// nucleic acid templates "AGTCaguc" for the sequence builder 20060511 TH
// there are 10 torsions, and the last one is for sidechains...

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

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

CONN:
ATOM 0x08: P 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 0x0008 0x0007 0x0006 0.160 109.6 +0 120.0 D
ATOM 0x11: O 0x0008 0x0007 0x0006 0.160 109.6 +0 240.0 S
ATOM 0x15: H 0x0001 0x0000 0xFF08 0.110 107.6 +2 120.0 S
ATOM 0x16: H 0x0001 0x0000 0xFF08 0.110 107.6 +2 240.0 S
ATOM 0x17: H 0x0002 0x0001 0x0000 0.110 104.1 +3 240.0 S
ATOM 0x18: H 0x0004 0x0003 0x0002 0.110 110.7 +5 120.0 S
ATOM 0x19: H 0x0005 0x0004 0x0003 0.110 116.4 +6 240.0 S
ATOM 0x1A: H 0x0006 0x0005 0x0004 0.110 117.7 +7 120.0 S
BOND: 0x02 0x06 S
END

HEAD_MOD:
ATOM 0x10: O 0x0008 0x0007 0x0006 0.160 109.6 +0 120.0 D
ATOM 0x11: O 0x0008 0x0007 0x0006 0.160 109.6 +0 240.0 S
ATOM 0x15: H 0x0001 0x0000 0xFF08 0.110 107.6 +2 120.0 S
ATOM 0x16: H 0x0001 0x0000 0xFF08 0.110 107.6 +2 240.0 S
ATOM 0x17: H 0x0002 0x0001 0x0000 0.110 104.1 +3 240.0 S
ATOM 0x18: H 0x0004 0x0003 0x0002 0.110 110.7 +5 120.0 S
ATOM 0x19: H 0x0005 0x0004 0x0003 0.110 116.4 +6 240.0 S
ATOM 0x1A: H 0x0006 0x0005 0x0004 0.110 117.7 +7 120.0 S
ATOM 0x1E: H 0x0000 0x0001 0x0002 0.110 109.5 -1 060.0 S	// cap
BOND: 0x02 0x06 S
END

TAIL_MOD:
ATOM 0x15: H 0x0001 0x0000 0xFF08 0.110 107.6 +2 120.0 S
ATOM 0x16: H 0x0001 0x0000 0xFF08 0.110 107.6 +2 240.0 S
ATOM 0x17: H 0x0002 0x0001 0x0000 0.110 104.1 +3 240.0 S
ATOM 0x18: H 0x0004 0x0003 0x0002 0.110 110.7 +5 120.0 S
ATOM 0x19: H 0x0005 0x0004 0x0003 0.110 116.4 +6 240.0 S
ATOM 0x1A: H 0x0006 0x0005 0x0004 0.110 117.7 +7 120.0 S
ATOM 0x1F: H 0x0007 0x0006 0x0005 0.110 109.5 -1 060.0 S	// cap
BOND: 0x02 0x06 S
END

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

RES 0xA1: dA_ A "deoxy-ADENINE"
ATOM 0x20: N 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21: C 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x22: N 0x0021 0x0020 0x0004 0.130 113.9 -1 180.0 D
ATOM 0x23: C 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x24: N 0x0023 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x25: C 0x0024 0x0023 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x26: N 0x0025 0x0024 0x0023 0.133 129.1 -1 000.0 S
ATOM 0x27: C 0x0026 0x0025 0x0024 0.134 118.8 -1 000.0 D
ATOM 0x28: C 0x0027 0x0026 0x0025 0.140 117.4 -1 000.0 S
BOND: 0x22 0x28 S
BOND: 0x23 0x28 D

ATOM 0x32: H 0x0005 0x0004 0x0003 0.110 116.4 +6 120.0 S	// 2' hydrogen

ATOM 0x40: N 0x0027 0x0026 0x0025 0.134 119.1 -1 180.0 S

ATOM 0x60: H 0x0021 0x0020 0x0004 0.110 120.0 -1 000.0 S
ATOM 0x61: H 0x0025 0x0024 0x0023 0.110 120.0 -1 180.0 S
ATOM 0x63: H 0x0040 0x0027 0x0026 0.110 120.0 -1 000.0 S
ATOM 0x64: H 0x0040 0x0027 0x0026 0.110 120.0 -1 180.0 S
END

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

RES 0xA2: dG_ G "deoxy-GUANINE"
ATOM 0x20: N 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21: C 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x22: N 0x0021 0x0020 0x0004 0.130 113.9 -1 180.0 D
ATOM 0x23: C 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x24: N 0x0023 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x25: C 0x0024 0x0023 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x26: N 0x0025 0x0024 0x0023 0.133 129.1 -1 000.0 S
ATOM 0x27: C 0x0026 0x0025 0x0024 0.134 118.8 -1 000.0 S
ATOM 0x28: C 0x0027 0x0026 0x0025 0.140 117.4 -1 000.0 S
BOND: 0x22 0x28 S
BOND: 0x23 0x28 D

ATOM 0x32: H 0x0005 0x0004 0x0003 0.110 116.4 +6 120.0 S	// 2' hydrogen

ATOM 0x40: N 0x0025 0x0024 0x0023 0.134 120.7 -1 180.0 S
ATOM 0x41: O 0x0027 0x0026 0x0025 0.123 119.8 -1 180.0 D

ATOM 0x60: H 0x0021 0x0020 0x0004 0.110 120.0 -1 000.0 S
ATOM 0x62: H 0x0026 0x0025 0x0024 0.110 120.0 -1 180.0 S
ATOM 0x65: H 0x0040 0x0025 0x0024 0.110 120.0 -1 000.0 S
ATOM 0x66: H 0x0040 0x0025 0x0024 0.110 120.0 -1 180.0 S
END

