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
25.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.56, H-bond role recall 0.17
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.180 kcal/mol/HA)
✓ Good fit quality (FQ -10.73)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (25.0 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Internal clashes (9)
Score
-29.510
kcal/mol
LE
-1.180
kcal/mol/HA
Fit Quality
-10.73
FQ (Leeson)
HAC
25
heavy atoms
MW
347
Da
LogP
2.92
cLogP
Interaction summary
HB 8
HY 19
PI 5
CLASH 2
Interaction summary
HB 8
HY 19
PI 5
CLASH 2
| Final rank | 0.906 | Score | -29.510 |
|---|---|---|---|
| Inter norm | -1.200 | Intra norm | 0.020 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 6 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 25.0 | ||
| Residues |
ARG17
GLY225
HIS241
LEU188
LEU226
NDP302
PHE113
TYR191
TYR194
TYR283
ARG287
| ||
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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 10 | Native recall | 0.59 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 484 | 0.28110153307647273 | -1.31495 | -32.5414 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 0.6106312707921285 | -1.25752 | -30.0688 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 459 | 0.9059983743946403 | -1.20032 | -29.5096 | 8 | 11 | 10 | 0.59 | 0.17 | - | no | Current |
| 490 | 1.4021700669349333 | -0.92032 | -22.5041 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 494 | 1.5668201695242128 | -0.749892 | -16.897 | 4 | 9 | 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
-29.510kcal/mol
Ligand efficiency (LE)
-1.1804kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.731
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.92
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
115.07kcal/mol
Minimised FF energy
90.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
580.6Ų
Total solvent-accessible surface area of free ligand
BSA total
465.5Ų
Buried surface area upon binding
BSA apolar
355.4Ų
Hydrophobic contacts buried
BSA polar
110.1Ų
Polar contacts buried
Fraction buried
80.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1627.9Ų
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
1016.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)