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List of molecules among the 133885 GDB9 molecules for which the Corina generated Cartesian coordinates and the B3LYP/6-31G(2df,p) equilibrium geometry lead to |
different SMILES and InChI strings when parsed through the program Openbabel. Given are the indices of these molecules in the database, the original GDB17 |
SMILES, the SMILES generated from the Cartesian coordinates using Openbabel, as well as the L1 norm of the difference between the Coulomb matrices (D_IJ in au) |
corresponding to the Corina and B3LYP coordinates. |
============================================================================================================================================================== |
# Index GDB17 SMILES SMILES for B3LYP XYZ SMILES for Corina generated XYZ D_IJ |
============================================================================================================================================================== |
58 NC(=N)C#N NC(=N)C#N [NH]C(=[NH2])C#N 6.036217 |
61 NC(=N)C=O NC(=N)C=O [NH]C(=[NH2])C=O 5.631463 |
80 [NH3+]CC([O-])=O NCC(=O)O [NH3]CC(=O)[O] 10.09360 |
185 N=C1NC=CO1 [NH][C@@H]1NC=CO1 N=c1occ[nH]1 1.588400 |
186 N=C1OC=CO1 [NH][C@@H]1OC=CO1 N=c1occo1 1.785040 |
245 NC(=N)NC=O NC(=N)NC=O [NH]C(=[NH2])NC=O 4.503399 |
267 C[NH2+]CC([O-])=O CNCC(=O)O C[NH2]CC(=O)[O] 8.290945 |
280 CC(=O)C(N)=N NC(=N)C(=O)C [NH]C(=[NH2])C(=O)C 10.12159 |
286 CC([NH3+])C([O-])=O C[C@H](C(=O)O)N C[C@H](C(=O)[O])[NH3] 12.34491 |
752 N=C1NC=NO1 [NH][C@H]1NC=NO1 N=c1onc[nH]1 5.453974 |
753 N=C1NN=NN1 [NH][C@@H]1NN=NN1 N=c1[nH]nn[nH]1 1.969069 |
754 N=C1OC=NO1 [NH][C@@H]1ON=CO1 N=c1onco1 5.516224 |
755 N=C1ON=NO1 [NH][C@@H]1ON=NO1 N=c1onno1 5.162241 |
881 CC1=CNC(=N)O1 CC1=CN[C@@H](O1)[NH] Cc1c[nH]c(=N)o1 2.128639 |
884 CC1=COC(=N)N1 CC1=CO[C@@H](N1)[NH] Cc1coc(=N)[nH]1 1.658691 |
885 CC1=COC(=N)O1 CC1=CO[C@H](O1)[NH] Cc1coc(=N)o1 2.221851 |
888 NC1=CNC(=N)O1 [NH][C@@H]1NC=C(O1)N Nc1c[nH]c(=N)o1 2.178052 |
891 NC1=COC(=N)O1 [NH][C@@H]1OC=C(O1)N Nc1coc(=N)o1 2.137957 |
894 OC1=CNC(=N)O1 [NH][C@H]1NC=C(O1)O Oc1c[nH]c(=N)o1 2.276974 |
897 OC1=COC(=N)N1 [NH][C@H]1NC(=CO1)O Oc1coc(=N)[nH]1 1.736408 |
898 OC1=COC(=N)O1 [NH][C@H]1OC(=CO1)O Oc1coc(=N)o1 2.413544 |
906 N=C1C=COC=N1 [NH]C1=CCOC=N1 N=c1ccocn1 1.854791 |
907 N=C1N=CNC=N1 [NH]C1=NCNC=N1 N=c1nc[nH]cn1 22.33349 |
908 N=C1N=COC=N1 [NH][C@@H]1N=COC=N1 N=c1ncocn1 21.21309 |
914 N=C1NC=NC=N1 [NH]C1=NC=NCN1 N=c1ncnc[nH]1 7.051838 |
1003 CN1C=COC1=N CN1C=CO[C@@H]1[NH] Cn1ccoc1=N 7.747874 |
