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 medium
Native strong
SASA done
Strain ΔE
11.0 kcal/mol
Protein clashes
1
Internal clashes
5
Native overlap
contact recall 0.58, Jaccard 0.55, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.841 kcal/mol/HA)
✓ Good fit quality (FQ -12.69)
✓ Good H-bonds (3 bonds)
✓ Deep burial (95% SASA buried)
✗ Moderate strain (11.0 kcal/mol)
✗ Geometry warnings
Score
-23.934
kcal/mol
LE
-1.841
kcal/mol/HA
Fit Quality
-12.69
FQ (Leeson)
HAC
13
heavy atoms
MW
222
Da
LogP
-0.86
cLogP
Final rank
0.9857
rank score
Inter norm
-1.991
normalised
Contacts
12
H-bonds 8
Interaction summary
HBD 1
HBA 2
HY 2
PI 2
CLASH 5
Interaction summary
HBD 1
HBA 2
HY 2
PI 2
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 0.55 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 493 | 0.985702875069024 | -1.99053 | -23.9339 | 8 | 12 | 11 | 0.58 | 0.40 | - | no | Current |
| 499 | 2.4338247235991908 | -1.81572 | -22.7289 | 5 | 12 | 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
-23.934kcal/mol
Ligand efficiency (LE)
-1.8411kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.690
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
13HA
Physicochemical properties
Molecular weight
222.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.86
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-51.41kcal/mol
Minimised FF energy
-62.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
384.2Ų
Total solvent-accessible surface area of free ligand
BSA total
366.1Ų
Buried surface area upon binding
BSA apolar
168.0Ų
Hydrophobic contacts buried
BSA polar
198.1Ų
Polar contacts buried
Fraction buried
95.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
45.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1328.3Ų
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
1022.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)