#----------------------------------------------------#
#     amino acids (IUPAC)                            #
#     extended                                       # 
#----------------------------------------------------#

AMINO_ACID ALA A
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB1 HB2 HB3   
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB1 CB-HB2 CB-HB3
      MExchange:    HN
	Alias:        HB HB1 HB2 HB3


AMINO_ACID GLU E
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG2 HG3 CD OE1 OE2 HE2
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG2 CG-HG3 CG-CD CD=OE1 CD-OE2 OE2-HE2
      FExchange:    HE2
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HG HG2 HG3


AMINO_ACID GLN Q
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG2 HG3 CD OE1 NE2 HE21 HE22
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG2 CG-HG3 CG-CD CD=OE1 CD-NE2 NE2-HE21 NE2-HE22
      FExchange:    HE21 H22 	
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HG HG2 HG3
      Alias:        HE2 HE21 HE22


AMINO_ACID ASP D
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG OD1 OD2 HD2
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG=OD1 CG-OD2 OD2-HD2
      FExchange:    HD2
      MExchange:    HN
	Alias:        HB HB2 HB3


AMINO_ACID ASN N
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG OD1 ND2 HD21 HD22
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG=OD1 CG-ND2 ND2-HD21 ND2-HD22
      FExchange:    HD21 HD22
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HD2 HD21 HD22


AMINO_ACID LEU L
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG CD1 HD11 HD12 HD13 CD2 HD21 HD22 HD23
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG CG-CD1 CD1-HD11 CD1-HD12 CD1-HD13 CG-CD2 CD2-HD21 CD2-HD22 CD2-HD23
      MExchange:    HN
	Alias:        HB  HB2 HB3
      Alias:        HD1 HD11 HD12 HD13
      Alias:        HD2 HD21 HD22 HD23
      Alias:        HD HD1 HD2


AMINO_ACID GLY G
	Backbone:     HN N CA HA2 HA3 C O
	Sidechain:   
	Bonds:        HN-N N-CA CA-HA2 CA-HA3 CA-C C=O
      MExchange:    HN
	Alias:        HA HA2 HA3


AMINO_ACID LYS K
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG2 CG-HG3 CG-CD CD-HD2 CD-HD3 CD-CE CE-HE2 CE-HE3 CE-NZ NZ-HZ1 NZ-HZ2 NZ-HZ3
      FExchange:    HZ1 HZ2 HZ3
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HG HG2 HG3
      Alias:        HD HD2 HD3
      Alias:        HE HE2 HE3
      Alias:        HZ HZ1 HZ2 HZ3


AMINO_ACID SER S
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 OG HG
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-OG OG-HG
      FExchange:    HG
      MExchange:    HN
	Alias:        HB HB2 HB3


AMINO_ACID VAL V
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB CB-CG1 CG1-HG11 CG1-HG12 CG1-HG13 CB-CG2 CG2-HG21 CG2-HG22 CG2-HG23
      MExchange:    HN
	Alias:        HG1 HG11 HG12 HG13
      Alias:        HG2 HG21 HG22 HG23
      Alias:        HG HG1 HG2


AMINO_ACID ARG R
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11 HH12 NH2 HH21 HH22 
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG2 CG-HG3 CG-CD CD-HD2 CD-HD3 CD-NE NE-HE NE-CZ CZ-NH1 NH1-HH11 NH1-HH12 CZ-NH2 NH2-HH21 NH2-HH22
      FExchange:    HE HH11 HH12 HH21 HH22
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HG HG2 HG3
      Alias:        HD HD2 HD3
      Alias:        HH1 HH11 HH12
      Alias:        HH2 HH21 HH22
      Alias:        HH HH1 HH2


AMINO_ACID THR T
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB OG1 HG1 CG2 HG21 HG22 HG23
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-OG1 OG1-HG1 CB-HB CB-CG2 CG2-HG21 CG2-HG22 CG2-HG23
      FExchange:    HG1
      MExchange:    HN
	Alias:        HG2 HG21 HG22 HG23


AMINO_ACID PRO P
	Backbone:     N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG2 HG3 CD HD2 HD3
	Bonds:        N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG2 CG-HG3 CG-CD CD-HD2 CD-HD3 CD-N
	Alias:        HB HB2 HB3
      Alias:        HG HG2 HG3
      Alias:        HD HD2 HD3


AMINO_ACID ILE I
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB CG1 HG12 HG13 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB CB-CG2 CG2-HG21 CG2-HG22 CG2-HG23 CB-CG1 CG1-HG12 CG1-HG13 CG1-CD1 CD1-HD11 CD1-HD12 CD1-HD13
      MExchange:    HN
	Alias:        HG2 HG21 HG22 HG23
      Alias:        HG1 HG12 HG13
      Alias:        HD1 HD11 HD12 HD13


AMINO_ACID MET M
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG2 CG-HG3 CG-SD SD-CE CE-HE1 CE-HE2 CE-HE3
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HG HG2 HG3
      Alias:        HE HE1 HE2 HE3


