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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
27.7 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.68, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.903 kcal/mol/HA)
✓ Good fit quality (FQ -8.62)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (27.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (10)
Score
-26.189
kcal/mol
LE
-0.903
kcal/mol/HA
Fit Quality
-8.62
FQ (Leeson)
HAC
29
heavy atoms
MW
416
Da
LogP
3.38
cLogP
Interaction summary
HB 2
HY 24
PI 4
CLASH 4
Interaction summary
HB 2
HY 24
PI 4
CLASH 4
| Final rank | 0.898 | Score | -26.189 |
|---|---|---|---|
| Inter norm | -0.956 | Intra norm | 0.053 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 2 |
| Artifact reason | geometry warning; 10 clashes; 4 protein contact clashes; 2 cofactor-context clashes; moderate strain Δ 27.7 | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR191
TYR194
VAL230
ARG287
| ||
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
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.68 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 67 | 0.639930200885836 | -0.897149 | -27.213 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 50 | 0.7239642042033002 | -0.897655 | -23.0785 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 33 | 0.8978064917464793 | -0.955789 | -26.1889 | 2 | 13 | 13 | 0.68 | 0.20 | - | no | Current |
| 47 | 1.2460564241284993 | -0.839896 | -23.0651 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 55 | 4.638616872500226 | -0.669129 | -18.4402 | 7 | 9 | 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
-26.189kcal/mol
Ligand efficiency (LE)
-0.9031kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.620
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
415.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.90kcal/mol
Minimised FF energy
14.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
662.6Ų
Total solvent-accessible surface area of free ligand
BSA total
527.6Ų
Buried surface area upon binding
BSA apolar
450.0Ų
Hydrophobic contacts buried
BSA polar
77.6Ų
Polar contacts buried
Fraction buried
79.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1716.6Ų
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
1032.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)