HGA1   : alphatic proton, CH
HGA2   : alphatic proton, CH2
HGA3   : alphatic proton, CH3
HGA4   : alkene proton; RHC=
HGA5   : alkene proton; H2C=CR
HGA6   : aliphatic H on fluorinated C, monofluoro
HGA7   : aliphatic H on fluorinated C, difluoro
HGAAM0 : aliphatic H, NEUTRAL trimethylamine (#)
HGAAM1 : aliphatic H, NEUTRAL dimethylamine (#)
HGAAM2 : aliphatic H, NEUTRAL methylamine (#)
HGP1   : polar H
HGP2   : polar H, +ve charge
HGP3   : polar H, thiol
HGP4   : polar H, neutral conjugated -NH2 group (NA bases)
HGP5   : polar H on quarternary ammonium salt (choline)
HGPAM1 : polar H, NEUTRAL dimethylamine (#)
HGPAM2 : polar H, NEUTRAL methylamine (#)
HGPAM3 : polar H, NEUTRAL ammonia (#)
HGR51  : nonpolar H, neutral 5-mem planar ring C, LJ based on benzene
HGR52  : Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge
HGR53  : nonpolar H, +ve charge HIS he1(+1)
HGR61  : aromatic H
HGR62  : nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom
HGR63  : nonpolar H, NAD+ nicotineamide all ring CH hydrogens
HGR71  : nonpolar H, neutral 7-mem arom ring, AZUL, azulene
HGTIP3 : polar H, TIPS3P WATER HYDROGEN
CG1T1  : alkyn C
CG1N1  : C for cyano group
CG2D1  : alkene; RHC= ; imine C
CG2D1O : double bond carbon adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2. If this cannot be satisfied, we have to introduce a second CG2D1O type, analoguous to CG2DC1 and CG2DC2.
CG2D2  : alkene; H2C=
CG2DC1 : conjugated alkenes, R2C=CR2
CG2DC2 : conjugated alkenes, R2C=CR2
CG2DC3 : conjugated alkenes, H2C=
CG2N1  : conjugated C in guanidine/guanidinium
CG2N2  : conjugated C in amidinium cation
CG2O1  : carbonyl C: amides
CG2O2  : carbonyl C: esters, [neutral] carboxylic acids
CG2O3  : carbonyl C: [negative] carboxylates
CG2O4  : carbonyl C: aldehydes
CG2O5  : carbonyl C: ketones
CG2O6  : carbonyl C: urea, carbonate
CG2O7  : CO2 carbon
CG2R51 : 5-mem ring, his CG, CD2(0), trp
CG2R52 : 5-mem ring, double bound to N, PYRZ, pyrazole
CG2R53 : 5-mem ring, double bound to N and adjacent to another heteroatom, purine C8, his CE1 (0,+1), 2PDO
CG2R61 : aromatic C
CG2R62 : aromatic C, type 2
CG2R63 : 6-mem ring carbonyl carbon
CG2R64 : 6-mem aromatic carbon to amine, between 2 Ns, from c22 FF
CG2R66 : 6-mem aromatic carbon bound to F
CG2R67 : 6-mem aromatic carbon of biphenyl
CG2RC0 : 6/5-mem ring bridging C, guanine C4,C5, trp
CG2R71 : 7-mem ring arom C, AZUL, azulene
CG2RC7 : sp2 ring connection with single bond(!), AZUL, azulene
CG301  : aliphatic C, no hydrogens, neopentane
CG302  : aliphatic C, no hydrogens, trifluoromethyl
CG311  : aliphatic C with 1 H, CH
CG312  : aliphatic C with 1 H, difluoromethyl
CG314  : aliphatic C with 1 H, adjacent to positive N (PROT NTER) (+)
CG321  : aliphatic C for CH2
CG322  : aliphatic C for CH2, monofluoromethyl
CG323  : aliphatic C for CH2, thiolate carbon
CG324  : aliphatic C for CH2, adjacent to positive N (piperidine) (+)
CG331  : aliphatic C for methyl group (-CH3)
CG334  : aliphatic C for methyl group (-CH3), adjacent to positive N (PROT NTER) (+)
CG3AM0 : aliphatic C for CH3, NEUTRAL trimethylamine methyl carbon (#)
CG3AM1 : aliphatic C for CH3, NEUTRAL dimethylamine methyl carbon (#)
CG3AM2 : aliphatic C for CH3, NEUTRAL methylamine methyl carbon (#)
CG3C31 : cyclopropyl carbon
CG3C50 : 5-mem ring aliphatic quaternary C (cholesterol, bile acids)
