
12.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
786.6Ų
Total solvent-accessible surface area of free ligand
BSA total
635.6Ų
Buried surface area upon binding
BSA apolar
560.5Ų
Hydrophobic contacts buried
BSA polar
75.0Ų
Polar contacts buried
Fraction buried
80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1715.2Ų
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
640.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)