aDAbe a-D-Abep.pdb a-abequose
aAbe a-D-Abep.pdb a-abequose
aDAll a-D-Allp.pdb a-D-allose
aDAllf a-D-Allf.pdb a-D-allose-f(furanose form)
aDAlt a-D-Altp.pdb a-D-altrose
aDAlt6d a-D-Altp6d.pdb 6-deoxy-a-D-altrose
aDAra a-D-Arap.pdb a-D-arabinose
aDAraf a-D-Araf.pdb a-D-arabofuranose
aDEry a-D-Eryf.pdb a-D-erythrose_(4_carbon_aldose)
aDFru a-D-Frup.pdb a-D-fructopyranose
aDFruf a-D-Fruf.pdb a-D-fructofuranose
aDFuc a-D-Fucp.pdb a-D-fucose
aDFucnac a-D-FucNAc.pdb
aDGal a-D-Galp.pdb a-D-galactopyranose
aDGalf a-D-Galf.pdb a-D-galactofuranose
aDGal23PyR aDGal23PyR.pdb -a-D-Galp23(R)Pyr
aDGal23PyS aDGal23PyS.pdb -a-D-Galp23(S)Pyr
aDGal46PyA aDGal46PyA.pdb a-D-pyruvyl-galactopyranose(axial)
aDGal46PyE aDGal46PyE.pdb a-D-pyruvyl-galactopyranose(equatorial)
aDGalA a-D-GalpA.pdb
aDGlc a-D-Glcp.pdb a-D-glucopyranose
aDGlc23PyR aDGlc23PyR.pdb -a-D-Glcp23(R)Pyr
aDGlc23PyS aDGlc23PyS.pdb -a-D-Glcp23(S)Pyr
aDGlc46PyA aDGlc46PyA.pdb
aDGlc46PyE aDGlc46PyE.pdb
aDGlcA a-D-GlcpA.pdb
aDGlc6A a-D-GlcpA.pdb
aDGlc4d a-D-Glc4d.pdb
aDGlcnac a-D-GlcpNAc.pdb
aDHep L-a-D-Hep.pdb
aDIdo a-D-Idop.pdb a-D-idopyranose
aDIdoA aidoa_olgun.pdb
aDKdo a-D-Kdop.pdb 3-Deoxy-D-manno-oct-2-ulosonic_acid
aKdo a-D-Kdop.pdb 3-Deoxy-D-manno-oct-2-ulosonic_acid
aDLyx a-D-Lyxp.pdb a-D-lyxopyranose
aDLyxf a-D-Lyxf.pdb a-D-lyxofuranose
aDMan a-D-Manp_gg.pdb a-D-manopyranose
aDMan23PyR aDMan23PyR.pdb -a-D-Manp23(R)Pyr
aDMan23PyS aDMan23PyS.pdb -a-D-Manp23(S)Pyr
aDMan46PyA aDMan46PyA.pdb a-D-pyruvyl-mannopyranose(axial)
aDMan46PyE aDMan46PyE.pdb a-D-pyruvyl-mannopyranose(equatorial)
aDManA a-D-ManpA.pdb
aDManf a-D-Manf.pdb a-D-manofuranose
aDMannac a-D-ManNAc.pdb
xDMdrvnac a-D-Mal.pdb
aDMurnac a-D-MurNAc.pdb N-Acetylmuramic_acid
aDNeu5Ac a-D-NeuNAc.pdb sialic_acid
aDNeu5ac aDNeuNAc.pdb 
aNeu5Ac a-D-NeuNAc.pdb sialic_acid
aDNeu5ac8Ac aDNeu5ac8Ac.pdb
aDJunk junk.pdb
aDPar a-D-Par.pdb a-paratose(3,6-dideoxy_D-glucose) 
aPar a-D-Par.pdb a-paratose(3,6-dideoxy_D-glucose) 
aDQui a-D-Quip.pdb a-quinovose(6-deoxy-D-glucose)
aQui a-D-Quip.pdb a-quinovose(6-deoxy-D-glucose)
aDRha a-D-Rhap.pdb a-D-rhamnose(6-deoxy-mannose)
