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
25.9 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.59, Jaccard 0.53, 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 (-1.042 kcal/mol/HA)
✓ Good fit quality (FQ -9.47)
✓ Good H-bonds (4 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (25.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-26.041
kcal/mol
LE
-1.042
kcal/mol/HA
Fit Quality
-9.47
FQ (Leeson)
HAC
25
heavy atoms
MW
346
Da
LogP
3.53
cLogP
Interaction summary
HB 4
HY 15
PI 3
CLASH 3
Interaction summary
HB 4
HY 15
PI 3
CLASH 3
| Final rank | 1.873 | Score | -26.041 |
|---|---|---|---|
| Inter norm | -1.123 | Intra norm | 0.082 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 4 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; 3 cofactor-context clashes; moderate strain Δ 25.9 | ||
| Residues |
ARG17
ASP181
GLY225
LEU226
LEU229
MET183
NDP302
PHE113
SER227
TYR194
VAL230
ARG287
| ||
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
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 | 10 | Native recall | 0.59 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 531 | 1.8731009528347602 | -1.1234 | -26.0407 | 4 | 12 | 10 | 0.59 | 0.33 | - | no | Current |
| 556 | 1.891007351008683 | -0.77488 | -19.1614 | 4 | 6 | 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
-26.041kcal/mol
Ligand efficiency (LE)
-1.0416kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.469
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
346.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.53
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.09kcal/mol
Minimised FF energy
88.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
580.3Ų
Total solvent-accessible surface area of free ligand
BSA total
485.8Ų
Buried surface area upon binding
BSA apolar
404.2Ų
Hydrophobic contacts buried
BSA polar
81.6Ų
Polar contacts buried
Fraction buried
83.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1629.3Ų
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
1046.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)