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
37.8 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.74, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.796 kcal/mol/HA)
✓ Good fit quality (FQ -7.42)
✓ Good H-bonds (3 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Very high strain energy (37.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-21.480
kcal/mol
LE
-0.796
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
27
heavy atoms
MW
380
Da
LogP
3.39
cLogP
Interaction summary
HB 3
HY 24
PI 5
CLASH 2
Interaction summary
HB 3
HY 24
PI 5
CLASH 2
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 | 1.669 | Score | -21.480 |
|---|---|---|---|
| Inter norm | -0.950 | Intra norm | 0.155 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; 1 severe cofactor-context clash; high strain Δ 37.8 | ||
| Residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
NDP302
PHE113
SER111
SER112
TYR191
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.74 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 78 | 1.6692729710025795 | -0.950213 | -21.4805 | 3 | 14 | 14 | 0.74 | 0.60 | - | no | Current |
| 103 | 2.960386822804398 | -1.13922 | -27.0542 | 8 | 18 | 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
-21.480kcal/mol
Ligand efficiency (LE)
-0.7956kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.422
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
380.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.39
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
32.31kcal/mol
Minimised FF energy
-5.45kcal/mol
SASA & burial
✓ computed
SASA (unbound)
613.5Ų
Total solvent-accessible surface area of free ligand
BSA total
491.1Ų
Buried surface area upon binding
BSA apolar
450.7Ų
Hydrophobic contacts buried
BSA polar
40.4Ų
Polar contacts buried
Fraction buried
80.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1642.8Ų
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
1109.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)