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 mixed
SASA done
Strain ΔE
24.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.36, H-bond role recall 0.20
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
91% of hydrophobic surface is solvent-exposed (21/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.913 kcal/mol/HA)
✓ Good fit quality (FQ -8.81)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (24.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-27.394
kcal/mol
LE
-0.913
kcal/mol/HA
Fit Quality
-8.81
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Interaction summary
HB 10
HY 2
PI 0
CLASH 4
⚠ Exposure 91%
Interaction summary
HB 10
HY 2
PI 0
CLASH 4
⚠ Exposure 91%
Solvent-exposed hydrophobic surface — desolvation penalty likely
91% of hydrophobic surface is solvent-exposed (21/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 23
Buried (contacted) 2
Exposed 21
LogP 3.8
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.503 | Score | -27.394 |
|---|---|---|---|
| Inter norm | -1.085 | Intra norm | 0.171 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; moderate strain Δ 24.9 | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
MET386
PHE284
PHE383
PRO338
SER282
THR241
THR285
VAL335
VAL336
| ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 8 | Native recall | 0.53 |
| Jaccard | 0.36 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| 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
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 233 | 1.8428601500822481 | -1.04592 | -26.5554 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 2.5467751268775465 | -0.65051 | -15.8541 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 268 | 2.7705616902011543 | -1.0526 | -28.622 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 212 | 2.863444887452424 | -0.948161 | -19.8913 | 14 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 327 | 2.987201405603104 | -0.919315 | -25.6982 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 206 | 3.2169290875610765 | -1.04357 | -26.4577 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 325 | 3.260669336411137 | -0.926625 | -22.6233 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 3.4667837154767405 | -0.975337 | -23.0078 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 285 | 4.189069699505982 | -0.841824 | -23.0251 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 309 | 4.503406492657552 | -1.08458 | -27.3937 | 10 | 15 | 8 | 0.53 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.394kcal/mol
Ligand efficiency (LE)
-0.9131kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.808
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.07kcal/mol
Minimised FF energy
8.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
688.1Ų
Total solvent-accessible surface area of free ligand
BSA total
530.7Ų
Buried surface area upon binding
BSA apolar
409.1Ų
Hydrophobic contacts buried
BSA polar
121.6Ų
Polar contacts buried
Fraction buried
77.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2517.6Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1380.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)