FAIRMol

NMT-TY0555

Pose ID 1018 Compound 515 Pose 340

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T02
Human DHFR Human
Ligand NMT-TY0555
PDB5SD8↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
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
24.8 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.40
Burial
91%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.208 kcal/mol/HA) ✓ Good fit quality (FQ -10.11) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (24.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-24.162
kcal/mol
LE
-1.208
kcal/mol/HA
Fit Quality
-10.11
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
cLogP
Strain ΔE
24.8 kcal/mol
SASA buried
91%
Lipo contact
74% BSA apolar/total
SASA unbound
472 Ų
Apolar buried
317 Ų

Interaction summary

HB 12 HY 17 PI 1 CLASH 2
Final rank1.520Score-24.162
Inter norm-1.304Intra norm0.096
Top1000noExcludedno
Contacts16H-bonds12
Artifact reasongeometry warning; 6 clashes; 1 protein clash; 1 cofactor-context clash; moderate strain Δ 24.8
Residues
ALA10 GLU31 ILE8 LEU23 LEU28 NAP201 PHE135 PHE32 PHE35 THR137 TRP25 TYR122 TYR34 VAL116 VAL136 VAL9

Protein summary

200 residues
Protein targetT02Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap11Native recall0.52
Jaccard0.42RMSD-
HB strict2Strict recall0.40
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
291 1.1342832901296953 -1.47243 -28.1213 7 13 0 0.00 0.00 - no Open
308 1.1407956598243199 -1.47271 -28.0966 7 13 0 0.00 0.00 - no Open
287 1.425854450107728 -1.57638 -29.017 10 15 0 0.00 0.00 - no Open
294 1.4368563653499584 -1.58614 -29.0417 10 15 0 0.00 0.00 - no Open
340 1.5199875327590986 -1.30421 -24.1616 12 16 11 0.52 0.40 - no Current
325 1.8929444358902847 -1.09972 -20.59 10 11 0 0.00 0.00 - no Open
264 2.0213778030470935 -1.28263 -24.1424 8 15 0 0.00 0.00 - no Open
272 2.07930378903586 -1.19931 -21.6886 10 17 0 0.00 0.00 - no Open
288 2.272686469792997 -1.20072 -21.8379 10 17 0 0.00 0.00 - no Open
255 2.604134178216891 -1.55444 -29.5672 11 18 0 0.00 0.00 - no Open
395 2.618228131873109 -1.34198 -25.4179 10 16 0 0.00 0.00 - no Open
307 2.6395815071657873 -1.216 -22.6881 12 17 0 0.00 0.00 - no Open
324 2.719858307570968 -0.962258 -19.339 7 11 0 0.00 0.00 - no Open
272 2.890185804928903 -1.24872 -23.3539 7 15 0 0.00 0.00 - no Open
354 2.894301988851109 -1.46517 -27.278 13 19 15 0.71 0.60 - no Open
248 2.9955573621189955 -1.44392 -27.8137 14 18 0 0.00 0.00 - no Open
346 3.086475756889026 -1.42333 -26.6003 13 19 15 0.71 0.60 - no Open
299 3.1992481359795537 -1.24642 -23.7166 13 17 0 0.00 0.00 - no Open
285 3.2187089349618714 -1.29682 -23.427 10 17 0 0.00 0.00 - no Open
379 3.2560466957189305 -1.35838 -25.6607 9 16 0 0.00 0.00 - no Open
369 3.4560880962334983 -1.32647 -25.5936 9 16 0 0.00 0.00 - no Open
254 3.4642926757389616 -1.30203 -24.5606 9 15 0 0.00 0.00 - no Open
406 3.67636034041161 -1.29246 -24.4616 10 16 0 0.00 0.00 - no Open
333 3.717795610400825 -1.4146 -26.5109 10 14 0 0.00 0.00 - no Open
241 3.724783035797209 -1.26416 -21.7498 15 13 0 0.00 0.00 - no Open
251 3.7829044977730146 -1.35705 -25.1409 11 19 0 0.00 0.00 - no Open
330 3.7929991462566486 -0.942708 -18.8834 6 11 0 0.00 0.00 - no Open
241 4.010694369049239 -1.38136 -25.2742 11 19 0 0.00 0.00 - no Open
226 4.299065349056032 -1.39557 -26.9943 14 15 0 0.00 0.00 - no Open
257 4.359761779337785 -1.65662 -30.294 16 22 0 0.00 0.00 - no Open
274 4.532558280468934 -1.63443 -31.073 16 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.
✓ Metrics available

Scoring & efficiency
Docking score -24.162kcal/mol
Ligand efficiency (LE) -1.2081kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.109
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.68
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -91.95kcal/mol
Minimised FF energy -116.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 472.3Ų
Total solvent-accessible surface area of free ligand
BSA total 430.0Ų
Buried surface area upon binding
BSA apolar 317.2Ų
Hydrophobic contacts buried
BSA polar 112.8Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1388.3Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 615.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)