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
21.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.36, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
76% of hydrophobic surface is solvent-exposed (19/25 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 (-0.710 kcal/mol/HA)
✓ Good fit quality (FQ -6.99)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (21.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-22.730
kcal/mol
LE
-0.710
kcal/mol/HA
Fit Quality
-6.99
FQ (Leeson)
HAC
32
heavy atoms
MW
438
Da
LogP
4.28
cLogP
Interaction summary
HB 9
HY 1
PI 0
CLASH 1
⚠ Exposure 76%
Interaction summary
HB 9
HY 1
PI 0
CLASH 1
⚠ Exposure 76%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
76% of hydrophobic surface is solvent-exposed (19/25 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 25
Buried (contacted) 6
Exposed 19
LogP 4.28
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (2/5 atoms exposed)aliphatic chain/group (8 atoms exposed)
| Final rank | 4.373 | Score | -22.730 |
|---|---|---|---|
| Inter norm | -0.903 | Intra norm | 0.192 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 9 |
| Artifact reason | geometry warning; 13 clashes; 3 protein clashes; moderate strain Δ 21.1 | ||
| Residues |
ALA283
ARG242
ARG337
ARG50
ASP243
ASP385
ASP44
ASP47
GLU384
LEU339
LEU382
MET386
PHE383
PRO338
SER282
THR21
THR241
THR285
VAL336
| ||
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.36 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 364 | 1.829900181254628 | -0.719662 | -18.3424 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 265 | 2.026313243924789 | -1.01026 | -23.2914 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 329 | 2.0373471110131636 | -0.869732 | -22.9516 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 330 | 2.058710961639984 | -0.909592 | -23.8784 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 2.6597483939163937 | -1.27139 | -31.6043 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 2.6953150877472445 | -0.847963 | -22.7415 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 3.6249745621726803 | -1.05167 | -23.8418 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 3.990038112087562 | -0.793892 | -22.5817 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 240 | 4.268181873602591 | -0.970374 | -21.8269 | 13 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 4.372928356142067 | -0.902686 | -22.7305 | 9 | 19 | 9 | 0.60 | 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
-22.730kcal/mol
Ligand efficiency (LE)
-0.7103kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.985
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.28
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
53.20kcal/mol
Minimised FF energy
32.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
706.9Ų
Total solvent-accessible surface area of free ligand
BSA total
564.5Ų
Buried surface area upon binding
BSA apolar
450.6Ų
Hydrophobic contacts buried
BSA polar
113.9Ų
Polar contacts buried
Fraction buried
79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2547.2Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1385.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)