#
# This file describes the connectivity of amino acid sidechains.
# The format uses commas to separate 4-character, PDB-style atom names
# and semi-colons to separate different polylines (like P in kinemage format).
# It uses the new PDB v3.X nomenclature.
#
aa.mc = " N  , CA , C  , O  , OXT"
aa.hy = " N  , H  ; CA , HA ; N  , H1 ; N  , H2 ; N  , H3 ;"

na.mc = " P  , OP1; P  , OP2; P  , O5', C5', C4', O4'; C4', C3', O3', C3', C2'; C2', O2'; O4', C1'; C2', C1', O3'"
na.hy = " C5', H5'; C5',H5''; C4', H4'; C3', H3'; C2', H2'; C2',H2''; O2',HO2'; O3',HO3'; C1', H1'; O5',HO5'"

dg.sc = " N9 , C8 , N7 , C5 , C6 , O6 ; C6 , N1 , C2 , N2 ; C2 , N3 , C4 ; N9 , C4 ; C5 , C4 "
dg.hy = " C8 , H8 ; N1 , H1 ; N2 , H21; N2 , H22; O6 , H69"

da.sc = " N9 , C8 , N7 , C5 , C6 , N6 ; C6 , N1 , C2 , N3 , C4 ; N9 , C4 ; C5 , C4 "
da.hy = " C8 , H8 ; N1 , H11; N6 , H61; N6 , H62"

dc.sc = " N1 , C2 , O2 ; C2 , N3 , C4 , N4 ; C4 , C5 , C6 ; N1 , C6 "
dc.hy = " N4 , H41; N4 , H42; C5 , H5 ; C6 , H6 "

dt.sc = " N1 , C2 , O2 ; C2 , N3 , C4 , O4 ; C4 , C5 , C7 ; N1 , C6 ; C5 , C6 "
dt.hy = " N3 , H3 ; C7 , H71; C7 , H72; C7 , H73; C6 , H6 "

gly.sc = ""
gly.hy = " CA , HA2; CA , HA3"
ala.sc = " CA , CB "
ala.hy = " CB , HB1; CB , HB2; CB , HB3"
val.sc = " CA , CB , CG1; CB , CG2"
val.hy = " CB , HB ; CG1,HG11; CG1,HG12; CG1,HG13; CG2,HG21; CG2,HG22; CG2,HG23"
leu.sc = " CA , CB , CG , CD1; CG , CD2"
leu.hy = " CB , HB2; CB , HB3; CG , HG ; CD1,HD11; CD1,HD12; CD1,HD13; CD2,HD21; CD2,HD22; CD2,HD23"
ile.sc = " CA , CB , CG1, CD1; CB , CG2"
ile.hy = " CB , HB ; CG1,HG11; CG1,HG12; CG1,HG13; CG2,HG21; CG2,HG22; CG2,HG23; CD1,HD11; CD1,HD12; CD1,HD13"
pro.sc = " CA , CB , CG , CD , N  "
pro.hy = " CB , HB2; CB , HB3; CG , HG2; CG , HG3; CD , HD2; CD , HD3;"

phe.sc = " CA , CB , CG , CD1, CE1, CZ , CE2, CD2, CG "
phe.hy = " CB , HB2; CB , HB3; CD1, HD1; CD2, HD2; CE1, HE1; CE2, HE2; CZ , HZ "
tyr.sc = " CA , CB , CG , CD1, CE1, CZ , CE2, CD2, CG ; CZ , OH "
tyr.hy = " CB , HB2; CB , HB3; CD1, HD1; CD2, HD2; CE1, HE1; CE2, HE2; OH , HH "
trp.sc = " CA , CB , CG , CD1, NE1, CE2, CD2, CG ; CD2, CE3, CZ3, CH2, CZ2, CE2"
trp.hy = " CB , HB2; CB , HB3; CD1, HD1; NE1, HE1; CZ2, HZ2; CH2, HH2; CE3, HE3; CZ3, HZ3"

ser.sc = " CA , CB , OG "
ser.hy = " CB , HB2; CB , HB3; OG , HG "
thr.sc = " CA , CB , OG1; CB , CG2"
thr.hy = " CB , HB ; OG1, HG1; CG2,HG21; CG2,HG22; CG2,HG23"
cys.sc = " CA , CB , SG "
cys.hy = " CB , HB2; CB , HB3; SG , HG "
met.sc = " CA , CB , CG , SD , CE "
met.hy = " CB , HB2; CB , HB3; CG , HG2; CG , HG3; CE , HE1; CE , HE2; CE , HE3"
mse.sc = " CA , CB , CG ,SED , CE ; CG ,SE  , CE "
mse.hy = " CB , HB2; CB , HB3; CG , HG2; CG , HG3; CE , HE1; CE , HE2; CE , HE3"

lys.sc = " CA , CB , CG , CD , CE , NZ "
lys.hy = " CB , HB2; CB , HB3; CG , HG2; CG , HG3; CD , HD2; CD , HD3; CE , HE2; CE , HE3; NZ , HZ1; NZ , HZ2; NZ , HZ3"
his.sc = " CA , CB , CG , ND1, CE1, NE2, CD2, CG "
his.hy = " CB , HB2; CB , HB3; ND1, HD1; CE1, HE1; NE2, HE2; CD2, HD2"
arg.sc = " CA , CB , CG , CD , NE , CZ , NH1; CZ , NH2"
arg.hy = " CB , HB2; CB , HB3; CG , HG2; CG , HG3; CD , HD2; CD , HD3; NE , HE ; NH1,HH11; NH1,HH12; NH2,HH21; NH2,HH22"

asp.sc = " CA , CB , CG , OD1; CG , OD2"
asp.hy = " CB , HB2; CB , HB3"
asn.sc = " CA , CB , CG , OD1; CG , ND2"
asn.hy = " CB , HB2; CB , HB3; ND2,HD21; ND2,HD22"
gln.sc = " CA , CB , CG , CD , OE1; CD , NE2"
gln.hy = " CB , HB2; CB , HB3; CG , HG2; CG , HG3; NE2,HE21; NE2,HE22"
glu.sc = " CA , CB , CG , CD , OE1; CD , OE2"
glu.hy = " CB , HB2; CB , HB3; CG , HG2; CG , HG3"

