PDB Chemical Component VNP

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 VNP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O2G PG 1.610 1.610
O2G H2G 0.950 0.967
PG O3G 1.607 1.480
PG O1G 1.481 1.610
PG N3B 1.625 1.683
O1G H1G 0.950 0.967
N3B PB 1.624 1.683
N3B H3B 1.000 1.009
PB O2B 1.480 1.481
PB O1B 1.479 1.610
PB O1 1.611 1.609
O1B H1B 0.950 0.967
O1 C7 1.433 1.429
C7 C12 1.529 1.530
C7 H71 1.100 1.090
C7 H72 1.100 1.090
C12 C11 1.532 1.507
C12 H121 1.100 1.090
C12 H122 1.100 1.090
C11 C10 1.531 1.336
C11 S1 1.823 1.762
C10 CM4 1.531 1.506
C10 N5 1.337 1.318
CM4 HM41 1.100 1.090
CM4 HM42 1.100 1.090
CM4 HM43 1.100 1.090
S1 C9 1.749 1.709
C9 N5 1.335 1.291
C9 H9 1.080 1.080
N5 C7A 1.472 1.465
C7A C5A 1.532 1.508
C7A H7A1 1.100 1.090
C7A H7A2 1.100 1.090
C5A C6A 1.389 1.381
C5A C4A 1.392 1.396
C6A N1A 1.320 1.326
C6A H6A 1.080 1.080
N1A C2A 1.340 1.317
C2A CM2 1.531 1.507
C2A N3A 1.340 1.317
CM2 HM21 1.100 1.090
CM2 HM22 1.100 1.091
CM2 HM23 1.100 1.089
N3A C4A 1.341 1.330
C4A N4A 1.331 1.385
N4A H4A1 0.999 0.970
N4A H4A2 1.000 0.970

Bond Angles for VNP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
PG O2G H2G 109.5 114.0
O2G PG O3G 105.8 109.5
O2G PG O1G 111.8 109.4
O2G PG N3B 107.8 109.5
O3G PG O1G 110.8 109.4
O3G PG N3B 108.4 109.5
O1G PG N3B 112.0 109.5
PG O1G H1G 109.5 114.0
PG N3B PB 114.2 111.0
PG N3B H3B 107.9 111.0
PB N3B H3B 107.9 111.0
N3B PB O2B 108.5 109.4
N3B PB O1B 108.0 109.5
N3B PB O1 104.2 109.5
O2B PB O1B 117.7 109.4
O2B PB O1 109.5 109.5
O1B PB O1 108.2 109.5
PB O1B H1B 109.5 114.0
PB O1 C7 124.1 123.0
O1 C7 C12 106.3 109.5
O1 C7 H71 110.5 109.5
O1 C7 H72 111.2 109.5
C12 C7 H71 110.5 109.5
C12 C7 H72 111.3 109.4
C7 C12 C11 117.0 109.5
C7 C12 H121 107.0 109.5
C7 C12 H122 105.3 109.4
H71 C7 H72 107.0 109.5
C11 C12 H121 107.0 109.5
C11 C12 H122 105.3 109.5
C12 C11 C10 116.4 126.0
C12 C11 S1 118.1 126.0
H121 C12 H122 115.6 109.5
C10 C11 S1 100.2 107.9
C11 C10 CM4 122.7 122.8
C11 C10 N5 114.3 114.5
C11 S1 C9 92.7 90.3
CM4 C10 N5 122.9 122.8
C10 CM4 HM41 109.5 109.5
C10 CM4 HM42 109.5 109.5
C10 CM4 HM43 109.5 109.5
C10 N5 C9 117.0 117.1
C10 N5 C7A 120.5 121.5
HM41 CM4 HM42 109.4 109.5
HM41 CM4 HM43 109.5 109.5
HM42 CM4 HM43 109.5 109.4
S1 C9 N5 109.4 110.2
S1 C9 H9 125.3 124.9
N5 C9 H9 125.3 124.9
C9 N5 C7A 122.4 121.4
N5 C7A C5A 113.8 109.5
N5 C7A H7A1 108.0 109.5
N5 C7A H7A2 107.1 109.5
C5A C7A H7A1 108.1 109.5
C5A C7A H7A2 107.1 109.4
C7A C5A C6A 116.3 120.9
C7A C5A C4A 126.7 120.8
H7A1 C7A H7A2 112.9 109.5
