amino_acids.yml

---
:amino_acids:
  :glycine:
  - "[$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]"
  - "N[CX4H2][CX3](=[OX1])[O,N]"
  :proline:
  - "[$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]"
  - "N1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[O,N]"
:generic_amino_acid: "[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]"
:side_chains:
  :arginine_side_chain:
  - "[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]"
  :aspargine_side_chain:
  - "[CH2X4][CX3](=[OX1])[NX3H2]"
  :aspartate_side_chain:
  - "[CH2X4][CX3](=[OX1])[OH0-,OH]"
  :cysteine_side_chain:
  - "[CH2X4][SX2H,SX1H0-]"
  :glutamate_side_chain:
  - "[CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]"
  :histidine_side_chain:
  - "[CX4H2][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1"
#  - "[CX4H2][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:"
  :isoleucine_side_chain:
  - "[CHX4]([CH3X4])[CH2X4][CH3X4]"
  :leucine_side_chain:
  - "[CH2X4][CHX4]([CH3X4])[CH3X4]"
  :lysine_side_chain:
  - "[CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]"
  :methionine_side_chain:
  - "[CH2X4][CH2X4][SX2][CH3X4]"
  :phenylalanine_side_chain:
  - "[CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1"
  :serine_side_chain:
  - "[CH2X4][OX2H]"
  :threonine_side_chain:
  - "[CHX4]([CH3X4])[OX2H]"
  :tryptophan_side_chain:
  - "[CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12"
  :tyrosine_side_chain:
  - "[CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1"
  :valine_side_chain:
  - "[CHX4]([CH3X4])[CH3X4]"
  :alanine_side_chain:
  - "[CH3X4]"