PDB Chemical Component YDJ

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 YDJ

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C1 C2 1.382 1.380
C1 C6 1.374 1.383
C2 C3 1.385 1.396
C3 C4 1.374 1.396
C3 C7 1.452 1.478
C4 C5 1.373 1.382
C5 C6 1.381 1.385
C5 F1 1.339 1.352
C7 C8 1.378 1.361
C7 S1 1.725 1.758
C8 C9 1.426 1.374
C9 C10 1.380 1.374
C9 N3 1.402 1.397
C10 S1 1.722 1.759
C10 C11 1.448 1.416
C11 O1 1.230 1.218
C11 N1 1.355 1.348
N1 C12 1.441 1.465
C12 C13 1.511 1.531
C12 C16 1.513 1.531
C13 C14 1.525 1.531
C14 C15 1.513 1.531
C15 N2 1.488 1.469
N2 C16 1.486 1.469
N3 C17 1.384 1.347
C17 O2 1.218 1.215
C17 N4 1.376 1.348
C1 H1 1.080 1.079
C2 H2 1.081 1.080
C6 H6 1.080 1.079
C4 H4 1.080 1.080
C8 H8 1.080 1.081
N3 H3 1.000 0.969
N1 HA 1.000 0.970
C12 H12 1.100 1.090
C13 H131 1.100 1.090
C13 H132 1.100 1.090
C16 H161 1.101 1.090
C16 H162 1.100 1.090
C14 H141 1.100 1.090
C14 H142 1.100 1.090
C15 H151 1.100 1.090
C15 H152 1.100 1.090
N2 HB 0.999 1.008
N4 H41N 1.000 0.970
N4 H42N 1.000 0.970

Bond Angles for YDJ

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 C1 C6 119.3 120.1
C1 C2 C3 121.2 119.9
C2 C1 H1 120.4 119.9
C1 C2 H2 119.4 120.1
C1 C6 C5 119.1 120.3
C6 C1 H1 120.3 120.0
C1 C6 H6 120.4 119.8
C2 C3 C4 119.3 119.7
C2 C3 C7 120.5 120.2
C3 C2 H2 119.4 120.0
C4 C3 C7 120.2 120.1
C3 C4 C5 119.2 119.8
C3 C4 H4 120.4 120.1
C3 C7 C8 128.0 125.1
C3 C7 S1 121.5 125.0
C4 C5 C6 121.8 120.1
C4 C5 F1 117.9 119.9
C5 C4 H4 120.4 120.1
C6 C5 F1 120.3 119.9
C5 C6 H6 120.4 119.9
C8 C7 S1 110.5 109.9
C7 C8 C9 113.5 114.8
C7 C8 H8 123.2 122.6
C7 S1 C10 92.6 91.3
C8 C9 C10 112.0 114.4
C8 C9 N3 127.9 122.8
C9 C8 H8 123.3 122.6
C10 C9 N3 120.2 122.7
C9 C10 S1 111.4 109.6
C9 C10 C11 124.3 125.2
C9 N3 C17 122.7 119.9
C9 N3 H3 118.6 120.0
S1 C10 C11 124.3 125.2
C10 C11 O1 122.2 120.0
C10 C11 N1 116.5 120.0
O1 C11 N1 121.2 120.0
C11 N1 C12 117.7 120.0
C11 N1 HA 121.1 120.0
N1 C12 C13 110.5 109.5
N1 C12 C16 107.4 109.5
C12 N1 HA 121.2 120.0
N1 C12 H12 110.8 109.5
C13 C12 C16 111.3 109.3
C12 C13 C14 112.3 109.2
C13 C12 H12 106.9 109.5
C12 C13 H131 108.6 109.6
C12 C13 H132 108.5 109.5
C12 C16 N2 108.8 109.5
C16 C12 H12 110.0 109.5
C12 C16 H161 109.7 109.5
C12 C16 H162 109.7 109.5
C13 C14 C15 110.6 109.3
C14 C13 H131 108.6 109.5
C14 C13 H132 108.6 109.5
C13 C14 H141 109.1 109.5
C13 C14 H142 109.1 109.5
C14 C15 N2 105.8 109.5
C15 C14 H141 109.1 109.4
C15 C14 H142 109.1 109.5
C14 C15 H151 110.7 109.5
C14 C15 H152 110.7 109.4
C15 N2 C16 113.4 111.2
N2 C15 H151 110.7 109.5
N2 C15 H152 110.7 109.4
C15 N2 HB 108.2 110.9
N2 C16 H161 109.7 109.5