C6A C5A C4A 116.9 118.4
C5A C6A N1A 121.1 119.2
C5A C6A H6A 119.4 120.4
C5A C4A N3A 120.0 118.9
C5A C4A N4A 121.0 120.6
N1A C6A H6A 119.5 120.4
C6A N1A C2A 120.9 121.0
N1A C2A CM2 119.6 119.0
N1A C2A N3A 120.2 121.9
CM2 C2A N3A 120.2 119.1
C2A CM2 HM21 109.5 109.5
C2A CM2 HM22 109.4 109.4
C2A CM2 HM23 109.5 109.5
C2A N3A C4A 120.9 120.7
HM21 CM2 HM22 109.5 109.5
HM21 CM2 HM23 109.4 109.5
HM22 CM2 HM23 109.5 109.5
N3A C4A N4A 119.0 120.5
C4A N4A H4A1 109.5 120.0
C4A N4A H4A2 109.5 120.0
H4A1 N4A H4A2 109.5 120.0

Torsion Angles for VNP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O3G PG O2G O1G 120.7 240.1
O3G PG O2G N3B 244.2 120.0
O1G PG O2G N3B 123.5 240.0
O2G PG O1G H1G 12.1 300.0
O2G PG N3B PB 279.0 60.0
O2G PG N3B H3B 39.0 183.9
H2G O2G PG O3G 295.5 180.0
H2G O2G PG O1G 174.8 299.9
H2G O2G PG N3B 51.3 59.9
O3G PG O2G H2G 295.5 180.0
O2G PG O3G O1G 238.6 119.9
O2G PG O3G N3B 115.4 240.0
O1G PG O3G N3B 236.8 120.0
O3G PG O1G H1G 254.4 60.0
O3G PG N3B PB 33.1 300.0
O3G PG N3B H3B 153.1 63.9
O1G PG O2G H2G 174.8 299.9
O2G PG O1G O3G 117.8 240.0
O2G PG O1G N3B 238.9 120.0
O3G PG O1G N3B 121.1 240.0
O1G PG N3B PB 155.6 180.0
O1G PG N3B H3B 275.6 303.9
N3B PG O2G H2G 51.3 59.9
O2G PG N3B O3G 245.9 120.0
O2G PG N3B O1G 123.4 240.0
O3G PG N3B O1G 237.5 120.0
N3B PG O1G H1G 133.3 180.0
PB N3B PG H3B 240.0 236.1
PG N3B PB O2B 170.1 60.0
PG N3B PB O1B 41.6 300.0
PG N3B PB O1 286.7 180.0
H1G O1G PG N3B 133.3 180.0
PG N3B PB H3B 120.0 123.9
O2B PB N3B O1B 128.5 119.9
O2B PB N3B O1 243.4 240.0
O1B PB N3B O1 114.9 120.1
N3B PB O1B H1B 172.7 300.0
N3B PB O1 C7 299.1 290.0
PG N3B H3B PB 236.1 236.1
H3B N3B PB O2B 50.1 296.1
H3B N3B PB O1B 281.6 176.1
H3B N3B PB O1 166.7 56.1
O2B PB N3B H3B 50.1 296.1
N3B PB O2B O1B 237.2 240.0
N3B PB O2B O1 113.1 120.0
O1B PB O2B O1 236.0 240.0
O2B PB O1B H1B 49.7 180.0
O2B PB O1 C7 54.9 50.0
O1B PB N3B H3B 281.6 176.1
N3B PB O1B O2B 123.1 119.9
N3B PB O1B O1 247.8 240.0
O2B PB O1B O1 124.7 120.0
O1B PB O1 C7 184.3 170.0
O1 PB N3B H3B 166.7 56.1
N3B PB O1 O2B 244.1 240.0
N3B PB O1 O1B 114.7 120.0
O2B PB O1 O1B 230.6 240.0
O1 PB O1B H1B 285.0 60.0
PB O1 C7 C12 208.3 180.0
PB O1 C7 H71 328.3 300.0
PB O1 C7 H72 87.0 60.0
H1B O1B PB O1 285.0 60.0
C12 C7 O1 H71 240.0 239.9
C12 C7 O1 H72 121.2 119.9
O1 C7 C12 C11 186.1 180.0
O1 C7 C12 H121 306.0 300.1
O1 C7 C12 H122 69.6 60.0
H71 C7 O1 H72 241.2 240.0
O1 C7 C12 H71 120.0 120.1
O1 C7 C12 H72 238.8 240.0
H71 C7 C12 H72 118.8 119.9
C11 C12 C7 H121 240.0 239.9
