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
19.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.17
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.809 kcal/mol/HA)
✓ Good fit quality (FQ -7.88)
✓ Good H-bonds (5 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (19.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-25.076
kcal/mol
LE
-0.809
kcal/mol/HA
Fit Quality
-7.88
FQ (Leeson)
HAC
31
heavy atoms
MW
424
Da
LogP
3.89
cLogP
Interaction summary
HB 5
HY 22
PI 3
CLASH 1
Interaction summary
HB 5
HY 22
PI 3
CLASH 1
| Final rank | 2.403 | Score | -25.076 |
|---|---|---|---|
| Inter norm | -0.909 | Intra norm | 0.100 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ARG17
HIS241
LEU188
LEU229
MET233
NDP302
PHE113
PRO115
SER111
TYR114
TYR191
TYR194
VAL230
| ||
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 259 | 2.186616249521787 | -0.767138 | -19.682 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 249 | 2.4030765412283297 | -0.909145 | -25.0763 | 5 | 13 | 12 | 0.71 | 0.17 | - | no | Current |
| 269 | 2.6372940514961205 | -1.01685 | -23.5396 | 9 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 312 | 3.2393473524780756 | -0.83684 | -17.5204 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 3.272332131596446 | -0.77267 | -17.6481 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 312 | 3.6488397918246784 | -0.752019 | -16.7004 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 266 | 3.7498473298653865 | -0.798347 | -21.5987 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 4.113009301054676 | -0.859307 | -18.827 | 12 | 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
-25.076kcal/mol
Ligand efficiency (LE)
-0.8089kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.881
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
423.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.68kcal/mol
Minimised FF energy
35.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
687.4Ų
Total solvent-accessible surface area of free ligand
BSA total
492.5Ų
Buried surface area upon binding
BSA apolar
373.8Ų
Hydrophobic contacts buried
BSA polar
118.7Ų
Polar contacts buried
Fraction buried
71.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1704.8Ų
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
1038.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)