N2 C16 H162 109.7 109.4
C16 N2 HB 108.2 111.0
N3 C17 O2 124.2 120.1
N3 C17 N4 114.3 120.0
C17 N3 H3 118.7 120.0
O2 C17 N4 121.5 120.0
C17 N4 H41N 120.0 120.0
C17 N4 H42N 120.0 120.0
H131 C13 H132 110.4 109.6
H161 C16 H162 109.3 109.5
H141 C14 H142 109.8 109.5
H151 C15 H152 108.2 109.4
H41N N4 H42N 120.0 120.0

Torsion Angles for YDJ

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2 C1 C6 C5 359.8 0.0
C6 C1 C2 H1 180.0 180.2
C2 C1 C6 H6 179.8 180.0
C1 C2 C3 C4 0.2 0.0
C1 C2 C3 C7 180.6 180.0
C3 C2 C1 H2 180.0 180.0
C6 C1 C2 C3 0.2 360.0
C2 C1 C6 H1 180.0 179.8
C6 C1 C2 H2 180.2 180.0
C4 C5 C6 C1 359.6 360.0
C1 C6 C5 F1 180.2 180.0
C5 C6 C1 H6 180.0 180.0
C3 C2 C1 C6 0.2 360.0
C3 C2 C1 H1 180.3 179.7
C1 C2 C3 H2 180.0 180.0
C4 C3 C2 C7 179.6 180.0
C2 C3 C4 C5 359.3 0.0
C2 C3 C4 H4 179.3 180.0
C2 C3 C7 C8 18.7 180.0
C2 C3 C7 S1 199.2 359.7
C2 C3 C4 C7 180.4 180.0
C4 C3 C2 H2 180.2 180.0
C4 C3 C7 C8 199.1 0.0
C4 C3 C7 S1 19.6 179.7
C3 C4 C5 C6 0.8 0.0
C3 C4 C5 F1 180.2 180.0
C5 C4 C3 H4 180.0 180.0
C2 C3 C7 C4 179.6 180.0
C7 C3 C2 H2 0.6 0.0
C7 C3 C4 C5 178.9 180.0
C7 C3 C4 H4 358.9 360.0
C8 C7 C3 S1 179.6 180.3
C3 C7 C8 C9 181.6 179.9
C3 C7 C8 H8 1.6 359.9
C3 C7 S1 C10 178.7 180.0
C1 C6 C5 C4 359.6 360.0
C5 C4 C3 C7 178.9 180.0
C3 C4 C5 H4 180.0 180.0
C6 C5 C4 F1 180.6 180.0
C4 C5 C6 H6 179.6 180.0
C5 C6 C1 H1 179.8 180.3
C1 C6 C5 H6 180.0 180.0
C4 C5 C6 F1 179.4 180.0
C6 C5 C4 H4 180.8 180.0
C4 C5 F1 C6 180.6 180.0
F1 C5 C4 H4 0.2 0.0
F1 C5 C6 H6 0.3 0.0
C3 C7 C8 S1 180.4 179.7
C8 C7 S1 C10 359.1 359.7
C7 C8 C9 C10 359.1 0.0
C7 C8 C9 N3 179.4 179.9
C9 C8 C7 H8 180.0 180.0
C3 C7 S1 C8 179.6 180.3
S1 C7 C8 C9 1.2 0.2
S1 C7 C8 H8 181.2 180.2
C9 C10 S1 C7 0.5 0.3
C7 S1 C10 C11 181.2 180.1
C9 C8 C7 S1 1.2 0.2
C7 C8 C9 H8 180.0 180.0
C10 C9 C8 N3 179.7 180.1
C8 C9 C10 S1 0.1 359.8
C8 C9 C10 C11 179.4 180.0
C8 C9 N3 C17 350.4 352.9
C8 C9 N3 H3 170.4 172.7
C7 S1 C10 C9 0.5 0.3
C8 C9 C10 N3 180.2 179.9
C10 C9 C8 H8 179.1 180.0
C10 C9 N3 C17 170.7 172.8
C10 C9 N3 H3 350.7 352.7
S1 C10 C9 C11 180.7 179.8
C9 C10 C11 O1 356.8 0.0
C9 C10 C11 N1 179.5 180.0
C8 C9 N3 C10 179.7 180.1
N3 C9 C8 H8 359.4 359.9
N3 C9 C10 S1 179.9 179.8
N3 C9 C10 C11 359.2 0.0
C9 N3 C17 O2 16.2 5.1
C9 N3 C17 N4 196.9 185.1
C17 N3 C9 H3 180.0 180.1
S1 C10 C9 N3 179.9 179.8
C9 C10 S1 C11 179.3 180.2
S1 C10 C11 O1 176.0 180.2
S1 C10 C11 N1 358.7 0.2
C11 C10 C9 N3 359.2 0.0
C9 C10 C11 S1 180.8 179.8
O1 C11 C10 N1 177.3 180.0
C10 C11 N1 C12 165.1 180.0
C10 C11 N1 HA 345.2 360.0
C10 C11 O1 N1 182.8 180.0
O1 C11 N1 C12 347.8 0.1
O1 C11 N1 HA 167.8 180.0
