PDB Chemical Component 5HT

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for 5HT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O5' C5' 1.418 1.429
O5' HO5' 0.949 0.967
C5' C4' 1.511 1.530
C5' H5' 1.116 1.090
C5' H5'' 1.115 1.090
C4' O4' 1.472 1.446
C4' C3' 1.512 1.548
C4' H4' 1.114 1.090
O4' C1' 1.431 1.437
C3' O3' 1.425 1.429
C3' C2' 1.513 1.548
C3' H3' 1.116 1.089
O3' HO3' 0.950 0.967
C2' C1' 1.533 1.541
C2' H2' 1.115 1.090
C2' H2'' 1.114 1.090
C1' N1 1.529 1.464
C1' H1' 1.114 1.090
N1 C2 1.272 1.341
N1 C6 1.541 1.464
C2 O2 1.207 1.215
C2 N3 1.402 1.343
N3 C4 1.412 1.346
N3 H3 1.020 0.970
C4 O4 1.214 1.214
C4 C5 1.513 1.506
C5 C5M 1.531 1.530
C5 O5 1.400 1.429
C5 C6 1.596 1.531
C5M H71 1.114 1.090
C5M H72 1.115 1.089
C5M H73 1.115 1.090
O5 HO5 0.950 0.967
C6 H61 1.115 1.089
C6 H62 1.116 1.090

Bond Angles for 5HT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C5' O5' HO5' 111.4 106.8
O5' C5' C4' 111.4 109.5
O5' C5' H5' 111.5 109.4
O5' C5' H5'' 111.5 109.5
C4' C5' H5' 111.5 109.4
C4' C5' H5'' 111.5 109.5
C5' C4' O4' 107.6 110.7
C5' C4' C3' 115.9 110.6
C5' C4' H4' 104.6 110.6
H5' C5' H5'' 98.9 109.5
O4' C4' C3' 103.3 103.6
O4' C4' H4' 117.0 110.5
C4' O4' C1' 109.8 106.9
C3' C4' H4' 108.9 110.7
C4' C3' O3' 114.2 110.9
C4' C3' C2' 104.2 102.1
C4' C3' H3' 111.3 111.0
O4' C1' C2' 106.3 107.4
O4' C1' N1 113.1 109.9
O4' C1' H1' 108.4 109.8
O3' C3' C2' 113.2 110.9
O3' C3' H3' 101.9 110.8
C3' O3' HO3' 114.2 106.8
C2' C3' H3' 112.3 110.9
C3' C2' C1' 105.2 104.2
C3' C2' H2' 113.8 110.5
C3' C2' H2'' 113.8 110.5
C1' C2' H2' 113.8 110.5
C1' C2' H2'' 113.9 110.4
C2' C1' N1 106.8 109.9
C2' C1' H1' 114.5 109.9
H2' C2' H2'' 96.6 110.5
N1 C1' H1' 108.0 109.9
C1' N1 C2 120.4 119.6
C1' N1 C6 115.7 119.5
C2 N1 C6 123.6 120.9
N1 C2 O2 121.2 119.2
N1 C2 N3 120.6 121.6
N1 C6 C5 108.5 109.5
N1 C6 H61 112.6 109.5
N1 C6 H62 112.5 109.4
O2 C2 N3 118.1 119.2
C2 N3 C4 123.8 121.0
C2 N3 H3 117.7 119.5
C4 N3 H3 118.4 119.5
N3 C4 O4 120.9 120.0
N3 C4 C5 116.1 120.0
O4 C4 C5 123.0 120.0
C4 C5 C5M 109.5 109.5
C4 C5 O5 108.7 109.5
C4 C5 C6 110.3 109.2
C5M C5 O5 109.7 109.6
C5M C5 C6 109.3 109.5
C5 C5M H71 109.4 109.4
C5 C5M H72 112.2 109.5
C5 C5M H73 112.2 109.4
O5 C5 C6 109.4 109.5
C5 O5 HO5 108.7 106.7
C5 C6 H61 112.6 109.5
