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
18.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.407 kcal/mol/HA)
✓ Good fit quality (FQ -11.27)
✓ Good H-bonds (3 bonds)
✓ Deep burial (87% SASA buried)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
Score
-25.319
kcal/mol
LE
-1.407
kcal/mol/HA
Fit Quality
-11.27
FQ (Leeson)
HAC
18
heavy atoms
MW
294
Da
LogP
3.38
cLogP
Interaction summary
HB 3
HY 16
PI 4
CLASH 1
Interaction summary
HB 3
HY 16
PI 4
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 | 0.476 | Score | -25.319 |
|---|---|---|---|
| Inter norm | -1.474 | Intra norm | 0.067 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 3 |
| Artifact reason | geometry warning; 3 clashes; 1 protein clash; 2 cofactor-context clashes | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR194
ARG287
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 11 | Native recall | 0.58 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 416 | -0.02197705513071642 | -1.35055 | -24.9974 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 398 | 0.4756929644349943 | -1.47357 | -25.319 | 3 | 11 | 11 | 0.58 | 0.40 | - | no | Current |
| 424 | 0.5658076263964957 | -1.25601 | -20.4768 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 0.9142477678312333 | -1.41951 | -23.8348 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 1.962238201095857 | -1.51574 | -25.6489 | 10 | 16 | 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
-25.319kcal/mol
Ligand efficiency (LE)
-1.4066kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.273
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
294.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.38
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
32.42kcal/mol
Minimised FF energy
13.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
493.6Ų
Total solvent-accessible surface area of free ligand
BSA total
431.5Ų
Buried surface area upon binding
BSA apolar
249.9Ų
Hydrophobic contacts buried
BSA polar
181.7Ų
Polar contacts buried
Fraction buried
87.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
57.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1466.2Ų
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
1022.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)