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
18.1 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.63, Jaccard 0.63, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.876 kcal/mol/HA)
✓ Good fit quality (FQ -7.97)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (18.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.907
kcal/mol
LE
-0.876
kcal/mol/HA
Fit Quality
-7.97
FQ (Leeson)
HAC
25
heavy atoms
MW
333
Da
LogP
2.66
cLogP
Final rank
1.8263
rank score
Inter norm
-1.105
normalised
Contacts
12
H-bonds 2
Interaction summary
HBD 1
HBA 1
HY 6
PI 2
CLASH 3
Interaction summary
HBD 1
HBA 1
HY 6
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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 | 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 | 0.63 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 585 | 1.8262933247315551 | -1.10505 | -21.9069 | 2 | 12 | 12 | 0.63 | 0.20 | - | no | Current |
| 572 | 2.0439671731543423 | -1.10015 | -26.0693 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 562 | 2.6867018007655448 | -1.24434 | -29.8034 | 5 | 9 | 8 | 0.42 | 0.60 | - | no | Open |
| 576 | 4.064891135826998 | -1.10482 | -21.3976 | 7 | 15 | 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
-21.907kcal/mol
Ligand efficiency (LE)
-0.8763kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.966
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
333.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-35.85kcal/mol
Minimised FF energy
-53.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
606.3Ų
Total solvent-accessible surface area of free ligand
BSA total
480.4Ų
Buried surface area upon binding
BSA apolar
408.6Ų
Hydrophobic contacts buried
BSA polar
71.9Ų
Polar contacts buried
Fraction buried
79.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1681.0Ų
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
1030.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)