Backbone fragment library
Assume that when it is a stereo-isomer, the fragment will have the final number 1 for the ( S ) configuration and 2 for the ( R ) configuration.
| FRAGMENT ID | Structure | Name | Notes |
| DPO |  | DPO | Standard dimethyl phosphate (regular backbone) Charge -1 Atom types from OL15/21 |
| RPO |  | RPO | Standard dimethyl phosphate (regular backbone) Charge -1 Atom types from OL3 |
| PSS |  | PSS | Phosphorodithioate Charge -1 |
| PS1 PS2 |  | PS1 (S) PS2 (R) | Thiophosphate Charge -1 Other names: phosphorothioate |
| MP1 MP2 |  | MP1 (S) MP2 (R) | Methylphosphate |
| NS1 NS2 |  | NS1 (S) NS2 (R) | Thio phosphoramidate Charge -1 |
| PR1 PR2 |  | PR1 (S) PR2 (R) | Propyl backbone |
| IB1 IB2 |  | IB1 (S) IB2 (R) | Isobutyl backbone |
| MO1 MO2 |  | MO1 (S) MO2 (R) | MOP backbone |
| PC1PC2 |  | PC1 (S) PC2 (R) | Phosphonoacetate Charge -1 |
| MXG |  | MXG | Methylene phosphonate Charge -1 |
| PN1 PN2 |  | PN1 (S) PN2 (R) | Phosphoryl guanidine |
| WX1 WX2 |  | MX1 (S) MX2 (R) | Mesyl phosphonate Charge -1 |
| VX1 VX2 |  | VX1 (S) VX2 (R) | Ethyl-mesyl phosphonate |
| XV1 XV2 |  | XV1 (S) XV2 (R) | Isopropyl mesyl phosphonate |
| ZV1 ZV2 |  | ZV1 (S) ZV2 (R) | Amine-mesyl phosphonate |
Base fragment library
| FRAGMENT ID | New 2D | Name | Notes |
| Canonical Nucleobases | |||
| DAA/RAA |  | Adenine | Ideal module Name HARDCODED Charges from OL3/OL15 |
| DCC/RCC |  | Cytidine | Ideal module Name HARDCODED Charges from OL3/OL15 |
| DGG/RCC |  | Guanine | Ideal module Name HARDCODED Charges from OL3/OL15 |
| DTT |  | Thymine | Ideal module Name HARDCODED Charges from OL3/OL15 |
| RUU |  | Uracil | Ideal module Name HARDCODED Charges from OL3/OL15 |
| Modified Adenine | |||
| 1DP |  | N1-deaza-adenosine-5′-monophosphate | |
| A6A |  | N6-acetyladenosine | |
| BII |  | Inosine | |
| C6A |  | N6-carbamoylmethyladenine | |
| CTA |  | cyclic N6-threonylcarbamoyladenosine | |
| DMA |  | 2,8-dimethyladenosine | |
| G6A |  | N6-glycinylcarbamoyladenosine | |
| E6A |  | N-ethylpiperidine-6’triazole modified adenine | +1 charge |
| E7A |  | N-ethylpiperidine-7’-EAA triazole modified adenine | +1 charge |
| F6A |  | N6-formyladenosine | |
| H6A |  | N6-hydroxynorvalylcarbamoyladenosine | |
| HNA |  | 6-hydroxyaminopurine | |
| HMA |  | N6-hydroxymethyladenosine | |
| HTA |  | Hydroxy-N6-threonylcarbamoyladenosine | |
| I6A |  | N6-isopentenyladenosine | |
| IGA |  | Isoguanosine | |
| IOA |  | N6-(cis-hydroxyisopentenyl)adenosine | |
| M1A |  | 1-methyladenosine | |
| M2A |  | 2-methyladenosine | |
| M3A |  | 3-methyladenosine | |
| M4A |  | 4-methyladenosine | |
| M6A |  | N6,N6-dimethyladenosine | |
| M7A |  | 7-methyladenosine | |
| M8A |  | 8-methyladenosine | |