1102 CC(C)([NH3+])C([O-])=O OC(=O)C(N)(C)C [O]C(=O)C([NH3])(C)C 13.85569 |
1115 CC(=O)NC(N)=N NC(=N)NC(=O)C [NH]C(=[NH2])NC(=O)C 11.23965 |
1117 NC(=[NH2+])CC([O-])=O [CH2]C(=[NH2])N.O=C=O NC(=[NH2])CC(=O)[O] 22.27789 |
1126 CC([NH3+])CC([O-])=O C[C@H](CC(=O)O)N C[C@H](CC(=O)[O])[NH3] 7.726201 |
1129 C[NH+](C)CC([O-])=O CN(CC(=O)O)C C[NH](CC(=O)[O])C 10.70834 |
1232 [O-]C(=O)CNC=[NH2+] NC=NCC(=O)O [O]C(=O)CNC=[NH2] 36.50570 |
1259 NC=[NH+]CC([O-])=O NC=NCC(=O)O [O]C(=O)CNC=[NH2] 36.24233 |
1265 [NH3+]CC#CC([O-])=O NCC#CC(=O)O [NH3]CC#CC(=O)[O] 10.17933 |
1281 CC[NH2+]CC([O-])=O CCNCC(=O)O CC[NH2]CC(=O)[O] 9.170403 |
1284 C[NH2+]CCC([O-])=O CNCCC(=O)O C[NH2]CCC(=O)[O] 14.01778 |
1290 [NH3+]CCCC([O-])=O NCCCC(=O)O [NH3]CCCC(=O)[O] 18.66856 |
1584 NC(=N)C(=O)C#C NC(=N)C(=O)C#C [NH]C(=[NH2])C(=O)C#C 1.895287 |
1585 NC(=N)C(=O)C#N NC(=N)C(=O)C#N [NH]C(=[NH2])C(=O)C#N 1.811070 |
1588 NC(=N)C(=O)C=O NC(=N)C(=O)C=O [NH]C(=[NH2])C(=O)C=O 1.779035 |
1596 NC(=N)C(O)C#N NC(=N)[C@H](C#N)O [NH]C(=[NH2])[C@H](C#N)O 7.136924 |
1600 [NH3+]C(C#C)C([O-])=O N[C@H](C(=O)O)C#C [NH3][C@H](C(=O)[O])C#C 13.27150 |
1637 CN(C=O)C(N)=N CN(C(=N)N)C=O CN(C(=[NH2])[NH])C=O 7.794703 |
1645 CCC(=O)C(N)=N CCC(=O)C(=N)N CCC(=O)C(=[NH2])[NH] 2.137097 |
1652 COC(=O)C(N)=N COC(=O)C(=N)N COC(=O)C(=[NH2])[NH] 2.198262 |
1654 NC(=N)C(=O)CO NC(=N)C(=O)CO [NH]C(=[NH2])C(=O)CO 2.031947 |
1675 CCC([NH3+])C([O-])=O CC[C@H](C(=O)O)N CC[C@H](C(=O)[O])[NH3] 13.06905 |
1680 C[NH2+]C(C)C([O-])=O C[C@@H](C(=O)O)NC C[C@@H](C(=O)[O])[NH2]C 13.91961 |
1684 [NH3+]C(CO)C([O-])=O OC[C@@H](C(=O)O)N OC[C@@H](C(=O)[O])[NH3] 13.85054 |
1685 NC(C[NH3+])C([O-])=O N[C@H](C(=O)O)CN N[C@H](C(=O)[O])C[NH3] 17.24594 |
1686 [NH3+]CC(O)C([O-])=O NC[C@H](C(=O)O)O [NH3]C[C@H](C(=O)[O])O 14.43758 |
1806 [NH3+]C1(CC1)C([O-])=O OC(=O)C1(N)CC1 [O]C(=O)C1([NH3])CC1 7.127893 |
1994 [O-]C(=O)CC1C[NH2+]1 OC(=O)C[C@H]1CN1 [O]C(=O)C[C@H]1C[NH2]1 7.843359 |
2356 [O-]C(=O)C1CC[NH2+]1 OC(=O)[C@H]1CCN1 [O]C(=O)[C@H]1CC[NH2]1 7.171507 |
2357 [O-]C(=O)C1C[NH2+]C1 OC(=O)C1CNC1 [O]C(=O)C1C[NH2]C1 12.60798 |
2386 [NH3+]C1CC1C([O-])=O N[C@H]1C[C@H]1C(=O)O [NH3][C@H]1C[C@H]1C(=O)[O] 8.873122 |
3704 CC1=NOC(=N)O1 CC1=NO[C@@H](O1)[NH] Cc1noc(=N)o1 23.19828 |
3751 CN1C=NOC1=N CN1C=NO[C@@H]1[NH] Cn1cnoc1=N 32.97848 |
3763 CN1N=COC1=N CN1[C@H]([NH])OC=N1 Cn1ncoc1=N 1.804659 |
3771 CN1N=NNC1=N CN1N=NN[C@H]1[NH] Cn1nn[nH]c1=N 2.478519 |
3773 CN1N=NOC1=N CN1N=NO[C@@H]1[NH] Cn1nnoc1=N 47.50930 |
3831 N=C1C=NNC=N1 [NH]C1=NCNN=C1 N=c1cn[nH]cn1 39.76283 |
3838 N=C1N=CON=N1 [NH][C][N]C=O.N#N [NH]C1=N[N]OC=N1 50.99306 |
