Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
26.6 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.47, Jaccard 0.40, H-bond role recall 0.33
Reason: 15 internal clashes
15 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.911 kcal/mol/HA)
✓ Good fit quality (FQ -8.79)
✓ Good H-bonds (3 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (94%)
✗ High strain energy (26.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-27.337
kcal/mol
LE
-0.911
kcal/mol/HA
Fit Quality
-8.79
FQ (Leeson)
HAC
30
heavy atoms
MW
407
Da
LogP
1.94
cLogP
Interaction summary
HB 3
HY 16
PI 1
CLASH 0
Interaction summary
HB 3
HY 16
PI 1
CLASH 0
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.
| Final rank | 2.397 | Score | -27.337 |
|---|---|---|---|
| Inter norm | -0.944 | Intra norm | 0.025 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; 2 cofactor-context clashes; moderate strain Δ 26.6 | ||
| Residues |
ARG17
LYS16
NDP302
PHE113
PRO115
SER111
SER112
TYR114
TYR191
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 | 8 | Native recall | 0.47 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 130 | 2.396689244992438 | -0.944417 | -27.3369 | 3 | 11 | 8 | 0.47 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.337kcal/mol
Ligand efficiency (LE)
-0.9112kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.790
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
406.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.94
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
143.37kcal/mol
Minimised FF energy
116.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
685.2Ų
Total solvent-accessible surface area of free ligand
BSA total
493.2Ų
Buried surface area upon binding
BSA apolar
462.6Ų
Hydrophobic contacts buried
BSA polar
30.6Ų
Polar contacts buried
Fraction buried
72.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1784.2Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1049.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)