AMINO_ACID PHE F
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG=CD1 CD1-HD1 CG-CD2 CD2-HD2 CD1-CE1 CE1-HE1 CD2=CE2 CE2-HE2 CE1=CZ CZ-HZ CE2-CZ
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HD HD1 HD2
      Alias:        HE HE1 HE2
      Alias:        HR HD HE


AMINO_ACID TYR Y
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG=CD1 CD1-HD1 CG-CD2 CD2-HD2 CD1-CE1 CE1-HE1 CD2=CE2 CE2-HE2 CE1=CZ CE2-CZ CZ-OH OH-HH
      FExchange:    HH
      MExchange:    HN
	Alias:        HB HB2 HB3
      Alias:        HE HE1 HE2
      Alias:        HD HD1 HD2
      Alias:        HR HD HE


AMINO_ACID CYS C
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 SG HG
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-SG SG-HG
      FExchange:    HG
      MExchange:    HN
	Alias:        HB HB2 HB3


AMINO_ACID TRP W
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG CD1 HD1 CD2 NE1 HE1 CE2 CE3 HE3 CZ2 HZ2 CZ3 HZ3 CH2 HH2
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG=CD1 CD1-HD1 CG-CD2 CD1-NE1 NE1-HE1 NE1-CE2 CD2=CE2 CD2-CE3 CE3-HE3 CE2-CZ2 CZ2-HZ2 CE3-CZ3 CZ3-HZ3 CZ2=CH2 CH2-HH2 CZ3-CH2
      FExchange:    HE1
      MExchange:    HN
	Alias:        HB HB2 HB3


AMINO_ACID HIS H
	Backbone:     HN N CA HA C O
	Sidechain:    CB HB2 HB3 CG ND1 HD1 CE1 HE1 NE2 HE2 CD2 HD2
	Bonds:        HN-N N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-ND1 ND1-HD1 ND1-CE1 CE1-HE1 CE1-NE2 NE2-HE2 NE2-CD2 CD2-HD2 CD2-CG
      FExchange:    HD1 HE2
      MExchange:    HN
	Alias:        HB HB2 HB3


AMINO_ACID HYP O
	Backbone:     N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG OD1 HD1 CD2 HD22 HD23     
	Bonds:        N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG CG-OD1 OD1-HD1 CG-CD2 CD2-HD22 CD2-HD23 CD2-N
      FExchange:    HD1
	Alias:        HB HB2 HB3
	Alias:        HD2 HD22 HD23


AMINO_ACID HYB B
	Backbone:     N CA HA C O
	Sidechain:    CB HB2 HB3 CG HG OD1 CD HD2 HD3 CFB HFB3 HFB2 CFG CFD1 HFD1 CFD2 HFD2 CFE1 HFE1 CFE2 HFE2 CFZ HFZ      
	Bonds:        N-CA CA-HA CA-C C=O CA-CB CB-HB2 CB-HB3 CB-CG CG-HG CG-OD1 CG-CD CD-HD2 CD-HD3 CD-N OD1-CFB CFB-HFB3 CFB-HFB2 CFB-CFG CFG=CFD1 CFD1-HFD1 CFD1-CFE1 CFE1-HFE1 CFE1=CFZ CFZ-HFZ CFZ-CFE2 CFE2-HFE2 CFE2=CFD2 CFD2-HFD2 CFD2-CFG	
      Alias:        HB HB2 HB3
	Alias:        HD HD2 HD3
      Alias:        HFB HFB2 HFB3 
	Alias:        HFD HFD1 HFD2
      Alias:        HFE HFE1 HFE2


AMINO_ACID DOW J
	Backbone:     HN N CB HB CA HA C O
	Sidechain:    CG HG CD OD1 OD2 CE HE1 HE2 HE3  
	Bonds:        HN-N N-CB CB-HB CB-CA CB-CG CA-C CA-HA CA-CG C=O CG-HG CG-CD CD=OD1 CD-OD2 OD2-CE CE-HE1 CE-HE2 CE-HE3
	Alias:        HE HE1 HE2 HE3

AMINO_ACID UP U
	Backbone:     HN N CB HB CA HA C O
	Sidechain:    CG HG CD OD1 OD2 CE HE1 HE2 HE3  
	Bonds:        HN-N N-CB CB-HB CB-CA CB-CG CA-C CA-HA CA-CG C=O CG-HG CG-CD CD=OD1 CD-OD2 OD2-CE CE-HE1 CE-HE2 CE-HE3
	Alias:        HE HE1 HE2 HE3

AMINO_ACID BZA Z
	Backbone:     OB CB HB3 HB2
	Sidechain:    CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ
	Bonds:        OB-CB CB-HB3 CB-HB2 CB-CG CG=CD1 CD1-HD1 CD1-CE1 CE1-HE1 CE1=CZ CZ-HZ CZ-CE2 CE2-HE2 CE2=CD2 CD2-HD2 CD2-CG
	Alias:        HD HD1 HD2
      Alias:        HE HE1 HE2




















