libghemical-data 3.0.0-2ubuntu1 / usr / share / libghemical / 3.0.0 / builder / amino.txt

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// amino acid templates "ARNDCQEGHILKMFPSTWYV" for the sequence builder 20070202 TH

// currently there are hard-coded fixes for these issues:
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
// * atoms 0x10 and 0x11 use incorrect torsion indices (see the index checks);
//   however this does not cause problems when psiPREV = psiNEXT (alpha-helix).
//
// * amino -NH3 group (is made???) by default (using formal_charge).
//
// * identification of met groups in LEU and VAL residues.
//
// * the 2nd ring in TRP residues can be identified in two different ways:
//
// this is the "correct way" (shown below):
//
//    23   29 - 28 - 27
//   /               |
//  22               |
//   \               |
//    21 - 24 - 25 - 26
//   /
// 20
//
// this is the "incorrect way" (shown below):
//
//    23   25 - 26 - 27
//   /     |         |
//  22     |         |
//   \     |         |
//    21 - 24   29 - 28
//   /
// 20

// most of the hydrogens have been left out from this file, and they will be
// added later based on valences and formal charges. only those hydrogens that
// either define the side chain (the GLY case) or define a unique conformation
// have been added here. the hydrogen numbering starts from 0x60.

// the formal charges are set by sb::Build() but are ignored by sb::Identify().

////////////////////////////////////////////////////////////////////////////////////////////////////

MAIN:
TORDEF 0x0000 0xFF02 0xFF01 0xFF00	// +0 psiPREV
TORDEF 0x0001 0x0000 0xFF02 0xFF01	// +1 omega
TORDEF 0x0002 0x0001 0x0000 0xFF02	// +2 phiNEXT
ATOM 0x00 N +0 0xFF02 0xFF01 0xFF00 0.134 116.6 +0 000.0 S (-C(-C(=O)))
ATOM 0x01 C +0 0x0000 0xFF02 0xFF01 0.145 121.9 +1 000.0 S (-N,-C(=O))
ATOM 0x02 C +0 0x0001 0x0000 0xFF02 0.152 111.1 +2 000.0 S (-C(-N),=O)
END

CONN:
END

////////////////////////////////////////////////////////////////////////////////////////////////////

HEAD:
(-C(-C(=O,-N)),nB=1)			// -NH3 or -NH2
(-C(-C(=O,-N),[-N-C-C-C-]),nB=2)	// proline at the beginning of sequence
(-C(-C(=O,-N)),-C(=O,-C(nB=1)))		// acetyl group (ACE) at the beginning of sequence
END

// this is an ACE-group at the beginning of sequence:
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
//   CH3
//   |
// O=C
//   |
//   N-H
//   |
//   C(alpha)
//   |

TAIL:
(-C(-N(-C(=O))),=O,-O(-H))		// -COOH
(-C(-N(-C(=O))),=O,-O)			// -COO (ionic or with a hydrogen missing)
(-C(-N(-C(=O))),=O,-N(-C(nB=1)))	// N-methyl group (NME) at the end of sequence
END

// this is an NME-group at the end of sequence:
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
//   |
//   C(alpha
//   |
//   C=O
//   |
// H-N
//   |
//   CH3

////////////////////////////////////////////////////////////////////////////////////////////////////

BODY_MOD:
ATOM 0x10 O +0 0x0002 0x0001 0x0000 0.123 120.5 +0 180.0 D	// not really tor +0 here!!!
END

HEAD_MOD:
ATOM 0x10 O +0 0x0002 0x0001 0x0000 0.123 120.5 +0 180.0 D	// not really tor +0 here!!!
END

TAIL_MOD:
ATOM 0x10 O +0 0x0002 0x0001 0x0000 0.123 120.5 +0 180.0 D	// not really tor +0 here!!!
ATOM 0x11 O -1 0x0002 0x0001 0x0000 0.123 119.5 +0 000.0 S	// not really tor +0 here!!!
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x01: ALA A "ALANINE"
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x02: ARG R "ARGININE (charged)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0023 0x0022 0x0021 0x0020	// +5
TORDEF 0x0024 0x0023 0x0022 0x0021	// +6
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S
ATOM 0x23 N +0 0x0022 0x0021 0x0020 0.148 111.0 +5 000.0 S
ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.133 123.0 +6 000.0 S
ATOM 0x25 N +1 0x0024 0x0023 0x0022 0.133 118.0 -1 000.0 D
ATOM 0x26 N +0 0x0024 0x0023 0x0022 0.133 118.0 -1 180.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x03: ASN N "ASPARAGINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 000.0 D
ATOM 0x23 N +0 0x0021 0x0020 0x0001 0.134 116.6 +4 180.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x04: ASP D "ASPARTIC ACID (charged)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 000.0 D
ATOM 0x23 O -1 0x0021 0x0020 0x0001 0.123 120.5 +4 180.0 S
END

RES 0x04: ASH D "ASPARTIC ACID (neutral)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0060 0x0023 0x0021 0x0020	// +5
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 000.0 D
ATOM 0x23 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 180.0 S
ATOM 0x60 H +0 0x0023 0x0021 0x0020 0.110 120.0 +5 000.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// the disulphide bridged cysteine residues will be identified
// as CYX residues, because there is no hydrogen that is required
// for CYS ; the formal charges are not tested by sb::Identify().

