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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
35.2 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.57, Jaccard 0.39, H-bond role recall 0.40
Reason: 16 internal clashes
16 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (11/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.662 kcal/mol/HA)
✓ Good fit quality (FQ -6.88)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Very high strain energy (35.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-25.839
kcal/mol
LE
-0.662
kcal/mol/HA
Fit Quality
-6.88
FQ (Leeson)
HAC
39
heavy atoms
MW
532
Da
LogP
3.79
cLogP
Interaction summary
HB 10
HY 24
PI 3
CLASH 0
⚠ Exposure 36%
Interaction summary
HB 10
HY 24
PI 3
CLASH 0
⚠ Exposure 36%
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (11/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30
Buried (contacted) 19
Exposed 11
LogP 3.79
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.778 | Score | -25.839 |
|---|---|---|---|
| Inter norm | -0.772 | Intra norm | 0.110 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 10 |
| Artifact reason | geometry warning; 16 clashes; 3 protein clashes; high strain Δ 35.2 | ||
| Residues |
ALA10
ARG29
ARG66
ARG71
ASN65
GLN36
GLU31
ILE8
LEU23
LEU28
LEU68
LYS64
LYS69
NAP201
PHE32
PHE35
PRO27
PRO62
PRO67
THR137
TRP25
TYR34
| ||
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 | 0.39 | RMSD | - |
| HB strict | 2 | Strict recall | 0.40 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 248 | 2.048813667607478 | -0.614374 | -9.73646 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 215 | 2.4577901811693255 | -0.623182 | -16.3266 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 206 | 2.7577601342615625 | -0.827558 | -20.9914 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 254 | 3.256604468418019 | -0.663495 | -10.5295 | 5 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 4.777589574511002 | -0.772139 | -25.8389 | 10 | 22 | 12 | 0.57 | 0.40 | - | no | Current |
| 273 | 5.650594001336309 | -0.575422 | -19.2044 | 8 | 11 | 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
-25.839kcal/mol
Ligand efficiency (LE)
-0.6625kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.876
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
531.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.79
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
119.59kcal/mol
Minimised FF energy
84.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
880.4Ų
Total solvent-accessible surface area of free ligand
BSA total
680.9Ų
Buried surface area upon binding
BSA apolar
568.6Ų
Hydrophobic contacts buried
BSA polar
112.3Ų
Polar contacts buried
Fraction buried
77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1811.1Ų
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
624.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)