C5 C6 H62 112.6 109.4
H71 C5M H72 112.3 109.5
H71 C5M H73 112.2 109.5
H72 C5M H73 98.3 109.5
H61 C6 H62 97.9 109.5

Torsion Angles for 5HT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C4' C5' O5' H5' 234.8 119.9
C4' C5' O5' H5'' 125.3 239.9
O5' C5' C4' O4' 348.4 65.7
O5' C5' C4' C3' 103.4 180.0
O5' C5' C4' H4' 223.3 303.0
H5' C5' O5' H5'' 250.5 120.0
HO5' O5' C5' C4' 180.1 180.0
HO5' O5' C5' H5' 305.3 60.0
HO5' O5' C5' H5'' 54.8 300.0
C4' C5' O5' HO5' 180.1 180.0
O5' C5' C4' H5' 125.3 240.1
O5' C5' C4' H5'' 234.7 120.1
H5' C5' C4' H5'' 109.4 240.0
O4' C4' C5' C3' 245.0 245.7
O4' C4' C5' H4' 125.1 122.8
C5' C4' O4' C1' 153.2 158.5
C3' C4' C5' H4' 240.1 237.1
C5' C4' C3' O3' 85.1 86.2
C5' C4' C3' C2' 209.2 204.4
C5' C4' C3' H3' 330.4 322.5
H5' C5' O5' HO5' 305.3 60.0
O5' C5' H5' C4' 234.8 120.0
O5' C5' H5' H5'' 117.4 240.0
C4' C5' H5' H5'' 242.6 120.0
H5' C5' C4' O4' 223.2 185.7
H5' C5' C4' C3' 338.2 299.9
H5' C5' C4' H4' 98.1 62.9
H5'' C5' O5' HO5' 54.8 300.0
O5' C5' H5'' C4' 125.3 239.9
O5' C5' H5'' H5' 242.6 120.0
C4' C5' H5'' H5' 117.3 240.1
H5'' C5' C4' O4' 113.7 305.6
H5'' C5' C4' C3' 228.8 59.9
H5'' C5' C4' H4' 348.7 182.9
O4' C4' C5' H5' 223.2 185.7
O4' C4' C5' H5'' 113.7 305.6
C5' C4' O4' C3' 123.1 118.6
C5' C4' O4' H4' 242.7 237.2
C3' C4' O4' H4' 119.6 118.5
O4' C4' C3' O3' 202.6 204.8
O4' C4' C3' C2' 326.6 323.0
O4' C4' C3' H3' 87.9 81.2
C4' O4' C1' C2' 345.9 333.7
C4' O4' C1' N1 229.0 214.2
C4' O4' C1' H1' 109.4 93.1
C3' C4' C5' H5' 338.2 299.9
C3' C4' C5' H5'' 228.8 59.9
C5' C4' C3' O4' 242.5 241.3
C5' C4' C3' H4' 117.5 122.9
O4' C4' C3' H4' 235.0 241.6
C3' C4' O4' C1' 30.0 39.9
O3' C3' C4' C2' 236.0 241.8
O3' C3' C4' H3' 114.7 123.6
C4' C3' O3' HO3' 180.0 174.1
C2' C3' C4' H3' 238.7 241.8
C4' C3' C2' C1' 25.3 20.9
C4' C3' C2' H2' 150.5 262.2
C4' C3' C2' H2'' 260.0 139.6
H4' C4' C5' H5' 98.1 62.9
H4' C4' C5' H5'' 348.7 182.9
C5' C4' H4' O4' 118.9 122.9
C5' C4' H4' C3' 235.5 237.1
O4' C4' H4' C3' 116.6 114.2
H4' C4' O4' C1' 270.4 281.3
H4' C4' C3' O3' 327.6 323.3
H4' C4' C3' C2' 91.6 81.5
H4' C4' C3' H3' 212.9 199.7
C1' O4' C4' C3' 30.0 39.9
C1' O4' C4' H4' 270.4 281.3
C3' C2' C1' O4' 352.5 1.9
O4' C1' C2' H2' 227.3 120.6
O4' C1' C2' H2'' 117.8 243.2
C2' C1' O4' N1 116.8 119.5
