PDB File Index
 
Acids
aceticacid
CHOOH
formicacid
HBr
H3O+
HCL
HCN
picricacid

Bases
NaOH
NH3
NH4+
OH-

Alcohols
methanol
ethanol
phenol

Aldehydes
formaldehyde

Alkanes
methane
ethane
propane
butane
pentane
hexane
heptane
octane
nonane
decane
2-methylpentane
3-methylpentane
2,2-dimethylpropane
2,2-dimethylbutane
2,3-dimethylbutane
2-methylbutane
Alkenes
ethene.pdb
propene.pdb
1-hexene.pdb
(E)-hex-3-ene.pdb
(Z)-hex-3-ene.pdb
1,3-hexadiene.pdb
1,3,5-hexatriene.pdb
butadiene.pdb
Alkynes
ethyne.pdb
propyne.pdb
hex-1-yne.pdb
hex-2-yne.pdb
hex-3-yne.pdb

VSEPR MOLECULES
name formula hybridization geometry
Berilium hydride BeH2 sp linear
Boron trifluoride BF3 sp2 trigonal planar
Water H20 sp3 bent tetrahedral (two lone pairs)
Ammonia NH3 sp3 tetrahedral (one lone pairs)
Methane CH4 sp3 tetrahedral
Phosphorous pentachloride PCl5 sp3d trigonal bipyramidal
Sulfur hexafluoride SF6 sp3d2 octahedral

Biological

AMINO ACIDS
alanine
arginine
asparagine
aspartic acid
cysteine
glutamic acid
glutamine
glycine
histidine
isoleucine
leucine
methione
phenylalanine
proline
serine
threonine
tryptophan
tyrosine
valine

NUCLEIC ACIDS
AMP
ATP
dATP
GMP
GTP
CMP
TMP
DNA helix (1 turn)

SUGARS
2-amino-2-deoxy-D-glucose
6-deoxy-D-glucose
D-fructose
D-galactose
D-glucose
D-mannose
D-xylose
L-glucose
straightglucose
sucrose

MISCELLANEOUS
1crn
3cro
caffeine
carotene
chlorphyll
carbon monoxide
carbon dioxide
cytochrome
DPPC
hemoglobin
NAD+
NADH
NADP+
NADPH
nicotinamide (niacin)
oxygen
pheophytin
phosynthetic reaction center
quinone
vitamin C


others