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 high
Native strong
SASA done
Strain ΔE
22.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.48, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.307 kcal/mol/HA)
✓ Good fit quality (FQ -11.35)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (22.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-28.761
kcal/mol
LE
-1.307
kcal/mol/HA
Fit Quality
-11.35
FQ (Leeson)
HAC
22
heavy atoms
MW
341
Da
LogP
1.09
cLogP
Interaction summary
HB 8
HY 12
PI 1
CLASH 2
Interaction summary
HB 8
HY 12
PI 1
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 | 2.088 | Score | -28.761 |
|---|---|---|---|
| Inter norm | -1.294 | Intra norm | -0.013 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes; 1 cofactor-context clash; moderate strain Δ 22.2 | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
LEU229
MET183
NDP302
PHE113
SER112
TYR114
TYR194
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 | 0.48 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 1.626499043761604 | -1.37094 | -30.1527 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 1.6518041180779013 | -1.37003 | -30.346 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 300 | 2.0875862514939527 | -1.29433 | -28.7606 | 8 | 14 | 10 | 0.59 | 0.50 | - | no | Current |
| 378 | 2.3075074574600802 | -1.36833 | -30.0855 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 2.606219346550542 | -1.13545 | -26.0457 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 2.8599754316936856 | -1.28494 | -28.9186 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 3.0559467618395817 | -1.44185 | -31.3269 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 282 | 4.254727390078342 | -1.16966 | -27.913 | 13 | 13 | 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
-28.761kcal/mol
Ligand efficiency (LE)
-1.3073kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.350
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-73.78kcal/mol
Minimised FF energy
-96.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
568.1Ų
Total solvent-accessible surface area of free ligand
BSA total
496.0Ų
Buried surface area upon binding
BSA apolar
341.5Ų
Hydrophobic contacts buried
BSA polar
154.5Ų
Polar contacts buried
Fraction buried
87.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1547.0Ų
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
1034.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)