C10 C11 N1 O1 177.3 180.0
C11 N1 C12 C13 146.2 155.0
C11 N1 C12 C16 267.8 274.8
C12 N1 C11 HA 180.0 180.1
C11 N1 C12 H12 28.0 34.9
C11 N1 C12 HA 180.0 179.9
C13 C12 N1 C16 238.4 240.2
N1 C12 C13 C14 170.8 177.6
C13 C12 N1 H12 118.3 120.1
N1 C12 C13 H131 290.8 297.5
N1 C12 C13 H132 50.8 57.7
N1 C12 C16 N2 186.2 180.9
C16 C12 N1 H12 239.8 239.9
N1 C12 C16 H161 306.2 300.9
N1 C12 C16 H162 66.2 60.9
N1 C12 C13 C16 119.3 119.9
C13 C12 N1 HA 326.2 335.0
N1 C12 C13 H12 239.4 239.9
C13 C12 C16 N2 307.3 300.8
C16 C12 C13 H12 120.1 120.0
C13 C12 C16 H161 67.3 60.8
C13 C12 C16 H162 187.3 180.8
C12 C13 C14 C15 304.5 302.4
C14 C13 C12 H131 240.0 240.1
C14 C13 C12 H132 120.0 119.9
C12 C13 C14 H141 64.5 62.3
C12 C13 C14 H142 184.4 182.4
H131 C13 C12 H132 240.0 239.8
N1 C12 C16 C13 238.9 240.1
C16 C12 N1 HA 87.8 94.9
N1 C12 C16 H12 120.6 120.1
C16 C12 C13 C14 51.5 57.6
C13 C12 C16 H12 241.7 240.0
C16 C12 C13 H131 171.5 177.6
C16 C12 C13 H132 291.5 297.8
C15 N2 C16 C12 61.7 61.7
N2 C16 C12 H161 240.0 240.0
N2 C16 C12 H162 120.0 120.0
C12 C16 N2 HB 301.7 297.7
H161 C16 C12 H162 240.0 240.0
C14 C13 C12 C16 51.5 57.6
C14 C13 C12 H12 291.4 297.6
C12 C13 C14 H131 120.0 120.0
C12 C13 C14 H132 240.0 240.1
C13 C14 C15 N2 59.1 59.1
C15 C14 C13 H141 240.0 240.1
C15 C14 C13 H142 120.0 120.0
C13 C14 C15 H151 179.1 179.2
C13 C14 C15 H152 299.1 299.1
H131 C13 C14 H132 120.0 120.2
H141 C14 C13 H142 240.0 239.8
C15 C14 C13 H131 184.4 182.4
C15 C14 C13 H132 64.4 62.3
C13 C14 C15 H141 120.0 119.9
C13 C14 C15 H142 240.0 240.0
C14 C15 N2 C16 295.5 298.3
N2 C15 C14 H151 240.0 239.9
N2 C15 C14 H152 120.0 120.0
C14 C15 N2 HB 55.5 62.4
H141 C14 C15 H142 120.0 120.1
H151 C15 C14 H152 240.0 240.0
C12 C16 N2 C15 61.7 61.7
N2 C15 C14 H141 299.1 299.2
N2 C15 C14 H142 179.1 179.1
C14 C15 N2 H151 120.0 120.1
C14 C15 N2 H152 240.0 240.0
C15 N2 C16 H161 301.7 301.7
C15 N2 C16 H162 181.7 181.7
C16 N2 C15 HB 240.0 235.9
H151 C15 N2 H152 120.0 119.9
N2 C16 C12 H12 65.6 60.8
C12 C16 N2 H161 120.0 120.0
C12 C16 N2 H162 240.0 240.0
C16 N2 C15 H151 175.5 178.2
C16 N2 C15 H152 55.6 58.3
C15 N2 C16 HB 120.0 124.1
H161 C16 N2 H162 120.0 120.0
C9 N3 C17 H3 180.0 179.9
O2 C17 N3 N4 179.2 180.0
N3 C17 N4 H41N 179.3 359.9
N3 C17 N4 H42N 359.2 180.0
N3 C17 O2 N4 180.8 180.0
O2 C17 N3 H3 196.2 185.2
O2 C17 N4 H41N 0.0 180.0
O2 C17 N4 H42N 180.0 0.1
N3 C17 N4 O2 179.3 180.0
N4 C17 N3 H3 16.9 5.2
H41N N4 C17 H42N 180.0 179.9
C2 C1 H1 C6 180.0 180.2
H1 C1 C2 C3 180.3 179.7
H1 C1 C2 H2 0.2 359.8
H1 C1 C6 C5 179.8 180.3
H1 C1 C6 H6 359.8 0.2
H2 C2 C1 C6 180.2 180.0
C1 C2 H2 C3 180.0 180.0