3842 N=C1NN=CC=N1 [NH]C1NCCNN1 [NH]C1=NCC=NN1 22.58177 |
3885 NC1=NOC(=N)N1 [NH][C@@H]1ON=C(N1)N Nc1noc(=N)[nH]1 5.839205 |
3886 NC1=NOC(=N)O1 [NH][C@H]1ON=C(O1)N Nc1noc(=N)o1 24.15656 |
3891 [NH3+]CC1=N[N-]N=N1 NCc1nnn[nH]1 [NH3]Cc1nnn[nH]1 24.79379 |
3895 O=C1C=CON=N1 [O][C][CH]C=O.N#N O=c1cconn1 35.63872 |
3899 O=C1N=CON=N1 O=CN=C=O.N#N O=c1nconn1 53.14760 |
3941 OC1=NNC(=N)N1 [NH][C@@H]1NC(=NN1)O Oc1n[nH]c(=N)[nH]1 22.48692 |
3945 OC1=NOC(=N)O1 [NH][C@@H]1OC(=NO1)O Oc1noc(=N)o1 24.61596 |
4010 C[NH2+]CC(C=O)=N[O-] CNC[C](C=O)N[O] C[NH2]CC(=N[O])C=O 32.62044 |
4232 NC(=N)C(F)(F)F NC(=N)C(F)(F)F [NH]C(=[NH2])C(F)(F)F 4.819105 |
4239 N=C1NC(=N)C=CO1 [NH][C@@H]1OCC=C(N1)[NH] N=C1OCC=C(N1)[NH] 2.303502 |
4240 N=C1NC(=N)N=CO1 [NH][C@H]1OC=N[C@@H](N1)[NH] N=c1ncoc(=N)[nH]1 2.578808 |
4266 CC1=NC(=N)N=CN1 C[C@@H]1NC=NC(=N1)[NH] Cc1nc(=N)nc[nH]1 2.409085 |
4267 CC1=NC(=N)N=CO1 CC1=N[C@@H](N=CO1)[NH] Cc1nc(=N)nco1 40.09121 |
4276 NC1=NC(=N)C=CO1 N[C@H]1OC=CC(=N1)[NH] Nc1nc(=N)cco1 2.383421 |
4277 NC1=[NH+]C(=N)N=C[N-]1 N[C@H]1N=CN=C(N1)[NH] Nc1ncnc(=N)[nH]1 31.41432 |
4278 NC1=NC(=N)N=CO1 N[C@H]1OC=NC(=N1)[NH] Nc1nc(=N)nco1 9.498572 |
4290 OC1=NC(=N)C=CN1 [NH]C1=N[C@H](NC=C1)O OC1=NC(=CCN1)[NH] 1.783895 |
4291 OC1=NC(=N)C=CO1 OC1=NC(=CCO1)[NH] Oc1nc(=N)cco1 2.604106 |
4292 OC1=NC(=N)N=CN1 [NH]C1=N[C@@H](O)NC=N1 Oc1nc(=N)nc[nH]1 2.484245 |
4293 OC1=NC(=N)N=CO1 [NH][C@@H]1N=C(O)OC=N1 Oc1nc(=N)nco1 2.837341 |
4303 CC1=NC(=N)NC=N1 C[C@@H]1N=C([NH])NC=N1 Cc1nc(=N)[nH]cn1 29.97388 |
4329 OC1=NC(=N)NC=N1 [NH]C1=NC(=NCN1)O [NH]C1=N[C@@H](N=CN1)O 2.240187 |
4392 CC1=NC=CC(=N)O1 [NH]C1=CCN=C(O1)C Cc1nccc(=N)o1 39.31768 |
4395 CC1=NC=NC(=N)N1 C[C@H]1N=CN=C(N1)[NH] Cc1ncnc(=N)[nH]1 2.387312 |
4396 CC1=NC=NC(=N)O1 C[C@@H]1N=CN=C(O1)[NH] CC1=NCN=C(O1)[NH] 2.736436 |
4422 OC1=NC=CC(=N)N1 [NH]C1=CCN=C(N1)O Oc1nccc(=N)[nH]1 2.059161 |
4423 OC1=NC=CC(=N)O1 [NH]C1=CCN=C(O1)O Oc1nccc(=N)o1 2.671334 |
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All-atom Diffusion Transformers - QM9 dataset
QM9 dataset from the paper "All-atom Diffusion Transformers: Unified generative modelling of molecules and materials", by Chaitanya K. Joshi, Xiang Fu, Yi-Lun Liao, Vahe Gharakhanyan, Benjamin Kurt Miller, Anuroop Sriram*, and Zachary W. Ulissi* from FAIR Chemistry at Meta (* Joint last author).
Original data source: https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.datasets.QM9.html (Adapted from MoleculeNet)
GitHub: https://github.com/facebookresearch/all-atom-diffusion-transformer
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