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 mixed
SASA done
Strain ΔE
4.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.21, Jaccard 0.21, 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.
✓ Low conformational strain (4.9 kcal/mol)
✓ Excellent LE (-2.506 kcal/mol/HA)
✓ Good fit quality (FQ -15.01)
✓ Good H-bonds (3 bonds)
✓ Deep burial (92% SASA buried)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
Score
-25.059
kcal/mol
LE
-2.506
kcal/mol/HA
Fit Quality
-15.01
FQ (Leeson)
HAC
10
heavy atoms
MW
137
Da
LogP
-0.96
cLogP
Interaction summary
HB 3
HY 5
PI 2
CLASH 1
Interaction summary
HB 3
HY 5
PI 2
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 | -1.559 | Score | -25.059 |
|---|---|---|---|
| Inter norm | -2.506 | Intra norm | 0.000 |
| Top1000 | no | Excluded | no |
| Contacts | 4 | H-bonds | 3 |
| Artifact reason | geometry warning; 3 clashes; 3 protein contact clashes; 1 severe cofactor-context clash | ||
| Residues |
ARG17
NDP302
PHE113
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 | 4 | Native recall | 0.21 |
| Jaccard | 0.21 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 222 | -1.5587348898944557 | -2.50595 | -25.0595 | 3 | 4 | 4 | 0.21 | 0.40 | - | no | Current |
| 223 | -0.6649180866808654 | -2.42457 | -24.2457 | 7 | 5 | 5 | 0.26 | 0.60 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.059kcal/mol
Ligand efficiency (LE)
-2.5059kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-15.006
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
10HA
Physicochemical properties
Molecular weight
137.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.96
Lipinski: ≤ 5
Rotatable bonds
0
Conformational strain (MMFF94s)
Strain energy (ΔE)
4.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-26.74kcal/mol
Minimised FF energy
-31.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
272.3Ų
Total solvent-accessible surface area of free ligand
BSA total
250.7Ų
Buried surface area upon binding
BSA apolar
118.0Ų
Hydrophobic contacts buried
BSA polar
132.7Ų
Polar contacts buried
Fraction buried
92.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
47.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1282.7Ų
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
1023.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)