aDRib a-D-Ribp.pdb a-D-ribose
aDTal a-D-Talp.pdb a-D-talose
aDTyv a-D-Tyvp.pdb a-tyvelose(3,6-dideoxy_mannose)
aTyv a-D-Tyvp.pdb a-tyvelose(3,6-dideoxy_mannose)
aDRibf a-D-Ribf.pdb a-D-ribofuranose
aDXyl a-D-Xylp.pdb a—D-xylose(6-deoxy-glucose)
aDXylf a-D-Xylf.pdb a-D-xylofuranose
aLAll a-L-Allp.pdb a-L-allose
aLAlt a-L-Altp.pdb a-L-altrose
aLAlt6d a-L-Altp6d.pdb 6-deoxy-a-L-altrose
aLAra a-L-Arap.pdb a-L-arabinose
aLAraf a-L-Araf.pdb a-L-arabofuranose
aLCol a-L-Colp.pdb a-colitose(3,6-dideoxy_L-galactose)
aCol a-L-Colp.pdb a-colitose(3,6-dideoxy_L-galactose)
aLFuc a-L-Fucp.pdb a-L-fucose
aLGal a-L-Galp.pdb a-L-galactose
aLGalA a-L-GalpA.pdb
aLGlcA a-L-GlcpA.pdb
aLGul a-L-Gulp.pdb a-L-gulose
aLIdo a-L-Ido.pdb a-L-idopyranose
aLIdoA a-L-IdoA.pdb
aLIdod aL6dIdo_4C1.pdb a-L-6-deoxy-Idose
aLIdod_1C4_ aL6dIdo_1C4.pdb a-L-6-deoxy-Idose(1C4_ring_conformation)
aLIdod_4C1_ aL6dIdo_4C1.pdb a-L-6-deoxy-Idose(4C1_ring_conformation)
aLLyx a-L-Lyxp.pdb a-L-lyxose
aLMan a-L-Manp.pdb a-L-mannose
aLManA a-L-ManpA.pdb
aLPneNAc a-L-PneNAc.pdb 2-acetamido-2,6-dideoxy-l-talose(pneumosamine)
aLRha a-L-Rhap.pdb a-rhamnose(6-deoxy_L-mannose)
xLRha a-L-Rha_hack.pdb
aLRib a-L-Ribp.pdb a-L-ribose
aLTal a-L-Talp.pdb a-L-talose
aLXyl a-L-Xylp.pdb a-L-xylose
bDAbe b-D-Abep.pdb b-abequose
bAbe b-D-Abep.pdb b-abequose
bDAll b-D-Allp.pdb b-D-allose
bDAllf b-D-Allf.pdb b-D-allose(furanose_form)
bDAlt b-D-Altp.pdb b-D-altrose
bDAlt6d b-D-Altp6d.pdb 6-deoxy-b-D-altrose
bDAra b-D-Arap.pdb b-D-arabinose
bDAraf b-D-Araf.pdb b-D-arabofuranose
bDEryf b-D-Eryf.pdb b-D-erythose(furanose_from)
bDFru b-D-Frup.pdb b-D-Fructose
bDFruf b-D-Fruf.pdb b-D-fructose(furanose_form)
bDFuc b-D-Fucp.pdb b-D-fucose
bDGal b-D-Galp.pdb b-D-galactose
bDGal23PyR bDGal23PyR.pdb -b-D-Galp23(R)Pyr
bDGal23PyS bDGal23PyS.pdb -b-D-Galp23(S)Pyr
bDGal46PyA bDGal46PyA.pdb b-D-pyruvyl-galactosepyranose(axial)
bDGal46PyE bDGal46PyE.pdb b-D-pyruvyl-galactosepyranose(equatorial)
bDGalA b-D-GalpA.pdb
bDGalf5Ac6Ac 
bDGalf b-D-Galf.pdb b-D-galactose(furanose_form)
bDGalnacOld b-D-GalNAc.pdb
bDGalnac galnac_olgun.pdb
