Backbone

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	2D Structure	Name (3D link)	Notes
5PO		5PO	5′-terminal cap
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
BPO		BPO
PSS		PSS	Phosphorodithioate Charge -1
PS1		PS1 (S)	Thiophosphate (S) Charge -1 Other names: phosphorothioate
PS2		PS2 (R)	Thiophosphate (R) Charge -1 Other names: phosphorothioate
MP1		MP1 (S)	Methylphosphate (S)
MP2		MP2 (R)	Methylphosphate (R)
NS1		NS1 (S)	Thio phosphoramidate (S) Charge -1
NS2		NS2 (R)	Thio phosphoramidate (R) Charge -1
PR1		PR1	Propyl backbone (S)
PR2		PR2	Propyl backbone (R)
IB1		IB1 (S)	Isobutyl backbone (S)
IB2		IB2 (R)	Isobutyl backbone (R)
MO1		MO1 (S)	MOP backbone (S)
MO2		MO2 (R)	MOP backbone (R)
PC1		PC1 (S)	Phosphonoacetate (S) Charge -1
PC2		PC2(R)	Phosphonoacetate (R) Charge -1
MES		MES	Charge -1
MXG		MXG	Methylene phosphonate Charge -1
PN1		PN1 (S)	Phosphoryl guanidine (S)
PN2		PN2 (R)	Phosphoryl guanidine (R)
WX1		MX1 (S)	Mesyl -N-phosphonate (S) Charge -1
WX2		MX2 (R)	Mesyl -N-phosphonate (R) Charge -1
VX1		VX1 (S)	Ethyl-mesyl phosphonate (S)
VX2		VX2 (R)	Ethyl-mesyl phosphonate (R)
XV1		XV1 (S)	Isopropyl mesyl phosphonate (S)
XV2		XV2 (R)	Isopropyl mesyl phosphonate (R)
ZV1		ZV1 (S)	Amine-mesyl phosphonate (S)
ZV2		ZV2 (R)	Amine-mesyl phosphonate (R)

Sugar / Linker

FRAGMENT ID	2D Structure	Name (3D link)	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
aDX		aDX
aXX		aXX
bLD		bLD
bYX		bYX
CET		“gapmer”	https://pubs.acs.org/doi/abs/10.1021/jo502320y
DBO		2′-O-benzyl	built-c2’endo
DDD		DDD
DMP		2′-O-methyl-4-pyridine	built-c2’endo
DMX		DMX	built-c2’endo
DS4		4′-thio-4′-deoxy-cytosine-5′-monophosphate,S4C
DUD		Unlocked nucleic acid	Built C2’endo without OH
GDS		GDS
GMS		GMS
GRS		GRS
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		NAI	Built C2’endo
OME		2’-O-methyl
P3S		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		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
UFB		UFB
UMO		2′-F-4′-OMe uridine 5′-monophosphate
YLX		YLX

A-based modification

FRAGMENT ID	2D Structure	Name (3D link)	Notes
DAA/RAA		Adenine (DAA) / Adenine (RAA)	Ideal module Name HARDCODED Charges from OL3/OL15
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		TMB
TMC		TMC
TIA		N2-trans-isosafrole-dA-adduct

C-based modification

FRAGMENT ID	2D Structure	Name (3D link)	Notes
DCC/RCC		Cytidine (DCC) / Cytidine (RCC)	Ideal module Name HARDCODED Charges from OL3/OL15
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
FMC		FMC
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

G-based modification

FRAGMENT ID	2D Structure	Name (3D link)	Notes
DGG/RGG		Guanine (DGG) / Guanine (RGG)	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
BQG		BQG
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
NMG		NMG
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

T-based modification

FRAGMENT ID	2D Structure	Name (3D link)	Notes
DTT		Cytidine	Ideal module Name HARDCODED Charges from OL3/OL15
APT		alpha-putrescinylthymine
DHT		5,6-dihydrothymine
M3T		3-methylthymine
O4T		O(4)-methylthymine

U-based modification

FRAGMENT ID	2D Structure	Name (3D link)	Notes
RUU		Uracil	Ideal module Name HARDCODED Charges from OL3/OL15
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		BNC
BOC		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		GXT
GYT		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

Other base modification

FRAGMENT ID	2D Structure	Name (3D link)	Notes
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		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		GCL
GC2		GC2