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
24.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.65, Jaccard 0.61, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.648 kcal/mol/HA)
✓ Good fit quality (FQ -6.04)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (76% SASA buried)
✗ High strain energy (24.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-17.491
kcal/mol
LE
-0.648
kcal/mol/HA
Fit Quality
-6.04
FQ (Leeson)
HAC
27
heavy atoms
MW
412
Da
LogP
1.80
cLogP
Final rank
2.5624
rank score
Inter norm
-1.037
normalised
Contacts
12
H-bonds 10
Interaction summary
HBD 1
HBA 7
PC 1
HY 6
PI 1
CLASH 1
Interaction summary
HBD 1
HBA 7
PC 1
HY 6
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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 | 11 | Native recall | 0.65 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 4 | Strict recall | 0.57 |
| HB same residue+role | 4 | HB role recall | 0.67 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 495 | 2.5624350645846876 | -1.03705 | -17.4906 | 10 | 12 | 11 | 0.65 | 0.67 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.491kcal/mol
Ligand efficiency (LE)
-0.6478kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.044
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
411.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.80
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
0.53kcal/mol
Minimised FF energy
-24.21kcal/mol
SASA & burial
✓ computed
SASA (unbound)
622.7Ų
Total solvent-accessible surface area of free ligand
BSA total
473.5Ų
Buried surface area upon binding
BSA apolar
269.2Ų
Hydrophobic contacts buried
BSA polar
204.3Ų
Polar contacts buried
Fraction buried
76.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
56.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1538.3Ų
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
1047.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)