#bDGalNAc galnac_olgun.pdb 
bDGalNAcA bDGalNAcA.pdb
bDGlc b-D-Glcp.pdb b-D-Glucose
bDGlc23PyR bDGlc23PyR.pdb -b-D-Glcp23(R)Pyr
bDGlc23PyS bDGlc23PyS.pdb -b-D-Glcp23(S)Pyr
bDGlc46PyA bDGlc46PyA.pdb b-D-pyruvyl-glucopyranose(axial)
bDGlc46PyE bDGlc46PyE.pdb b-D-pyruvyl-glucopyranose(equatorial)
bDGlcA bglca_olgun.pdb
bDGlc6A b-D-GlcpA.pdb
bDGlc3OAH b-D-Glc3OAH.pdb b-D-Glc3OAH(protonated)
bDGlc3OA b-D-Glc3OA.pdb b-D-Glc3OA(unprotonated)
bDGlcf b-D-Glcf.pdb b-D-glucose(furanose_form)
#bDGlcNAc b-D-GlcNAc_olgun.pdb
bDGlcNAc b-D-GlcNAc_alt.pdb
bDGlcnac b-D-GlcNAc.pdb
bDIdo b-D-Idop.pdb b-D-idose
bDKdo b-D-Kdop.pdb 3-Deoxy-D-manno-oct-2-ulosonic_acid
bKdo b-D-Kdop.pdb 3-Deoxy-D-manno-oct-2-ulosonic_acid
bDLyx b-D-Lyxp.pdb b-L-lyxose
bDLyxf b-D-Lyxf.pdb b-L-lyoxse(furanose_form)
bDMan b-D-Manp.pdb b-D-mannose
bDMan23PyR bDMan23PyR.pdb -b-D-Manp23(R)Pyr
bDMan23PyS bDMan23PyS.pdb -b-D-Manp23(S)Pyr
bDMan46PyA bDMan46PyA.pdb b-D-pyruvyl-mannopyranose(axial)
bDMan46PyE bDMan46PyE.pdb b-D-pyruvyl-mannopyranose(equatorial)
bDManA bDManA.pdb
bDManf b-D-Manf.pdb b-D-mannose(furanose_form)
#bDManNAc6Gly bDManNAc6Gly.pdb
bDMannac b-D-ManNAc.pdb
#bDMan6Gly bDMan6Gly.pdb
#bDManNAcA bDManNAcA.pdb
bDMurnac b-D-MurNAc.pdb N-Acetylmuramic_acid
bDPar b-D-Parp.pdb b-paratose(3,6-dideoxy_glucose) 
bPar b-D-Parp.pdb b-paratose(3,6-dideoxy_glucose) 
bDQui b-D-Quip.pdb b-quinovose(6-deoxy_D-glucose)
bQui b-D-Quip.pdb b-quinovose(6-deoxy_D-glucose)
bDRib b-D-Ribp.pdb b-D-ribose
bDRibf b-D-Ribf.pdb b-D-ribose (furanose_form)
bDSug b-D-Sug.pdb 2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose	
bDTal b-D-Talp.pdb b—D-talose
bDTyv b-D-Tyvp.pdb b-tyvelose(3,6-dideoxy_mannose)
bTyv b-D-Tyvp.pdb b-tyvelose(3,6-dideoxy_mannose)
bDXyl b-D-Xylp.pdb b-D-xylose
bDXylf b-D-Xylf.pdb b-D-xylose (furanose_form)
bLAll b-L-Allp.pdb b-L-allose
bLAlt b-L-Altp.pdb B-L-altrose
bLAlt6d b-L-Altp6d.pdb 6-deoxy-b-L-altrose
bLAra b-L-Arap.pdb b-L-arabinose
bLAraf b-L-Araf.pdb b-L-arabinose(furanose_form)
bLCol b-L-Colp.pdb b-colitose(3,6-dideoxy_L-galactose)
bCol b-L-Colp.pdb b-colitose(3,6-dideoxy_L-galactose)