RES 0x05: CYS C "CYSTEINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0060 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 S +0 0x0020 0x0001 0x0000 0.181 116.0 +3 000.0 S
ATOM 0x60 H +0 0x0021 0x0020 0x0001 0.110 109.5 +4 000.0 S
END

RES 0x05: CYX C "CYSTEINE (charged)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 S -1 0x0020 0x0001 0x0000 0.181 116.0 +3 000.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x06: GLN Q "GLUTAMINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0023 0x0022 0x0021 0x0020	// +5
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S
ATOM 0x23 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 000.0 D
ATOM 0x24 N +0 0x0022 0x0021 0x0020 0.134 116.6 +5 180.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x07: GLU E "GLUTAMIC ACID (charged)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0023 0x0022 0x0021 0x0020	// +5
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S
ATOM 0x23 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 000.0 D
ATOM 0x24 O -1 0x0022 0x0021 0x0020 0.123 120.5 +5 180.0 S
END

RES 0x07: GLH E "GLUTAMIC ACID (neutral)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0023 0x0022 0x0021 0x0020	// +5
TORDEF 0x0060 0x0024 0x0022 0x0021	// +6
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S
ATOM 0x23 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 000.0 D
ATOM 0x24 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 180.0 S
ATOM 0x60 H +0 0x0024 0x0022 0x0021 0.110 120.0 +6 000.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x08: GLY G "GLYCINE"
ATOM 0x60 H +0 0x0001 0x0000 0xFF02 0.110 109.5 +2 240.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x09: HIE H "HISTIDINE (e-form)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0001 0.139 122.5 +4 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 108.0 -1 180.0 D
ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.131 109.0 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.136 110.0 -1 000.0 S
ATOM 0x60 H +0 0x0024 0x0023 0x0022 0.110 120.0 -1 180.0 S
BOND 0x21 0x25 D
END

RES 0x09: HID H "HISTIDINE (d-form)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0001 0.139 122.5 +4 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 108.0 -1 180.0 S
ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.131 109.0 -1 000.0 D
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.136 110.0 -1 000.0 S
ATOM 0x60 H +0 0x0022 0x0021 0x0020 0.110 120.0 -1 000.0 S
BOND 0x21 0x25 D
END

RES 0x09: HIP H "HISTIDINE (charged)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0001 0.139 122.5 +4 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 108.0 -1 180.0 S
ATOM 0x24 N +1 0x0023 0x0022 0x0021 0.131 109.0 -1 000.0 D
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.136 110.0 -1 000.0 S
ATOM 0x60 H +0 0x0022 0x0021 0x0020 0.110 120.0 -1 000.0 S
ATOM 0x61 H +0 0x0024 0x0023 0x0022 0.110 120.0 -1 180.0 S
BOND 0x21 0x25 D
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// this is a CHIRAL amino acid!
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

RES 0x0A: ILE I "ISOLEUCINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S
ATOM 0x23 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 240.0 S	// met
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// the -CH3 groups must be always assigned in the
// following way (the H atom is projected down):
//
// 22    23     ; the 20-22-23 turn is clockwise.
//   \  /       ; this is an IUPAC rule...
//    21
//    |
//    20

RES 0x0B: LEU L "LEUCINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S	// 1st met
ATOM 0x23 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 120.0 S	// 2nd met
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x0C: LYS K "LYSINE (charged)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0023 0x0022 0x0021 0x0020	// +5
TORDEF 0x0024 0x0023 0x0022 0x0021	// +6
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.153 109.5 +5 000.0 S
ATOM 0x24 N +1 0x0023 0x0022 0x0021 0.147 109.5 +6 000.0 S
ATOM 0x60 H +0 0x0024 0x0023 0x0022 0.110 109.5 -1 060.0 S
ATOM 0x61 H +0 0x0024 0x0023 0x0022 0.110 109.5 -1 180.0 S
ATOM 0x62 H +0 0x0024 0x0023 0x0022 0.110 109.5 -1 300.0 S
END