| MIA |  | 2-methylthio-N6-isopentenyl-adenosine-5′-monophosphate | |
| MSA |  | 2-methylthio-N6-methyladenosine | |
| MTA |  | 2-methylthio cyclic N6-threonylcarbamoyladenosine | |
| M1I |  | 1-methylinosine | |
| M3I |  | 3-methylhypoxyanthine | |
| M7I |  | 7-methylhypoxanthine | |
| N1A |  | N1-protonated adenosine | +1 charge |
| N2A |  | 2-aminoadenine | |
| N6A |  | N6-methyladenosine | |
| NHA |  | 2-amino-6-hydroxyaminopurine | |
| S6A |  | 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine | |
| SIA |  | 2-methylthio-N6-isopentenyladenosine | |
| SHA |  | 2-methylthio-N6-hydroxynorvalylcarbamoyladenosine | |
| STA |  | 2-methylthio-N6-threonylcarbamoyladenosine | |
| T6A |  | N6-methyl-N6-threonylcarbamoyladenosine | |
| TCA |  | N6-threonylcarbamoyladenosine-5′-monophosphate | |
| TMA |  | 2- methylthiomethylenethio-N6-isopentenyl-adenosine | |
| TMB |  | ||
| TMC |  | ||
| TIA |  | N2-trans-isosafrole-dA-adduct | |
| Modified Cytidine | |||
| 5FC |  | 5-fluorocytidine 5′-(dihydrogen phosphate) | |
| A4C |  | N4-acetylcytidine | |
| B5C |  | 5-bromocytidine 5′-(dihydrogen phosphate) | |
| BIC |  | isocytidine-5′-monophosphate | |
| BPC |  | agmatidine | |
| C5C |  | 5-carboxylcytosine | |
| E3C |  | 3-ethylcytosine | |
| F5C |  | 5-formylcytosine | |
| G5C |  | 5-glucosylmethylcytosine | |
| H5C |  | 5-hydroxymethylcytosine | |
| K2C |  | 2-lysidine | |
| M2C |  | 2-O-methylcytosine | |
| M3C |  | 3-methylcytosine | |
| M4C |  | N4,N4-dimethylcytidine | |
| M5C |  | 5’-methylcytidine | |
| N3C |  | N3-protonated cytidine | Charge +1 |
| N4C |  | N4-methylcytosine | |
| N5C |  | 5-nitrocytidine 5′-(dihydrogen phosphate) | Charge +1 |
| NEC |  | 3,N4-ethenocytosine | |
| O5C |  | 5-hydroxycytidine | |
| PPC |  | 6’-phenylpyrrolo-cytosine | |
| RYC |  | 5′-3,6-dihydrocytidylic acid | |
| S2C |  | 2-thiocytidine | |
| FRC |  | 5-Formyl dC III CE | |
| FQC |  | Ac-5-Me-dC-CE | |
| FSC |  | 5-Formyl-dC-CE | |
| FUC |  | 5-Hydroxymethyl-dC II-CE | |
| FVC |  | 5-I-dC-CE | 5′-Dimethoxytrityl-N-benzoyl-5-iodo-2′-deoxyCytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| FWC |  | 5-Br-dC-CE | 5′-Dimethoxytrityl-N-benzoyl-5-bromo-2′-deoxyCytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| FYC |  | 5-Carboxy-dC-CE | 5′-Dimethoxytrityl-N-benzoyl-5-ethylcarboxy-2′-deoxyCytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| FZC |  | 5-Hydroxymethyl-dC-CE | 5′-Dimethoxytrityl-N-benzoyl-5-cyanoethoxy-methyl-2′-deoxyCytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| FTC |  | 5-Me-dC-CE | 5′-Dimethoxytrityl-N-benzoyl-5-methyl-2′-deoxyCytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| Modified Guanine | |||
| TIG |  | N2-trans-isosafrole-dG-adduct | |
| 1NE |  | 1,N2-ethenoguanine | |
