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
22.6 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.74, H-bond role recall 0.60
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.436 kcal/mol/HA)
✓ Good fit quality (FQ -4.11)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ High strain energy (22.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-12.202
kcal/mol
LE
-0.436
kcal/mol/HA
Fit Quality
-4.11
FQ (Leeson)
HAC
28
heavy atoms
MW
397
Da
LogP
3.04
cLogP
Interaction summary
HB 7
HY 24
PI 2
CLASH 2
Interaction summary
HB 7
HY 24
PI 2
CLASH 2
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
| Final rank | 2.947 | Score | -12.202 |
|---|---|---|---|
| Inter norm | -0.918 | Intra norm | 0.482 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; 5 cofactor-context clashes; moderate strain Δ 22.6 | ||
| Residues |
ARG17
ASP181
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR191
TYR194
VAL230
ARG287
| ||
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 | 0.74 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 412 | 2.2282048565114194 | -0.9349 | -25.578 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 400 | 2.9471794262273776 | -0.917555 | -12.2021 | 7 | 14 | 14 | 0.74 | 0.60 | - | no | Current |
| 408 | 3.2597862975616207 | -0.820251 | -21.3582 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 391 | 5.01401130935189 | -0.987817 | -22.1215 | 9 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 373 | 5.1435904455655335 | -0.97996 | -23.9874 | 10 | 16 | 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
-12.202kcal/mol
Ligand efficiency (LE)
-0.4358kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.114
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
397.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.04
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.31kcal/mol
Minimised FF energy
40.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.2Ų
Total solvent-accessible surface area of free ligand
BSA total
530.6Ų
Buried surface area upon binding
BSA apolar
327.0Ų
Hydrophobic contacts buried
BSA polar
203.6Ų
Polar contacts buried
Fraction buried
85.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1537.0Ų
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
1039.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)