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
8.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.59, Jaccard 0.56, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.349 kcal/mol/HA)
✓ Good fit quality (FQ -12.09)
✓ Good H-bonds (4 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (8.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-32.380
kcal/mol
LE
-1.349
kcal/mol/HA
Fit Quality
-12.09
FQ (Leeson)
HAC
24
heavy atoms
MW
354
Da
LogP
4.65
cLogP
Interaction summary
HB 4
HY 20
PI 3
CLASH 1
Interaction summary
HB 4
HY 20
PI 3
CLASH 1
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 | 2.252 | Score | -32.380 |
|---|---|---|---|
| Inter norm | -1.359 | Intra norm | 0.010 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes; 2 cofactor-context clashes | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
LEU229
NDP302
PHE113
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 | 0.56 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 389 | -0.18784752275886354 | -1.01592 | -23.8653 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 0.044810234807672045 | -1.09043 | -25.2406 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 471 | 0.05669390183562073 | -1.09591 | -25.194 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 0.2488068813182308 | -1.18196 | -27.8753 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 1.2946467321758754 | -1.18634 | -27.2383 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 2.0117884778778174 | -1.01577 | -22.8536 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 2.25182953308986 | -1.35937 | -32.3799 | 4 | 11 | 10 | 0.59 | 0.33 | - | no | Current |
| 390 | 2.8542622317418695 | -1.17081 | -26.8659 | 9 | 15 | 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
-32.380kcal/mol
Ligand efficiency (LE)
-1.3492kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.091
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
354.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.65
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
11.20kcal/mol
Minimised FF energy
3.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
578.2Ų
Total solvent-accessible surface area of free ligand
BSA total
488.5Ų
Buried surface area upon binding
BSA apolar
349.6Ų
Hydrophobic contacts buried
BSA polar
138.9Ų
Polar contacts buried
Fraction buried
84.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1583.4Ų
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
1024.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)