| 2NE |  | N2,3-ethenoguanine | |
| 2MG |  | N2,N2-dimethylguanosine | |
| 7MG |  | N2,7-dimethylguanosine | +1 charge |
| 8OG |  | 8-oxoguanine | |
| ADG |  | 7-amido-7-deazaguanosine | |
| BGM |  | 8-bromo-2′-deoxyguanosine-5′-monophosphate | |
| C7G |  | 7-cyano-7-carbaguanine | |
| CEG |  | N2-carboxyethylguanine | |
| ISG |  | Iso-guanine | |
| M1G |  | 1-methylguanine | |
| M2G |  | 2-methylguanine | |
| M3G |  | 3-methylguanine | |
| M6G |  | 6-O-methylguanine | |
| M7G |  | 7-methylguanine | +1 charge |
| PQG |  | 7-aminomethyl-7-carbaguanine | |
| TMG |  | N2,N2,7-trimethylguanosine | +1 charge |
| ACG |  | archaeosine | |
| WYB |  | wybutosine | |
| HWB |  | hydroxywybutosine | |
| IPG |  | peroxywybutosine | |
| OHW |  | undermodified hydroxywybutosine | |
| OMW |  | methylated undermodified hydroxywybutosine | |
| PYW |  | wybutosine[C15(S)]-5′-monophosphate | |
| IMG |  | wyosine | |
| IG2 |  | isowyosine | |
| I4G |  | 4-demethylwyosine | |
| MWG |  | methylwyosine | |
| YW5 |  | 7-aminocarboxypropylwyosine methyl ester | |
| YW7 |  | 7-aminocarboxypropylwyosine | |
| YW8 |  | 7-aminocarboxypropyl-demethylwyosine | |
| QUE |  | queuosine | |
| EOQ |  | epoxyqueuosine | |
| GAQ |  | galactosyl-queuosine | |
| GLQ |  | glutamyl-queuosine | |
| MQG |  | mannosyl-queuosine | |
| XAN |  | Xantine | |
| BRG |  | 8-Br-dG-CE Phosphoramidite | |
| BSG |  | 8-Amino-dA-CE Phosphoramidite | |
| BTH |  | 7-Deaza-8-aza-dG-CE Phosphoramidite | |
| BTG |  | 7-deaza-dG-CE | |
| BUG |  | 8-Amino-dG-CE | 5′-Dimethoxytrityl-N2,N8-bis(dimethylaminomethylidine)-8-amino-2′-deoxyGuanosine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| Modified Thymine | |||
| APT |  | alpha-putrescinylthymine | |
| DHT |  | 5,6-dihydrothymine | |
| M3T |  | 3-methylthymine | |
| O4T |  | O(4)-methylthymine | |
| Modified Uracil | |||
| 5BU |  | 5-bromo-uridine | |
| 6BU |  | 6-bromo-uridine | |
| I6U |  | 6-iodouridine | |
| I5U |  | 5-iodouridine | |
| 5CU |  | 5-cyanomethyluridine | |
| SSU |  | 2-thiouridine | |
| 5SU |  | 5-methyl-2-thiouridine | |
| CGU |  | 5-carboxymethylaminomethyl-2-geranylthiouridine | |
| C5U |  | 5-carboxymethyluridine | |
| CHU |  | 5-carboxyhydroxymethyluridine | |
| CMU |  | 5-carbamoylmethyluridine | |
| CNU |  | 5-carboxymethylaminomethyl-2-thiouridine | |
| COU |  | 5-carboxymethylaminomethyluridine | |
| CSU |  | 5-carboxymethyl-2-thiouridine | |
| FDU |  | 5’-fluoro-uridine | |
| FHU |  | (5S,6R)-5-fluoro-6-hydroxy-pseudouridine-5′-monophosphate | |
| GSU |  | 2-geranylthiouridine | |
| H5U |  | 5-hydroxyuridine | |
| HMU |  | 5-(carboxyhydroxymethyl)uridine methyl ester | |
| HOU |  | 5-carbamoylhydroxymethyluridine | |
| BNC |  | ||
| BOC |  | ||