C11 C12 C7 H122 116.5 120.0
C7 C12 C11 C10 76.7 90.0
C7 C12 C11 S1 317.3 269.8
H121 C12 C7 H122 236.5 240.1
O1 C7 H71 C12 242.6 239.9
O1 C7 H71 H72 121.3 120.0
C12 C7 H71 H72 238.7 240.1
H71 C7 C12 C11 66.1 59.9
H71 C7 C12 H121 186.0 180.0
H71 C7 C12 H122 309.6 299.9
O1 C7 H72 C12 118.3 120.0
O1 C7 H72 H71 239.1 240.0
C12 C7 H72 H71 120.8 119.9
H72 C7 C12 C11 307.3 300.0
H72 C7 C12 H121 67.3 60.1
H72 C7 C12 H122 190.8 180.0
C11 C12 C7 H71 66.1 59.9
C11 C12 C7 H72 307.3 300.0
C7 C12 C11 H121 120.0 120.0
C7 C12 C11 H122 243.5 240.1
H121 C12 C11 H122 123.5 120.0
C10 C11 C12 S1 119.4 180.3
C12 C11 C10 CM4 30.1 0.0
C12 C11 C10 N5 211.1 180.0
C12 C11 S1 C9 149.6 180.0
H121 C12 C7 H71 186.0 180.0
H121 C12 C7 H72 67.3 60.1
C7 C12 H121 C11 233.8 239.9
C7 C12 H121 H122 116.9 119.9
C11 C12 H121 H122 243.1 240.0
H121 C12 C11 C10 316.7 330.0
H121 C12 C11 S1 197.3 149.7
H122 C12 C7 H71 309.6 299.9
H122 C12 C7 H72 190.8 180.0
C7 C12 H122 C11 124.3 120.0
C7 C12 H122 H121 242.1 240.1
C11 C12 H122 H121 117.9 120.0
H122 C12 C11 C10 193.2 210.0
H122 C12 C11 S1 73.8 29.7
C10 C11 C12 H121 316.7 330.0
C10 C11 C12 H122 193.2 210.0
C12 C11 C10 S1 231.4 179.8
C10 C11 S1 C9 22.1 359.7
CM4 C10 C11 N5 179.0 180.0
C11 C10 CM4 HM41 228.7 90.0
C11 C10 CM4 HM42 348.7 210.0
C11 C10 CM4 HM43 108.7 330.0
C11 C10 N5 C9 6.3 359.9
C11 C10 N5 C7A 182.4 180.0
S1 C11 C12 H121 197.3 149.7
S1 C11 C12 H122 73.8 29.7
C12 C11 S1 C10 127.5 180.2
S1 C11 C10 CM4 158.7 180.3
S1 C11 C10 N5 339.8 0.3
C11 S1 C9 N5 338.7 0.2
C11 S1 C9 H9 158.7 179.9
CM4 C10 C11 S1 158.7 180.3
C11 C10 CM4 N5 181.1 180.0
CM4 C10 N5 C9 187.3 179.9
CM4 C10 N5 C7A 3.4 360.0
HM41 CM4 C10 HM42 240.1 240.0
HM41 CM4 C10 HM43 120.0 120.0
HM42 CM4 C10 HM43 239.9 240.0
N5 C10 C11 S1 339.8 0.3
C11 C10 N5 CM4 179.0 180.0
N5 C10 CM4 HM41 47.6 270.0
N5 C10 CM4 HM42 167.6 30.0
N5 C10 CM4 HM43 287.6 150.0
S1 C9 N5 C10 12.4 359.9
C10 N5 C9 H9 192.4 180.2
C9 N5 C10 C7A 184.0 179.9
C10 N5 C7A C5A 156.1 85.0
C10 N5 C7A H7A1 276.1 205.0
C10 N5 C7A H7A2 38.0 325.0
HM41 CM4 C10 N5 47.6 270.0
C10 CM4 HM41 HM42 120.0 120.0
C10 CM4 HM41 HM43 240.0 240.0
HM42 CM4 HM41 HM43 120.0 120.0
HM42 CM4 C10 N5 167.6 30.0
C10 CM4 HM42 HM41 240.0 240.0
C10 CM4 HM42 HM43 120.0 120.0
HM41 CM4 HM42 HM43 240.0 240.0
HM43 CM4 C10 N5 287.6 150.0
C10 CM4 HM43 HM41 120.0 120.0
C10 CM4 HM43 HM42 240.0 240.0
HM41 CM4 HM43 HM42 120.0 120.0
C10 N5 C9 S1 12.4 359.9
N5 C9 S1 H9 180.0 180.3
S1 C9 N5 C7A 196.4 179.8
C10 N5 C9 C7A 176.0 180.1
S1 C9 N5 H9 180.0 179.7