H2 C2 C1 H1 0.2 359.8
H2 C2 C3 C4 180.2 180.0
H2 C2 C3 C7 0.6 0.0
C1 C6 H6 C5 180.0 180.0
H6 C6 C1 H1 359.8 0.2
H6 C6 C5 F1 0.3 0.0
H4 C4 C3 C7 358.9 360.0
C3 C4 H4 C5 180.0 180.0
H4 C4 C5 C6 180.8 180.0
H4 C4 C5 F1 0.2 0.0
H8 C8 C7 S1 181.2 180.2
C7 C8 H8 C9 180.0 180.0
H8 C8 C9 C10 179.1 180.0
H8 C8 C9 N3 359.4 359.9
C9 N3 H3 C17 180.0 180.1
H3 N3 C17 O2 196.2 185.2
H3 N3 C17 N4 16.9 5.2
C11 N1 HA C12 180.0 180.1
HA N1 C12 C13 326.2 335.0
HA N1 C12 C16 87.8 94.9
HA N1 C12 H12 207.9 215.0
N1 C12 H12 C13 120.4 120.1
N1 C12 H12 C16 241.4 240.0
H12 C12 N1 HA 207.9 215.0
C13 C12 H12 C16 120.9 119.9
H12 C12 C13 C14 291.4 297.6
H12 C12 C13 H131 51.4 57.6
H12 C12 C13 H132 171.4 177.8
H12 C12 C16 N2 65.6 60.8
H12 C12 C16 H161 185.6 180.8
H12 C12 C16 H162 305.6 300.8
H131 C13 C12 C16 171.5 177.6
C12 C13 H131 C14 237.7 240.3
H131 C13 C12 H12 51.4 57.6
C12 C13 H131 H132 118.8 120.2
H131 C13 C14 C15 184.4 182.4
C14 C13 H131 H132 241.1 239.9
H131 C13 C14 H141 304.4 302.3
H131 C13 C14 H142 64.4 62.5
H132 C13 C12 C16 291.5 297.8
C12 C13 H132 C14 122.3 119.7
H132 C13 C12 H12 171.4 177.8
C12 C13 H132 H131 241.2 239.8
H132 C13 C14 C15 64.4 62.3
C14 C13 H132 H131 118.9 120.1
H132 C13 C14 H141 184.5 182.2
H132 C13 C14 H142 304.4 302.3
C12 C16 H161 N2 240.5 240.0
H161 C16 C12 H12 185.6 180.8
C12 C16 H161 H162 120.3 120.0
N2 C16 H161 H162 239.7 240.1
H161 C16 N2 HB 181.7 177.6
C12 C16 H162 N2 119.4 120.0
H162 C16 C12 H12 305.6 300.8
C12 C16 H162 H161 239.7 240.0
N2 C16 H162 H161 120.3 120.0
H162 C16 N2 HB 61.7 57.7
C13 C14 H141 C15 239.1 240.2
H141 C14 C13 H131 304.4 302.3
H141 C14 C13 H132 184.5 182.2
C13 C14 H141 H142 119.5 120.1
H141 C14 C15 N2 299.1 299.2
C15 C14 H141 H142 240.4 239.9
H141 C14 C15 H151 59.1 59.3
H141 C14 C15 H152 179.1 179.2
C13 C14 H142 C15 120.9 119.9
H142 C14 C13 H131 64.4 62.5
H142 C14 C13 H132 304.4 302.3
C13 C14 H142 H141 240.5 239.9
H142 C14 C15 N2 179.1 179.1
C15 C14 H142 H141 119.6 120.0
H142 C14 C15 H151 299.1 299.2
H142 C14 C15 H152 59.1 59.1
C14 C15 H151 N2 243.0 239.9
H151 C15 C14 H141 59.1 59.3
H151 C15 C14 H142 299.1 299.2
C14 C15 H151 H152 121.5 120.0
H151 C15 N2 C16 175.5 178.2
N2 C15 H151 H152 238.5 240.1
H151 C15 N2 HB 295.5 302.3
C14 C15 H152 N2 117.0 120.0
H152 C15 C14 H141 179.1 179.2
H152 C15 C14 H142 59.1 59.1
C14 C15 H152 H151 238.5 240.0
H152 C15 N2 C16 55.6 58.3
N2 C15 H152 H151 121.5 120.0
H152 C15 N2 HB 175.5 182.4
C15 N2 HB C16 236.8 235.8
HB N2 C15 H151 295.5 302.3
HB N2 C15 H152 175.5 182.4
HB N2 C16 H161 181.7 177.6
HB N2 C16 H162 61.7 57.7
C17 N4 H41N H42N 180.0 180.1
C17 N4 H42N H41N 180.0 179.9