| INU |  | 5-(isopentenylaminomethyl)uridine | |
| ISU |  | 5-(isopentenylaminomethyl)-2-thiouridine | |
| M3U |  | 3-methyluridine | |
| M5U |  | 5-methyluridine | |
| M6U |  | uracil-6-ylacetic acid: DNAmod | |
| MCU |  | 5-methoxycarbonylmethyluridine | |
| MGU |  | 5-methylaminomethyl-2-geranylthiouridine | |
| MMU |  | 5-methoxycarbonylmethyl-2-thiouridine | |
| MNU |  | 5-methylaminomethyluridine | |
| MOU |  | 5-methoxyuridine | |
| MSU |  | 5-methylaminomethyl-2-thiouridine | |
| N3U |  | 3-(3-amino-3-carboxypropyl)uridine | |
| N5U |  | 5-aminomethyluridine | |
| NCD |  | 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine | |
| NGU |  | 5-aminomethyl-2-geranylthiouridine | |
| NMU |  | 5-carbamoylmethyl-2-thiouridine | |
| NSU |  | 5-aminomethyl-2-thiouridine | |
| O5U |  | uridine 5-oxyacetic acid | |
| OMU |  | uridine 5-oxyacetic acid methyl ester | |
| S2U |  | 2’-thiouridine | |
| S4U |  | 4-thiouridine | |
| T5U |  | 5-taurinomethyluridine | |
| TSU |  | 5-taurinomethyl-2-thiouridine | |
| B8N |  | (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid | |
| BDD |  | Dihydrouridine | |
| M5D |  | 5-methyldihydrouridine | |
| PUU |  | Pseudouridine | |
| C3Y |  | 3-(3-amino-3-carboxypropyl)pseudouridine | |
| MCY |  | 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine | |
| M1Y |  | 1-methylpseudouridine | |
| M3Y |  | 3-methylpseudouridine | |
| GXT |  | ||
| GYT |  | ||
| TIP |  | Tipiracil | |
| SFF |  | Saflufenacil | |
| OAU |  | Orotic acid | |
| OBU |  | Orotate | |
| EMU |  | Emivirine | |
| PVU |  | 6-methyl-2-thiouracil | |
| PSU |  | 6-ethyl-2-thiouracil | |
| PTU |  | 6-propyl-2-thiouracil | |
| PWU |  | 6-butyl-2-thiouracil | |
| 5NU |  | 5-nitrouracil | |
| RAU |  | 5-cyclohexane-uracil | |
| RBU |  | 5-phenyl-uracil | |
| RCU |  | p-methylphenyl-5-uracil | |
| RDU |  | p-ethylphenyl-5-uracil | |
| REU |  | p-propyl phenyl-5 uracil | |
| RFU |  | C=4 | |
| RGU |  | C=5 | |
| Unclassified Modifications | |||
| 1RN |  | (E)-N-{[4-oxo-1-(5-O-phosphono-beta-D-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycin | |
| 3TD |  | (1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol | |
| 2PR |  | 2-amino-9-[2-deoxyribofuranosyl]-9H-purine-5′-monophosphate | |
| 5NI |  | 5’-nitroindole | |
| 7AT |  | 1-(5-O-phosphono-beta-D-ribofuranosyl)-3-(1H-1,2,3-triazol-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine | |
| 8AZ |  | 8-aza-nebularine-5′-monophosphate | |
| A7C |  | 3-[1-(4-bromophenyl)-1H-1,2,3-triazol-4-yl]-1-[5-O-(trihydroxy-lambda~5~-phosphanyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine | |
| A7E |  | 3-ethynyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine | |
| B8H |  | [(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate | |
