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 and worth follow-up
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
15.2 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.005 kcal/mol/HA)
✓ Good fit quality (FQ -8.41)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Moderate strain (15.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-20.103
kcal/mol
LE
-1.005
kcal/mol/HA
Fit Quality
-8.41
FQ (Leeson)
HAC
20
heavy atoms
MW
263
Da
LogP
3.82
cLogP
Interaction summary
HB 1
HY 24
PI 3
CLASH 3
Interaction summary
HB 1
HY 24
PI 3
CLASH 3
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 | -0.221 | Score | -20.103 |
|---|---|---|---|
| Inter norm | -1.372 | Intra norm | 0.367 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 1 |
| Artifact reason | geometry warning; 9 clashes; 1 protein contact clash; 2 cofactor-context clashes | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
TYR191
TYR194
VAL230
| ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 538 | -0.22129243544498237 | -1.3719 | -20.1031 | 1 | 10 | 10 | 0.53 | 0.20 | - | no | Current |
| 521 | 0.5477762713696871 | -1.16376 | -22.086 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 521 | 1.8894076082925473 | -1.10288 | -19.5901 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 542 | 3.4157421864499886 | -1.21168 | -22.0034 | 8 | 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
-20.103kcal/mol
Ligand efficiency (LE)
-1.0052kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.411
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
263.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.82
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
71.41kcal/mol
Minimised FF energy
56.21kcal/mol
SASA & burial
✓ computed
SASA (unbound)
489.3Ų
Total solvent-accessible surface area of free ligand
BSA total
425.2Ų
Buried surface area upon binding
BSA apolar
388.1Ų
Hydrophobic contacts buried
BSA polar
37.1Ų
Polar contacts buried
Fraction buried
86.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1591.8Ų
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
1032.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)