libghemical-data 3.0.0-4.1build2 / usr / share / libghemical / 3.0.0 / builder / nucleic.txt

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// nucleic acid templates "AGTCaguc" for the sequence builder 20070201 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 torPREV = torNEXT (symmetry).

// all hydrogen atoms have been left out from this file, and they will be
// added later based on valences and formal charges.

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

MAIN:
TORDEF 0x0000 0xFF08 0xFF07 0xFF06	// +0
TORDEF 0x0001 0x0000 0xFF08 0xFF07	// +1
TORDEF 0x0002 0x0001 0x0000 0xFF08	// +2
TORDEF 0x0003 0x0002 0x0001 0x0000	// +3
TORDEF 0x0004 0x0003 0x0002 0x0001	// +4
TORDEF 0x0005 0x0004 0x0003 0x0002	// +5
TORDEF 0x0006 0x0005 0x0004 0x0003	// +6
TORDEF 0x0007 0x0006 0x0005 0x0004	// +7
ATOM 0x00 O +0 0xFF08 0xFF07 0xFF06 0.160 101.5 +0 000.0 S (-C(-C([-O-C-C-C-])))
ATOM 0x01 C +0 0x0000 0xFF08 0xFF07 0.144 119.0 +1 000.0 S (-O,-C([-O-C-C-C-]))
ATOM 0x02 C +0 0x0001 0x0000 0xFF08 0.152 110.0 +2 000.0 S ([-O-C-C-C-])
ATOM 0x03 O +0 0x0002 0x0001 0x0000 0.146 108.9 +3 000.0 S ([-C-C-C-C-])
ATOM 0x04 C +0 0x0003 0x0002 0x0001 0.142 110.0 +4 000.0 S (-N,[-O-C-C-C-])
ATOM 0x05 C +0 0x0004 0x0003 0x0002 0.153 107.8 +5 000.0 S ([-C-O-C-C-])
ATOM 0x06 C +0 0x0005 0x0004 0x0003 0.153 101.9 +6 000.0 S (-O,[-C-O-C-C-])
ATOM 0x07 O +0 0x0006 0x0005 0x0004 0.142 107.4 +7 000.0 S (-C([-C-O-C-C-]))
END

CONN:
TORDEF 0x0008 0x0007 0x0006 0x0005	// +8
ATOM 0x08 P +1 0x0007 0x0006 0x0005 0.160 119.1 +8 000.0 S (-O,-O,=O,-O)
END

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

HEAD:
(-C(-C([-O-C-C-C-]),nB=2),nB=1)
END

TAIL:
(-C(-C(-C(-N)),-C(-C(-O(-P)),-O)),nB=1)
END

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

BODY_MOD:
ATOM 0x10 O +0 0x0008 0x0007 0x0006 0.160 109.6 +0 120.0 D	// not really tor +0 here!!!
ATOM 0x11 O -1 0x0008 0x0007 0x0006 0.160 109.6 +0 240.0 S	// not really tor +0 here!!!
BOND 0x02 0x06 S
END

HEAD_MOD:
ATOM 0x10 O +0 0x0008 0x0007 0x0006 0.160 109.6 +0 120.0 D	// not really tor +0 here!!!
ATOM 0x11 O -1 0x0008 0x0007 0x0006 0.160 109.6 +0 240.0 S	// not really tor +0 here!!!
BOND 0x02 0x06 S
END

TAIL_MOD:
BOND 0x02 0x06 S
END

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

RES 0xA1: dA_ A "deoxy-ADENINE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 D	// D in A/a
ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S
ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D
BOND 0x21 0x26 D
BOND 0x28 0x26 S

ATOM 0x40 N +0 0x0025 0x0024 0x0023 0.134 119.1 -1 180.0 S
END

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

RES 0xA2: dG_ G "deoxy-GUANINE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 S	// S in G/g
ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S
ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D
BOND 0x21 0x26 D
BOND 0x28 0x26 S

ATOM 0x40 N +0 0x0023 0x0022 0x0021 0.134 120.7 -1 180.0 S
ATOM 0x41 O +0 0x0025 0x0024 0x0023 0.123 119.8 -1 180.0 D
END

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

RES 0xA3: dT_ T "deoxy-THYMINE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 S
ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D
BOND 0x20 0x25 S

ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D
ATOM 0x41 O +0 0x0023 0x0022 0x0021 0.122 118.1 -1 180.0 D
ATOM 0x42 C +0 0x0024 0x0023 0x0022 0.150 117.6 -1 180.0 S
END

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

RES 0xA4: dC_ C "deoxy-CYTOSINE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 D
ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D
BOND 0x20 0x25 S

ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D
ATOM 0x41 N +0 0x0023 0x0022 0x0021 0.132 117.8 -1 180.0 S
END

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

RES 0xB1: ra_ a "ADENINE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 D	// D in A/a
ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S
ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D
BOND 0x21 0x26 D
BOND 0x28 0x26 S

ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl

ATOM 0x40 N +0 0x0025 0x0024 0x0023 0.134 119.1 -1 180.0 S
END

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

RES 0xB2: rg_ g "GUANINE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 S	// S in G/g
ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S
ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D
BOND 0x21 0x26 D
BOND 0x28 0x26 S

ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl

ATOM 0x40 N +0 0x0023 0x0022 0x0021 0.134 120.7 -1 180.0 S
ATOM 0x41 O +0 0x0025 0x0024 0x0023 0.123 119.8 -1 180.0 D
END

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

RES 0xB3: ru_ u "URACILE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 S
ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D
BOND 0x20 0x25 S

ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl

ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D
ATOM 0x41 O +0 0x0023 0x0022 0x0021 0.122 118.1 -1 180.0 D
END

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

RES 0xB4: rc_ c "CYTOSINE"
TORDEF 0x0021 0x0020 0x0004 0x0003	// +9
ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S
ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S
ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S
ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 D
ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S
ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D
BOND 0x20 0x25 S

ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl

ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D
ATOM 0x41 N +0 0x0023 0x0022 0x0021 0.132 117.8 -1 180.0 S
END

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

END

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