bLFuc b-L-Fucp.pdb b-L-fucose
bLGal b-L-Galp.pdb b-L-galactose
bLGalA b-L-GalpA.pdb
bLGlc b-L-Glcp.pdb b-L-glucose
bLGlcA b-L-GlcpA.pdb
bLIdo b-L-Ido.pdb b-L-idose
bLIdoA b-L-IdoA.pdb
bLIdod bL6dIdo_4C1.pdb b-L-6-deoxy-Idose
bLIdod_1C4_ bL6dIdo_1C4.pdb b-L-6-deoxy-Idose(1C4_ring_conformation)
bLIdod_4C1_ bL6dIdo_4C1.pdb b-L-6-deoxy-Idose(4C1_ring_conformation)
bLLyx b-L-Lyxp.pdb b-L-lyxose
bLMan b-L-Manp.pdb b-L-mannose
bLRha b-L-Rhap.pdb b-rhamnose(6-deoxy_L-mannose)
bRha b-L-Rhap.pdb b-rhamnose(6-deoxy_L-mannose)
bLRib b-L-Ribp.pdb b-L-ribose
bLTal b-L-Talp.pdb b-L-talose
bLXyl b-L-Xylp.pdb b-L-xylose
———LINEAR_ALDITOLS——— + one_form
DGlcol D-glucitol.pdb D-glucitol
DGro D-glycerol.pdb D-glycerol
LGro1P GL1P.pdb
Gro3P G3P_2R.pdb
LGro3P G3P_2R.pdb
DGro1P G3P_2R.pdb
Gro1P GL1P.pdb
LGro1P GL1P.pdb
DGro2P D-glycerol2P.pdb 2P-linked-D-glycerol
Gro2P D-glycerol2P.pdb
NDGroA ND-GroA.pdb N-linked-D-glycerol-A
NLGroA NL-GroA.pdb N-linked-L-glycerol-A
DRibol D-ribitol.pdb D-ribitol
DRibol5P D-ribitol5-phosphate.pdb
Ribol D-ribitol.pdb D-ribitol
Ribol5P D-ribitol5-phosphate.pdb
Ribol1P D-ribitol1-phosphate.pdb

——other molecules——
CycHex13diol cyclohexane13diol.pdb Cyclohexane-1,3-diol
———Substituents——— + position
NAc NAc.pdb NAcetyl_substituent
NAm NAm.pdb N-amindino_substituent
NFo NFo.pdb N-formyl_substituent
NFoZ NFo.pdb N-formyl_substituent
NFoE NFoE.pdb N-formyl_substituent
NS NS.pdb NS_substituent
N NH3.pdb Nitrogen_substituent 
Ac Ac.pdb acetyl_substituent
A A.pdb uronic_acid_substituent:POSITION_6_only
OMe OMe.pdb O-Methyl_substituent
Me OMe.pdb O_methyl
PEtN PEtN.pdb phosphoethanolamine_substituent
PO4 PO4.pdb phosphate_substituent
SO4 SO4.pdb sulphate_substituent
Asn Asn.pdb Asparagine-N-linked
Ser Ser.pdb Serine-O-linked
Thr Thr.pdb Threonine-O-linked
6Gly glycine.pdb Glycine
#Hacky stuff
#CRM strepBIII_CRM.pdb 
#CRM strepBIII_CRM_GSKversion_4carb.pdb
CRM CRM_builder.pdb
#CRM CRM_fix.pdb CORRECTED_CRM_WITH _COMPLETE_IMPORTANT_LYSINES
#CRM CRM_4ae0_original.pdb CRM_RECOMBINANT_DIPHTHERIA_TOXIN
lysin Lys_frag.pdb
prot Prot.pdb