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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
30.8 kcal/mol
Protein clashes
6
Internal clashes
8
Native overlap
contact recall 0.71, Jaccard 0.55, H-bond role recall 0.33
Reason: 2 severe internal clashes, 8 internal clashes
2 severe internal clashes
6 protein-contact clashes
8 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.615 kcal/mol/HA)
✓ Good fit quality (FQ -6.10)
✓ Good H-bonds (5 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Very high strain energy (30.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-20.288
kcal/mol
LE
-0.615
kcal/mol/HA
Fit Quality
-6.10
FQ (Leeson)
HAC
33
heavy atoms
MW
457
Da
LogP
3.92
cLogP
Final rank
6.3510
rank score
Inter norm
-0.857
normalised
Contacts
17
H-bonds 10
Interaction summary
HBD 3
HBA 2
HY 9
PI 2
CLASH 8
Severe 2
Interaction summary
HBD 3
HBA 2
HY 9
PI 2
CLASH 8
Severe 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 12 | Native recall | 0.71 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 363 | 4.5505637977431235 | -0.972896 | -25.7285 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 5.107114005005125 | -0.935919 | -21.9802 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 5.391120897130467 | -0.735467 | -20.287 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 344 | 5.521545929099955 | -0.891439 | -22.0875 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 373 | 5.8719996082640895 | -0.798435 | -18.9584 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 319 | 6.351016053385534 | -0.856986 | -20.288 | 10 | 17 | 12 | 0.71 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.288kcal/mol
Ligand efficiency (LE)
-0.6148kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.100
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
457.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.92
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.77kcal/mol
Minimised FF energy
74.01kcal/mol
SASA & burial
✓ computed
SASA (unbound)
712.2Ų
Total solvent-accessible surface area of free ligand
BSA total
592.5Ų
Buried surface area upon binding
BSA apolar
500.9Ų
Hydrophobic contacts buried
BSA polar
91.6Ų
Polar contacts buried
Fraction buried
83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1692.7Ų
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
1060.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)