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 high
Native strong
SASA done
Strain ΔE
16.5 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.798 kcal/mol/HA)
✓ Good fit quality (FQ -7.53)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (16.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.342
kcal/mol
LE
-0.798
kcal/mol/HA
Fit Quality
-7.53
FQ (Leeson)
HAC
28
heavy atoms
MW
379
Da
LogP
1.76
cLogP
Interaction summary
HB 1
HY 16
PI 1
CLASH 2
Interaction summary
HB 1
HY 16
PI 1
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 | 2.000 | Score | -22.342 |
|---|---|---|---|
| Inter norm | -0.876 | Intra norm | 0.078 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 1 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ARG17
ASP181
ASP232
HIS241
LEU188
LEU226
LEU229
MET233
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.60 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 500 | 1.9998018606086565 | -0.876097 | -22.3424 | 1 | 13 | 12 | 0.63 | 0.20 | - | no | Current |
| 482 | 2.4285791188077326 | -0.955649 | -16.389 | 2 | 16 | 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
-22.342kcal/mol
Ligand efficiency (LE)
-0.7979kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.533
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
379.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.76
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-11.80kcal/mol
Minimised FF energy
-28.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
660.3Ų
Total solvent-accessible surface area of free ligand
BSA total
495.2Ų
Buried surface area upon binding
BSA apolar
389.6Ų
Hydrophobic contacts buried
BSA polar
105.6Ų
Polar contacts buried
Fraction buried
75.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1670.2Ų
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
1056.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)