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
13.9 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.45, H-bond role recall 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.273 kcal/mol/HA)
✓ Good fit quality (FQ -11.73)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (13.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-33.093
kcal/mol
LE
-1.273
kcal/mol/HA
Fit Quality
-11.73
FQ (Leeson)
HAC
26
heavy atoms
MW
367
Da
LogP
2.95
cLogP
Interaction summary
HB 10
HY 14
PI 2
CLASH 4
Interaction summary
HB 10
HY 14
PI 2
CLASH 4
| Final rank | 2.647 | Score | -33.093 |
|---|---|---|---|
| Inter norm | -1.261 | Intra norm | -0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 10 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
LYS16
MET183
NDP302
PHE113
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 | 9 | Native recall | 0.53 |
| Jaccard | 0.45 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 313 | 0.8712913457919358 | -1.07999 | -25.8552 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 259 | 1.0887783330232708 | -1.16095 | -30.3355 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 310 | 1.5345591015763724 | -0.726221 | -16.5713 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 229 | 2.0704697110349266 | -0.998736 | -19.793 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 256 | 2.3416472278121194 | -1.03745 | -25.3269 | 2 | 11 | 10 | 0.59 | 0.17 | - | no | Open |
| 245 | 2.6468222692756207 | -1.26083 | -33.0935 | 10 | 12 | 9 | 0.53 | 0.50 | - | no | Current |
| 191 | 3.0336689687352054 | -1.09429 | -28.6535 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 277 | 3.806776809599375 | -0.815034 | -16.965 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 214 | 3.8581501940359018 | -1.22756 | -28.0706 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 3.8864053339831193 | -0.911524 | -23.3962 | 3 | 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
-33.093kcal/mol
Ligand efficiency (LE)
-1.2728kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.727
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
367.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.95
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-70.08kcal/mol
Minimised FF energy
-83.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
598.6Ų
Total solvent-accessible surface area of free ligand
BSA total
505.9Ų
Buried surface area upon binding
BSA apolar
371.0Ų
Hydrophobic contacts buried
BSA polar
134.9Ų
Polar contacts buried
Fraction buried
84.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1580.6Ų
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
1045.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)