Update ligand structures and add new PDB files for A7, A8, and A9 AMP complexes

- Modified ligand SMILES representations in ligands_amp_fep.smi to reflect updated structures.
- Introduced new PDB files for A7, A8, and A9 AMP complexes, enhancing the dataset for molecular simulations.
- Ensured consistency in ligand naming across the new PDB files and the SMILES definitions.

Author: FridrichMethod

examples/openfe/ligands_amp_fep.smi

@@ -1,9 +1,13 @@
 smiles title
-O=C(CCCCNC(OC[C@@H]1[C@]2([C@@]1(CCC#CCC2)[H])[H])=O)OP(OC[C@H]3O[C@@H](n4cnc5c4ncnc5N)[C@H](O)[C@@H]3O)([O-])=O BCN_AMP
-O=C(OP(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n2c3ncnc(N)c3nc2)([O-])=O)CCCCCCCC#C A7_AMP
-O=P(OC(CCCC[C@@H]1CCSS1)=O)(OC[C@H]2O[C@H]([C@@H]([C@@H]2O)O)n3c4ncnc(N)c4nc3)[O-] LA_AMP
-O=P([O-])(OC(CCCCNC(OCC#C)=O)=O)OC[C@H]1O[C@@H](n2cnc3c2ncnc3N)[C@H](O)[C@@H]1O C5_AMP
-[O-]P(OC(CCCCCCC)=O)(OC[C@H]1O[C@@H](n2cnc3c2ncnc3N)[C@H](O)[C@@H]1O)=O OCTA_AMP
-[O-]P(OC[C@H]1O[C@@H](n2cnc3c2ncnc3N)[C@H](O)[C@@H]1O)(OC(CCCCNC(C[C@@]4(O)CCCC=C(CC4))=O)=O)=O ACO_AMP
-[O-]P(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n2c3ncnc(N)c3nc2)(OC(CCCCNC(C[C@@]4(CC/C([H])=C([H])\CCC4)O)=O)=O)=O ACCO_AMP
-[O-]P(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n2c3ncnc(N)c3nc2)(OC(CCCCNC(c4ccc(C#C)cc4)=O)=O)=O P5_AMP
+C#CCCCCCCCC(=O)OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O A7_AMP
+C#CCOC(=O)NCCCCC(=O)OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O C5_AMP
+C#CCOc1ccc(C(=O)NCCCCC(=O)OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](O)[C@@H]2O)cc1 Pb5_AMP
+C#C[C@H]1CC[C@H](C(=O)NCCCCC(=O)OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](O)[C@@H]2O)CC1 Ch5_AMP
+C#Cc1ccc(C(=O)NCCCCC(=O)OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](O)[C@@H]2O)c(O)c1 OP5_AMP
+C#Cc1ccc(C(=O)NCCCCC(=O)OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](O)[C@@H]2O)cc1 P5_AMP
+C#Cc1ccc(C(=O)NCCCCC(=O)OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](O)[C@@H]2O)cc1C MP5_AMP
+C#Cc1cccc(C(=O)NCCCCC(=O)OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](O)[C@@H]2O)c1 M5_AMP
+CCCCCCCC(=O)OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O OCTA_AMP
+Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])OC(=O)CCCCNC(=O)C[C@]2(O)CC/C=C\CCC2)[C@@H](O)[C@H]1O ACCO_AMP
+Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])OC(=O)CCCCNC(=O)OC[C@@H]2[C@@H]3CCC#CCC[C@@H]32)[C@@H](O)[C@H]1O BCN_AMP
+Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])OC(=O)CCCC[C@@H]2CCSS2)[C@@H](O)[C@H]1O LA_AMP