C9 N5 C7A C5A 331.9 265.1
C9 N5 C7A H7A1 91.9 25.1
C9 N5 C7A H7A2 213.8 145.1
S1 C9 H9 N5 180.0 180.3
H9 C9 N5 C7A 16.5 0.1
C10 N5 C7A C9 184.2 179.9
C7A N5 C9 H9 16.5 0.1
C5A C7A N5 H7A1 240.0 239.9
C5A C7A N5 H7A2 118.1 119.9
N5 C7A C5A C6A 118.9 265.0
N5 C7A C5A C4A 294.3 84.7
H7A1 C7A N5 H7A2 238.1 240.0
N5 C7A C5A H7A1 120.0 120.1
N5 C7A C5A H7A2 241.9 240.0
H7A1 C7A C5A H7A2 121.9 119.9
C6A C5A C7A C4A 184.6 180.3
C7A C5A C6A N1A 175.4 179.9
C7A C5A C6A H6A 355.4 359.9
C7A C5A C4A N3A 185.0 179.8
C7A C5A C4A N4A 4.8 0.1
N5 C7A H7A1 C5A 236.5 240.0
N5 C7A H7A1 H7A2 118.2 120.0
C5A C7A H7A1 H7A2 241.8 240.1
H7A1 C7A C5A C6A 358.9 145.0
H7A1 C7A C5A C4A 174.3 324.6
N5 C7A H7A2 C5A 122.4 120.0
N5 C7A H7A2 H7A1 241.2 239.9
C5A C7A H7A2 H7A1 118.8 120.0
H7A2 C7A C5A C6A 237.0 25.0
H7A2 C7A C5A C4A 52.4 204.7
C6A C5A C7A H7A1 358.9 145.0
C6A C5A C7A H7A2 237.0 25.0
C7A C5A C6A C4A 175.9 179.7
C6A C5A C4A N3A 0.4 359.5
C6A C5A C4A N4A 180.2 179.8
N1A C6A C5A H6A 180.0 180.0
C5A C6A N1A C2A 0.1 360.0
C4A C5A C7A H7A1 174.3 324.6
C4A C5A C7A H7A2 52.4 204.7
C7A C5A C4A C6A 184.6 180.3
C4A C5A C6A N1A 359.5 0.3
C4A C5A C6A H6A 179.5 180.3
C2A N3A C4A C5A 360.0 0.5
N3A C4A C5A N4A 180.3 179.7
C5A C4A N4A H4A1 264.2 360.0
C5A C4A N4A H4A2 24.2 180.0
N1A C6A C5A C4A 359.5 0.3
C5A C6A N1A H6A 180.0 180.0
C6A N1A C2A CM2 181.6 180.0
C6A N1A C2A N3A 0.3 360.0
H6A C6A C5A C4A 179.5 180.3
C5A C6A H6A N1A 180.0 180.0
H6A C6A N1A C2A 180.1 180.0
C2A N1A C6A H6A 180.1 180.0
CM2 C2A N1A N3A 181.3 180.0
N1A C2A CM2 HM21 25.1 90.1
N1A C2A CM2 HM22 145.2 210.0
N1A C2A CM2 HM23 265.2 330.0
N1A C2A N3A C4A 359.6 359.8
N1A C2A CM2 N3A 178.7 180.0
CM2 C2A N3A C4A 178.3 179.8
HM21 CM2 C2A HM22 240.0 240.0
HM21 CM2 C2A HM23 120.0 120.1
HM22 CM2 C2A HM23 240.0 240.0
C5A C4A N3A C2A 360.0 0.5
N1A C2A N3A CM2 181.3 180.0
N3A C2A CM2 HM21 206.4 270.1
N3A C2A CM2 HM22 326.5 30.0
N3A C2A CM2 HM23 86.5 150.0
C2A N3A C4A N4A 180.2 180.2
HM21 CM2 C2A N3A 206.4 270.1
C2A CM2 HM21 HM22 120.0 119.9
C2A CM2 HM21 HM23 240.0 239.9
HM22 CM2 HM21 HM23 120.0 120.0
HM22 CM2 C2A N3A 326.5 30.0
C2A CM2 HM22 HM21 240.0 240.0
C2A CM2 HM22 HM23 120.0 120.0
HM21 CM2 HM22 HM23 240.0 240.0
HM23 CM2 C2A N3A 86.5 150.0
C2A CM2 HM23 HM21 120.0 120.1
C2A CM2 HM23 HM22 240.0 240.0
HM21 CM2 HM23 HM22 120.0 120.0
C5A C4A N3A N4A 179.7 180.3
N3A C4A N4A H4A1 83.9 180.2
N3A C4A N4A H4A2 204.0 0.3
C5A C4A N4A N3A 180.3 179.7
H4A1 N4A C4A H4A2 240.0 179.9
C4A N4A H4A1 H4A2 120.0 180.1
C4A N4A H4A2 H4A1 239.9 179.9