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
23.4 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.696 kcal/mol/HA)
✓ Good fit quality (FQ -6.71)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (23.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-20.878
kcal/mol
LE
-0.696
kcal/mol/HA
Fit Quality
-6.71
FQ (Leeson)
HAC
30
heavy atoms
MW
418
Da
LogP
4.30
cLogP
Final rank
1.9448
rank score
Inter norm
-0.856
normalised
Contacts
15
H-bonds 2
Interaction summary
HBA 2
HY 6
PI 5
CLASH 2
Interaction summary
HBA 2
HY 6
PI 5
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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: 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 | 0.70 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 501 | 0.6818248824134601 | -0.870183 | -22.6709 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 1.1696575870053978 | -1.09557 | -32.502 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 1.9447900786079562 | -0.856086 | -20.8782 | 2 | 15 | 14 | 0.74 | 0.20 | - | no | Current |
| 526 | 2.18086980307911 | -0.986616 | -23.3532 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 498 | 4.110887622816772 | -1.00704 | -25.3241 | 14 | 17 | 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
-20.878kcal/mol
Ligand efficiency (LE)
-0.6959kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.713
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.30
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
100.86kcal/mol
Minimised FF energy
77.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
684.4Ų
Total solvent-accessible surface area of free ligand
BSA total
530.8Ų
Buried surface area upon binding
BSA apolar
402.8Ų
Hydrophobic contacts buried
BSA polar
128.0Ų
Polar contacts buried
Fraction buried
77.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1692.2Ų
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
1041.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)