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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
16.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.44, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.280 kcal/mol/HA)
✓ Good fit quality (FQ -11.12)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (16.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-28.168
kcal/mol
LE
-1.280
kcal/mol/HA
Fit Quality
-11.12
FQ (Leeson)
HAC
22
heavy atoms
MW
298
Da
LogP
1.43
cLogP
Interaction summary
HB 6
HY 18
PI 2
CLASH 2
Interaction summary
HB 6
HY 18
PI 2
CLASH 2
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 | 1.340 | Score | -28.168 |
|---|---|---|---|
| Inter norm | -1.351 | Intra norm | 0.071 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 6 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 2 severe cofactor-context clashes | ||
| Residues |
ARG17
LEU229
MET233
NDP302
PHE113
SER111
TYR194
VAL228
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 | 0.44 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 348 | 0.42852216441102114 | -1.51718 | -31.4288 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 333 | 1.339614803622845 | -1.35118 | -28.1684 | 6 | 9 | 8 | 0.47 | 0.33 | - | no | Current |
| 413 | 3.765212929298701 | -1.33975 | -26.3127 | 10 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 433 | 4.545002909003321 | -1.05952 | -24.126 | 7 | 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
-28.168kcal/mol
Ligand efficiency (LE)
-1.2804kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.116
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
298.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.43
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.32kcal/mol
Minimised FF energy
87.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
489.8Ų
Total solvent-accessible surface area of free ligand
BSA total
406.8Ų
Buried surface area upon binding
BSA apolar
264.0Ų
Hydrophobic contacts buried
BSA polar
142.7Ų
Polar contacts buried
Fraction buried
83.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1472.7Ų
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
1026.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)