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

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

ATOM 0x32: H 0x0005 0x0004 0x0003 0.110 116.4 +6 120.0 S	// 2' hydrogen

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

ATOM 0x60: H 0x0022 0x0021 0x0020 0.110 120.0 -1 180.0 S
ATOM 0x61: H 0x0042 0x0024 0x0023 0.110 109.5 -1 000.0 S
ATOM 0x62: H 0x0042 0x0024 0x0023 0.110 109.5 -1 120.0 S
ATOM 0x63: H 0x0042 0x0024 0x0023 0.110 109.5 -1 240.0 S
ATOM 0x64: H 0x0025 0x0024 0x0023 0.110 120.0 -1 180.0 S
END

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

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

ATOM 0x32: H 0x0005 0x0004 0x0003 0.110 116.4 +6 120.0 S	// 2' hydrogen

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

ATOM 0x60: H 0x0024 0x0023 0x0022 0.110 120.0 -1 180.0 S
ATOM 0x61: H 0x0025 0x0024 0x0023 0.110 120.0 -1 180.0 S
ATOM 0x62: H 0x0041 0x0023 0x0022 0.110 120.0 -1 000.0 S
ATOM 0x63: H 0x0041 0x0023 0x0022 0.110 120.0 -1 180.0 S
END

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

RES 0xB1: ra_ a "ADENINE"
ATOM 0x20: N 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21: C 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x22: N 0x0021 0x0020 0x0004 0.130 113.9 -1 180.0 D
ATOM 0x23: C 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x24: N 0x0023 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x25: C 0x0024 0x0023 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x26: N 0x0025 0x0024 0x0023 0.133 129.1 -1 000.0 S
ATOM 0x27: C 0x0026 0x0025 0x0024 0.134 118.8 -1 000.0 D
ATOM 0x28: C 0x0027 0x0026 0x0025 0.140 117.4 -1 000.0 S
BOND: 0x22 0x28 S
BOND: 0x23 0x28 D

ATOM 0x30: O 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl
ATOM 0x31: H 0x0030 0x0005 0x0004 0.110 110.0 -1 060.0 S

ATOM 0x40: N 0x0027 0x0026 0x0025 0.134 119.1 -1 180.0 S

ATOM 0x60: H 0x0021 0x0020 0x0004 0.110 120.0 -1 000.0 S
ATOM 0x61: H 0x0025 0x0024 0x0023 0.110 120.0 -1 180.0 S
ATOM 0x63: H 0x0040 0x0027 0x0026 0.110 120.0 -1 000.0 S
ATOM 0x64: H 0x0040 0x0027 0x0026 0.110 120.0 -1 180.0 S
END

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

RES 0xB2: rg_ g "GUANINE"
ATOM 0x20: N 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S
ATOM 0x21: C 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S
ATOM 0x22: N 0x0021 0x0020 0x0004 0.130 113.9 -1 180.0 D
ATOM 0x23: C 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S
ATOM 0x24: N 0x0023 0x0020 0x0004 0.135 126.7 -1 000.0 S
ATOM 0x25: C 0x0024 0x0023 0x0020 0.132 110.8 -1 180.0 D
ATOM 0x26: N 0x0025 0x0024 0x0023 0.133 129.1 -1 000.0 S
ATOM 0x27: C 0x0026 0x0025 0x0024 0.134 118.8 -1 000.0 S
ATOM 0x28: C 0x0027 0x0026 0x0025 0.140 117.4 -1 000.0 S
BOND: 0x22 0x28 S
BOND: 0x23 0x28 D

ATOM 0x30: O 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl
ATOM 0x31: H 0x0030 0x0005 0x0004 0.110 110.0 -1 060.0 S

ATOM 0x40: N 0x0025 0x0024 0x0023 0.134 120.7 -1 180.0 S
ATOM 0x41: O 0x0027 0x0026 0x0025 0.123 119.8 -1 180.0 D

ATOM 0x60: H 0x0021 0x0020 0x0004 0.110 120.0 -1 000.0 S
ATOM 0x62: H 0x0026 0x0025 0x0024 0.110 120.0 -1 180.0 S
ATOM 0x65: H 0x0040 0x0025 0x0024 0.110 120.0 -1 000.0 S
ATOM 0x66: H 0x0040 0x0025 0x0024 0.110 120.0 -1 180.0 S
END

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

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

ATOM 0x30: O 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl
ATOM 0x31: H 0x0030 0x0005 0x0004 0.110 110.0 -1 060.0 S

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

ATOM 0x60: H 0x0022 0x0021 0x0020 0.110 120.0 -1 180.0 S
ATOM 0x61: H 0x0024 0x0023 0x0022 0.110 120.0 -1 180.0 S
ATOM 0x62: H 0x0025 0x0024 0x0023 0.110 120.0 -1 180.0 S
END

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

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

ATOM 0x30: O 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S	// 2' hydroxyl
ATOM 0x31: H 0x0030 0x0005 0x0004 0.110 110.0 -1 060.0 S

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

ATOM 0x60: H 0x0024 0x0023 0x0022 0.110 120.0 -1 180.0 S
ATOM 0x61: H 0x0025 0x0024 0x0023 0.110 120.0 -1 180.0 S
ATOM 0x62: H 0x0041 0x0023 0x0022 0.110 120.0 -1 000.0 S
ATOM 0x63: H 0x0041 0x0023 0x0022 0.110 120.0 -1 180.0 S
END

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

END
