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
Promising
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
17.7 kcal/mol
Protein clashes
0
Internal clashes
6
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Reason: 6 internal clashes
6 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.398 kcal/mol/HA)
✓ Good fit quality (FQ -11.20)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (17.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.165
kcal/mol
LE
-1.398
kcal/mol/HA
Fit Quality
-11.20
FQ (Leeson)
HAC
18
heavy atoms
MW
256
Da
LogP
2.40
cLogP
Interaction summary
HB 2
HY 21
PI 4
CLASH 0
Interaction summary
HB 2
HY 21
PI 4
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | -0.480 | Score | -25.165 |
|---|---|---|---|
| Inter norm | -1.395 | Intra norm | -0.003 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 2 |
| Artifact reason | geometry warning; 6 clashes; 1 protein contact clash | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 545 | -0.4801230573225261 | -1.39516 | -25.1647 | 2 | 10 | 10 | 0.53 | 0.20 | - | no | Current |
| 524 | 2.10908688481874 | -1.55214 | -26.0245 | 5 | 11 | 10 | 0.53 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.165kcal/mol
Ligand efficiency (LE)
-1.3980kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.204
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
256.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.40
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
124.03kcal/mol
Minimised FF energy
106.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
451.3Ų
Total solvent-accessible surface area of free ligand
BSA total
386.7Ų
Buried surface area upon binding
BSA apolar
276.4Ų
Hydrophobic contacts buried
BSA polar
110.2Ų
Polar contacts buried
Fraction buried
85.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1503.9Ų
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
1013.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)