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 strong
SASA done
Strain ΔE
14.5 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.50, H-bond role recall 0.33
Reason: no major geometry red flags detected
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.278 kcal/mol/HA)
✓ Good fit quality (FQ -11.09)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (14.5 kcal/mol)
✗ Geometry warnings
Score
-28.106
kcal/mol
LE
-1.278
kcal/mol/HA
Fit Quality
-11.09
FQ (Leeson)
HAC
22
heavy atoms
MW
335
Da
LogP
3.81
cLogP
Interaction summary
HB 6
HY 17
PI 3
CLASH 2
Interaction summary
HB 6
HY 17
PI 3
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 | 2.749 | Score | -28.106 |
|---|---|---|---|
| Inter norm | -1.426 | Intra norm | 0.149 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 3 clashes; 3 protein clashes; 3 cofactor-context clashes | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
MET183
NDP302
PHE113
SER111
TYR194
TYR283
VAL230
ARG287
| ||
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 | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 628 | 2.748826267904254 | -1.4263 | -28.1057 | 6 | 13 | 10 | 0.59 | 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
-28.106kcal/mol
Ligand efficiency (LE)
-1.2775kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.091
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
335.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.81
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
24.39kcal/mol
Minimised FF energy
9.91kcal/mol
SASA & burial
✓ computed
SASA (unbound)
578.9Ų
Total solvent-accessible surface area of free ligand
BSA total
471.6Ų
Buried surface area upon binding
BSA apolar
305.1Ų
Hydrophobic contacts buried
BSA polar
166.4Ų
Polar contacts buried
Fraction buried
81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1552.2Ų
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
1031.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)