C2' C1' O4' H1' 236.5 240.6
N1 C1' O4' H1' 119.6 121.1
O4' C1' N1 C2 224.8 58.4
O4' C1' N1 C6 50.8 238.3
O3' C3' C4' H4' 327.6 323.3
C4' C3' O3' C2' 119.1 112.7
C4' C3' O3' H3' 239.9 236.3
C2' C3' O3' H3' 120.8 123.5
O3' C3' C2' C1' 149.9 139.2
O3' C3' C2' H2' 275.2 20.5
O3' C3' C2' H2'' 24.6 257.8
C2' C3' C4' H4' 91.6 81.5
C4' C3' C2' O3' 235.3 241.8
C4' C3' C2' H3' 120.6 118.3
O4' C1' C2' C3' 352.5 1.9
O3' C3' C2' H3' 245.3 236.5
C2' C3' O3' HO3' 61.0 61.4
C1' C2' C3' H2' 234.8 118.7
C1' C2' C3' H2'' 125.3 241.4
C3' C2' C1' N1 113.5 121.4
C3' C2' C1' H1' 232.9 242.5
H2' C2' C3' H2'' 250.6 122.7
H3' C3' C4' H4' 212.9 199.7
C4' C3' H3' O3' 122.1 123.7
C4' C3' H3' C2' 243.6 247.3
O3' C3' H3' C2' 121.4 123.6
H3' C3' O3' HO3' 300.2 297.9
H3' C3' C2' C1' 264.7 262.7
H3' C3' C2' H2' 29.9 144.0
H3' C3' C2' H2'' 139.4 21.3
HO3' O3' C3' C2' 61.0 61.4
HO3' O3' C3' H3' 300.2 297.9
O4' C1' C2' N1 239.0 240.5
O4' C1' C2' H1' 119.6 119.4
C1' C2' C3' H3' 264.7 262.7
C3' C2' C1' H2' 125.2 241.3
C3' C2' C1' H2'' 234.7 118.7
H2' C2' C1' H2'' 109.5 237.4
N1 C1' C2' H1' 240.6 238.9
C2' C1' N1 C2 108.2 300.4
C2' C1' N1 C6 294.3 120.3
H2' C2' C3' H3' 29.9 144.0
C3' C2' H2' C1' 239.5 114.8
C3' C2' H2' H2'' 119.7 237.3
C1' C2' H2' H2'' 240.2 122.5
H2' C2' C1' N1 348.3 240.1
H2' C2' C1' H1' 107.7 1.2
H2'' C2' C3' H3' 139.4 21.3
C3' C2' H2'' C1' 120.5 245.2
C3' C2' H2'' H2' 240.3 122.7
C1' C2' H2'' H2' 119.8 237.4
H2'' C2' C1' N1 238.7 2.7
H2'' C2' C1' H1' 358.1 123.8
O4' C1' N1 C2' 116.6 118.0
O4' C1' N1 H1' 240.1 239.0
N1 C1' C2' H2' 348.3 240.1
N1 C1' C2' H2'' 238.7 2.7
C2' C1' N1 H1' 123.6 121.0
C2 N1 C1' C6 173.9 180.1
C1' N1 C2 O2 355.2 5.6
C1' N1 C2 N3 176.7 185.7
C1' N1 C6 C5 207.5 144.2
C1' N1 C6 H61 332.8 24.1
C1' N1 C6 H62 82.2 264.2
O4' C1' H1' C2' 241.5 242.1
O4' C1' H1' N1 122.8 121.0
H1' C1' C2' H2' 107.7 1.2
H1' C1' C2' H2'' 358.1 123.8
C2' C1' H1' N1 241.3 239.0
H1' C1' N1 C2 344.6 179.4
H1' C1' N1 C6 170.7 359.3
C2 N1 C1' H1' 344.6 179.4
C1' N1 C2 C6 186.6 179.9
C2 N1 C6 C5 33.8 324.1
C2 N1 C6 H61 159.0 204.1
C2 N1 C6 H62 268.5 84.1
O2 C2 N1 N3 178.5 180.0
N1 C2 N3 C4 358.6 12.1
N1 C2 N3 H3 178.6 192.0
C6 N1 C1' H1' 170.7 359.3
C1' N1 C6 C2 173.7 180.1
C6 N1 C2 O2 168.6 185.7
C6 N1 C2 N3 350.1 5.7
C4 C5 C6 N1 314.6 46.6