RES 0x0C: LYN K "LYSINE (neutral)"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0023 0x0022 0x0021 0x0020	// +5
TORDEF 0x0024 0x0023 0x0022 0x0021	// +6
TORDEF 0x0060 0x0024 0x0023 0x0022	// +7
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.153 109.5 +5 000.0 S
ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.147 109.5 +6 000.0 S
ATOM 0x60 H +0 0x0024 0x0023 0x0022 0.110 109.5 +7 000.0 S
ATOM 0x61 H +0 0x0024 0x0023 0x0022 0.110 109.5 +7 120.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x0D: MET M "METHIONINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0023 0x0022 0x0021 0x0020	// +5
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S
ATOM 0x22 S +0 0x0021 0x0020 0x0001 0.181 110.0 +4 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.178 100.5 +5 000.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// has 2-fold symmetry so that...
// ...d-atoms are equivalent and
// ...e-atoms are equivalent

RES 0x0E: PHE F "PHENYLALANINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.140 120.0 +4 000.0 D	// d
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.140 120.0 -1 180.0 S	// e
ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.140 120.0 -1 000.0 D
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.140 120.0 -1 000.0 S	// e
ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 120.0 -1 000.0 D	// d
BOND 0x21 0x26 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// the torsion +3 value should be set to about 15.0 deg!
// the torsion +4 value should be set to about 0.0 deg!

RES 0x0F: PRO P "PROLINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.150 106.0 +4 000.0 S
BOND 0x00 0x22 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

RES 0x10: SER S "SERINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0060 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S
ATOM 0x21 O +0 0x0020 0x0001 0x0000 0.143 109.5 +3 000.0 S
ATOM 0x60 H +0 0x0021 0x0020 0x0001 0.110 109.5 +4 000.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// this is a CHIRAL amino acid!
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

RES 0x11: THR T "THREONINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0060 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S
ATOM 0x21 O +0 0x0020 0x0001 0x0000 0.143 109.5 +3 000.0 S
ATOM 0x22 C +0 0x0020 0x0001 0x0000 0.150 109.5 +3 240.0 S	// met
ATOM 0x60 H +0 0x0021 0x0020 0x0001 0.110 109.5 +4 000.0 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

//    23   29 - 28 - 27		this is how
//   /               |		the builder
//  22               |		makes the
//   \               |		2nd ring.
//    21 - 24 - 25 - 26
//   /
// 20

RES 0x12: TRP W "TRYPTOPHAN"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.134 127.0 +4 000.0 D
ATOM 0x23 N +0 0x0022 0x0021 0x0020 0.143 107.0 -1 180.0 S
ATOM 0x24 C +0 0x0021 0x0020 0x0001 0.140 127.5 +4 180.0 S
ATOM 0x25 C +0 0x0024 0x0021 0x0020 0.140 129.5 -1 000.0 S
ATOM 0x26 C +0 0x0025 0x0024 0x0021 0.141 117.0 -1 180.0 D
ATOM 0x27 C +0 0x0026 0x0025 0x0024 0.135 122.0 -1 000.0 S
ATOM 0x28 C +0 0x0027 0x0026 0x0025 0.139 121.0 -1 000.0 D
ATOM 0x29 C +0 0x0028 0x0027 0x0026 0.140 116.0 -1 000.0 S
BOND 0x23 0x29 S
BOND 0x24 0x29 D
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// has 2-fold symmetry so that...
// ...d-atoms are equivalent and
// ...e-atoms are equivalent

RES 0x13: TYR Y "TYROSINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
TORDEF 0x0022 0x0021 0x0020 0x0001	// +4
TORDEF 0x0060 0x0027 0x0024 0x0023	// +5
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S
ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.140 120.0 +4 000.0 D	// d
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.140 120.0 -1 180.0 S	// e
ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.140 120.0 -1 000.0 D
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.140 120.0 -1 000.0 S	// e
ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 120.0 -1 000.0 D	// d
ATOM 0x27 O +0 0x0024 0x0023 0x0022 0.136 120.0 -1 180.0 S
ATOM 0x60 H +0 0x0027 0x0024 0x0023 0.110 120.0 +5 000.0 S
BOND 0x21 0x26 S
END

////////////////////////////////////////////////////////////////////////////////////////////////////

// the -CH3 groups must be always assigned in the
// following way (the H atom is projected down):
//
// 21    22     ; the 01-21-22 turn is clockwise.
//   \  /       ; this is an IUPAC rule...
//    20
//    |
//    01

RES 0x14: VAL V "VALINE"
TORDEF 0x0021 0x0020 0x0001 0x0000	// +3
ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S
ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S	// 1st met
ATOM 0x22 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 120.0 S	// 2nd met
END

////////////////////////////////////////////////////////////////////////////////////////////////////

END

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