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 mixed
SASA done
Strain ΔE
26.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.33, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (25/25 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 (-0.704 kcal/mol/HA)
✓ Good fit quality (FQ -7.04)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (26.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-23.920
kcal/mol
LE
-0.704
kcal/mol/HA
Fit Quality
-7.04
FQ (Leeson)
HAC
34
heavy atoms
MW
474
Da
LogP
4.20
cLogP
Interaction summary
HB 8
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Interaction summary
HB 8
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (25/25 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) 0
Exposed 25
LogP 4.2
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.219 | Score | -23.920 |
|---|---|---|---|
| Inter norm | -0.712 | Intra norm | 0.009 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 8 |
| Artifact reason | geometry warning; 19 clashes; 1 protein clash; moderate strain Δ 26.7 | ||
| Residues |
ALA283
ARG22
ARG242
ARG337
ARG50
ASN20
ASP243
ASP385
ASP44
ASP47
GLU384
GLY240
LYS51
SER282
THR21
THR241
THR285
| ||
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 | 0.33 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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
No hy · hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 435 | 1.9301717756467363 | -0.72761 | -23.752 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 334 | 2.0263869649204853 | -0.930222 | -27.1777 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 2.0501377984473983 | -0.787007 | -19.7508 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 2.752858282721569 | -0.800489 | -23.9414 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 396 | 2.7601535713818413 | -0.591573 | -16.9942 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 381 | 2.9359635508409108 | -0.793642 | -19.3973 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 3.1523302745872246 | -0.760382 | -22.134 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 379 | 3.2188609293194674 | -0.712407 | -23.9203 | 8 | 17 | 8 | 0.53 | 0.20 | - | no | Current |
| 418 | 3.4321465037133247 | -0.816749 | -26.4904 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 407 | 3.5524489581677203 | -0.633858 | -18.4382 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 3.7807067079968997 | -0.979467 | -27.5375 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 3.8486675627744926 | -0.726729 | -19.7364 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 4.10912935177256 | -0.834923 | -27.5266 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 336 | 4.160825631036783 | -0.993151 | -30.1156 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 5.0362869852581325 | -0.819442 | -25.2435 | 6 | 21 | 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
-23.920kcal/mol
Ligand efficiency (LE)
-0.7035kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.040
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.20
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
83.76kcal/mol
Minimised FF energy
57.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
740.4Ų
Total solvent-accessible surface area of free ligand
BSA total
551.7Ų
Buried surface area upon binding
BSA apolar
385.4Ų
Hydrophobic contacts buried
BSA polar
166.4Ų
Polar contacts buried
Fraction buried
74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2475.5Ų
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
1425.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)