C5M C5 C6 N1 74.9 166.6
O5 C5 C6 N1 195.1 286.7
C5 C6 N1 H61 234.7 120.1
C5 C6 N1 H62 125.3 240.1
H61 C6 N1 H62 250.5 120.0
O2 C2 N1 C6 168.6 185.7
N1 C2 O2 N3 181.5 180.0
O2 C2 N3 C4 180.1 192.1
O2 C2 N3 H3 0.0 12.0
N3 C2 N1 C6 350.1 5.7
N1 C2 N3 O2 178.5 180.0
C4 N3 C2 H3 180.1 180.1
C2 N3 C4 O4 164.2 184.5
C2 N3 C4 C5 344.7 4.3
C2 N3 C4 H3 179.9 179.9
O4 C4 N3 C5 179.5 180.2
N3 C4 C5 C5M 278.5 206.0
N3 C4 C5 O5 158.7 85.8
N3 C4 C5 C6 38.7 325.9
C2 N3 H3 C4 180.1 180.1
H3 N3 C4 O4 344.3 4.5
H3 N3 C4 C5 164.8 184.4
O4 C4 N3 H3 344.3 4.5
N3 C4 O4 C5 180.6 179.8
O4 C4 C5 C5M 99.0 25.8
O4 C4 C5 O5 339.2 265.6
O4 C4 C5 C6 219.3 145.7
N1 C6 C5 C4 314.6 46.6
C5 C4 N3 H3 164.8 184.4
N3 C4 C5 O4 179.5 180.2
C5M C5 C4 O5 119.8 120.2
C5M C5 C4 C6 239.8 240.1
C4 C5 C5M H71 180.0 299.9
C4 C5 C5M H72 305.3 59.9
C4 C5 C5M H73 54.8 179.9
O5 C5 C4 C6 119.9 119.9
C4 C5 O5 HO5 180.0 60.2
C4 C5 C6 H61 189.3 166.7
C4 C5 C6 H62 79.8 286.7
N1 C6 C5 C5M 74.9 166.6
C4 C5 C5M O5 240.8 239.8
C4 C5 C5M C6 120.9 119.8
O5 C5 C5M C6 240.0 239.9
C5M C5 O5 HO5 60.4 300.1
C5M C5 C6 H61 309.6 286.7
C5M C5 C6 H62 200.2 46.7
H71 C5M C5 H72 234.7 240.0
H71 C5M C5 H73 125.2 120.0
H72 C5M C5 H73 250.5 240.0
N1 C6 C5 O5 195.1 286.7
C4 C5 O5 C5M 119.7 120.2
C4 C5 O5 C6 239.5 240.3
C5M C5 O5 C6 119.9 120.1
O5 C5 C5M H71 299.2 60.0
O5 C5 C5M H72 64.4 180.0
O5 C5 C5M H73 173.9 300.1
O5 C5 C6 H61 69.8 46.8
O5 C5 C6 H62 320.3 166.8
N1 C6 C5 H61 125.3 239.9
N1 C6 C5 H62 234.8 119.9
C4 C5 C6 C5M 239.6 240.0
C4 C5 C6 O5 119.5 119.9
C5M C5 C6 O5 239.8 239.9
C6 C5 C5M H71 59.1 180.1
C6 C5 C5M H72 184.4 300.1
C6 C5 C5M H73 293.9 60.1
C6 C5 O5 HO5 300.5 180.0
H61 C6 C5 H62 109.5 240.0
H71 C5M C5 O5 299.2 60.0
H71 C5M C5 C6 59.1 180.1
C5 C5M H71 H72 125.2 120.0
C5 C5M H71 H73 234.8 240.1
H72 C5M H71 H73 109.6 120.1
H72 C5M C5 O5 64.4 180.0
H72 C5M C5 C6 184.4 300.1
C5 C5M H72 H71 236.3 240.0
C5 C5M H72 H73 118.1 120.0
H71 C5M H72 H73 241.8 240.0
H73 C5M C5 O5 173.9 300.1
H73 C5M C5 C6 293.9 60.1
C5 C5M H73 H71 123.6 119.9
C5 C5M H73 H72 241.9 240.0
H71 C5M H73 H72 118.2 120.0
HO5 O5 C5 C6 300.5 180.0
N1 C6 H61 C5 236.9 120.1
N1 C6 H61 H62 118.5 240.0
C5 C6 H61 H62 241.5 120.0
N1 C6 H62 C5 123.0 240.0
N1 C6 H62 H61 241.5 120.0
C5 C6 H62 H61 118.5 240.0