CG3C51 : 5-mem ring aliphatic CH  (proline CA, furanoses)
CG3C52 : 5-mem ring aliphatic CH2 (proline CB/CG/CD, THF, deoxyribose)
CG3C53 : 5-mem ring aliphatic CH  adjacent to positive N (proline.H+ CA) (+)
CG3C54 : 5-mem ring aliphatic CH2 adjacent to positive N (proline.H+ CD) (+)
CG3RC1 : bridgehead in bicyclic systems containing at least one 5-membered or smaller ring
NG1T1  : N for cyano group
NG2D1  : N for neutral imine/Schiff's base (C=N-R, acyclic amidine, gunaidine)
NG2S0  : N,N-disubstituted amide, proline N (CO=NRR')
NG2S1  : peptide nitrogen (CO=NHR)
NG2S2  : terminal amide nitrogen (CO=NH2)
NG2S3  : external amine ring nitrogen (planar/aniline), phosphoramidate
NG3N1  : N in hydrazine, HDZ1
NG2O1  : NITB, nitrobenzene
NG2P1  : N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium)
NG2R50 : unprotonated neutral 5-mem planar ring, purine N7
NG2R51 : protonated neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused)
NG2R52 : protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP
NG2R53 : amide in 5-memebered ring (slightly pyramidized), 2PDO
NG2R60 : unprotonated neutral 6-mem planar ring, pyr1, pyzn
NG2R61 : protonated neutral 6-mem planar ring imino nitrogen; glycosyl linkage
NG2R62 : unprotonated 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm
NG2RC0 : 6/5-mem ring bridging N, indolizine, INDZ
NG3C51 : secondary sp3 amine in 5-membered ring
NG301  : neutral trimethylamine nitrogen
NG311  : neutral dimethylamine nitrogen
NG321  : neutral methylamine nitrogen
NG331  : neutral ammonia nitrogen
NG3P0  : quarternary N+, choline
NG3P1  : tertiary NH+ (PIP)
NG3P2  : secondary NH2+ (proline)
NG3P3  : primary NH3+, phosphatidylethanolamine
OG2D1  : carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera
OG2D2  : carbonyl O: negative groups: carboxylates, carbonate
OG2D3  : carbonyl O: ketones
OG2D4  : 6-mem heterocycle carbonyl oxygen
OG2D5  : CO2 oxygen
OG2N1  : NITB, nitrobenzene
OG2P1  : =O in phosphate or sulfate
OG2R50 : FURA, furan
OG3R60 : O in 6-mem cyclic enol ether (basically pyran only)
OG301  : ether -O-
OG302  : ester -O-
OG303  : phosphate/sulfate ester oxygen
OG311  : hydroxyl oxygen
OG312  : ionized alcohol oxygen
OG3C51 : 5-mem furanose ring oxygen (ether)
OG3C61 : DIOX, dioxane, ether in 6-membered ring
OGTIP3 : TIPS3P WATER OXYGEN
SG2R50 : THIP, thiophene
SG3O1  : sulfate sulfur
SG301  : sulfur C-S-S-C type
SG302  : thiolate sulfur (-1)
SG311  : sulphur, SH, -S-
CLGA1  : CLET, DCLE, chloroethane, 1,1-dichloroethane
CLGA3  : TCLE, 1,1,1-trichloroethane
CLGR1  : CHLB, chlorobenzene
BRGA1  : BRET, bromoethane
BRGA2  : DBRE, 1,1-dibromoethane
BRGA3  : TBRE, 1,1,1-dibromoethane
BRGR1  : BROB, bromobenzene
IGR1   : IODB, iodobenzene
FGA1   : aliphatic fluorine, monofluoro
FGA2   : aliphatic fluorine, difluoro
FGA3   : aliphatic fluorine, trifluoro
FGP1   : anionic F, for ALF4 AlF4-
FGR1   : aromatic flourine
DUM    : dummy atom
HE     : helium
NE     : neon
PG1    : phosphorus
PG2    : pyrophosphate
PG3    : protonated pyrophosphate
ALG1   : Aluminum, for ALF4, AlF4-

(#) extremE care is required when doing atom typing on compounds that look like this. Use ONLY
on NEUTRAL METHYLAMINE groups, NOT Schiff Bases, but DO use on 2 out of 3 guanidine nitrogens
(+) Includes protonated Shiff base (NG3D5, NG2R52 in 2HPP) but NOT amidinium (NG2R52 in IMIM),
guanidinium nitrogens