| BRF |  | 2’,4’-difluorotoluyl ribonucleoside | |
| F4F |  | ||
| C4J |  | (5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol | |
| MTU |  | 9-beta-D-ribofuranosyl-9H-purin-2-amine | |
| N6G |  | ((2R,3S,4R,5S)-5-(2,6-diamino-9H-purin-9-YL)-3,4-dihydroxy-tetrahydrofuran-2-YL)methyl dihydrogen phosphate | |
| NF2 |  | (1S)-1,4-anhydro-1-(2,4-difluoro-5-methylphenyl)-5-O-phosphono-D-ribitol | |
| O2Z |  | [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-diazanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxyphosphinic acid | |
| ONE |  | 1-(beta-D-ribofuranosyl)-pyridin-4-one-5′-phosphate | |
| P5P |  | purine riboside-5′-monophosphate | |
| PYO |  | 1-(beta-D-ribofuranosyl)-pyrimidin-2-one-5′-phosphate | |
| PYY |  | D-ribofuranosyl-benzene-5′-monophosphate | |
| GCL |  | ||
| GC2 |  | ||
Sugar/linkers
| FRAGMENT ID | Structure | Name | Notes |
| DC2 |  | Standard deoxyribose | Atom types from OL15 |
| 2AD |  | 2’amino-2’deoxy | |
| A5L |  | (2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl) | 2’FANA, built C2’endo |
| A5O |  | arabinose | *note the 2’OH group points “up” instead of “down” |
| A9Z |  | 2′-(4-ethyl-1H-1,2,3-triazol-1-yl) | |
| AF2 |  | 2′-deoxy-2′-fluoro | Built C3’endo |
| CET |  | “gapmer” | https://pubs.acs.org/doi/abs/10.1021/jo502320y |
| DBO |  | 2′-O-benzyl | built-c2’endo |
| DMP |  | 2′-O-methyl-4-pyridine | built-c2’endo |
| DMX |  | built-c2’endo | |
| DS4 |  | 4′-thio-4′-deoxy-cytosine-5′-monophosphate,S4C | |
| DUD |  | Unlocked nucleic acid | Built C2’endo without OH |
| LNA |  | Locked nucleic acid | Built C2’endo (but C3’endo also optimizes to C2’endo) |
| M5M |  | 2′-(N-acetamide)-cytidine-5′-monophosphate | |
| MOE |  | 2′-O-methoxyethyl | built-C3’endo only |
| NAI |  | Built C2’endo | |
| OME |  | 2’-O-methyl | |
| P3S |  | Sulfonyl ester on O2′, Built C2’endo | |
| RBO |  | 2′-O-benzyl | Built C3’endo |
| RC3 |  | Standard ribose sugar | C3’endo, atom types from OL3 |
| RMP |  | 2′-O-methyl-4-pyridine | Built C3’endo |
| RMX |  | 2-amino-9-(6-deoxy-5-O-phosphono-beta-D-allofuranosyl)-3,9-dihydro-6H-purin-6-one | Built C3’endo |
| RS4 |  | S4C, 4′-thio-4′-deoxy-cytosine-5′-monophosphate | |
| RUR |  | Unlocked nucleic acid | Built c3’endo with 2’OH |
| TAE |  | Triazole aryl ether on O2′, Built with C2’endo | |
| U4M |  | 1-{2,5-dideoxy-2-fluoro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione | Methyl group on C4’, fluorine on C2’ |
| U5M |  | 1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione | Methyl group on C5’, fluorine on C2’ |
| U5R |  | 1-(2,6-dideoxy-2-fluoro-5-O-phosphono-beta-D-allofuranosyl)pyrimidine-2,4(1H,3H)-dione | D-enantiomer version of U5M |
| UMO |  | 2′-F-4′-OMe uridine 5′-monophosphate |