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
19.2 kcal/mol
Protein clashes
4
Internal clashes
2
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.187 kcal/mol/HA)
✓ Good fit quality (FQ -11.07)
✓ Good H-bonds (4 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (19.2 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (9)
Score
-32.038
kcal/mol
LE
-1.187
kcal/mol/HA
Fit Quality
-11.07
FQ (Leeson)
HAC
27
heavy atoms
MW
361
Da
LogP
2.25
cLogP
Interaction summary
HB 4
HY 20
PI 5
CLASH 2
Interaction summary
HB 4
HY 20
PI 5
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 | 0.638 | Score | -32.038 |
|---|---|---|---|
| Inter norm | -1.089 | Intra norm | -0.097 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 4 protein contact clashes; 2 cofactor-context clashes | ||
| Residues |
ARG17
ASP181
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
PRO115
SER111
TYR114
TYR191
TYR194
| ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.60 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 243 | 0.6383642184233481 | -1.0895 | -32.0384 | 4 | 13 | 12 | 0.63 | 0.40 | - | no | Current |
| 201 | 0.8514219575329248 | -1.05836 | -31.6861 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 226 | 0.9119370131705961 | -1.00589 | -29.0088 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 252 | 0.9771214741373022 | -0.806834 | -22.1243 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 230 | 1.2472816895024497 | -0.89324 | -26.0279 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 212 | 1.2689902355634186 | -1.20655 | -34.7324 | 8 | 25 | 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
-32.038kcal/mol
Ligand efficiency (LE)
-1.1866kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.071
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
361.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.25
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
77.42kcal/mol
Minimised FF energy
58.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
650.2Ų
Total solvent-accessible surface area of free ligand
BSA total
495.5Ų
Buried surface area upon binding
BSA apolar
425.3Ų
Hydrophobic contacts buried
BSA polar
70.2Ų
Polar contacts buried
Fraction buried
76.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1710.2Ų
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
1038.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)