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 mixed
SASA done
Strain ΔE
12.1 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.41, Jaccard 0.39, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.288 kcal/mol/HA)
✓ Good fit quality (FQ -11.37)
✓ Good H-bonds (4 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (61%)
✗ Moderate strain (12.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Internal clashes (6)
Score
-29.636
kcal/mol
LE
-1.288
kcal/mol/HA
Fit Quality
-11.37
FQ (Leeson)
HAC
23
heavy atoms
MW
361
Da
LogP
3.69
cLogP
Interaction summary
HB 4
HY 15
PI 3
CLASH 3
Interaction summary
HB 4
HY 15
PI 3
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 | 0.355 | Score | -29.636 |
|---|---|---|---|
| Inter norm | -1.259 | Intra norm | -0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 8 | H-bonds | 4 |
| Artifact reason | geometry warning; 6 clashes; 5 protein contact clashes; 1 severe cofactor-context clash | ||
| Residues |
ARG17
LEU229
NDP302
PHE113
SER111
SER112
TYR194
VAL230
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 7 | Native recall | 0.41 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 471 | 0.35494554851377064 | -1.25875 | -29.6357 | 4 | 8 | 7 | 0.41 | 0.33 | - | no | Current |
| 515 | 4.109660491598755 | -1.04273 | -25.1959 | 7 | 15 | 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
-29.636kcal/mol
Ligand efficiency (LE)
-1.2885kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.372
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
360.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.69
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
2.96kcal/mol
Minimised FF energy
-9.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
517.1Ų
Total solvent-accessible surface area of free ligand
BSA total
409.6Ų
Buried surface area upon binding
BSA apolar
248.0Ų
Hydrophobic contacts buried
BSA polar
161.6Ų
Polar contacts buried
Fraction buried
79.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1447.1Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1057.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)