PDB Chemical Component 2PD

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 2PD

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
O30	S33	1.444	1.420
S33	O29	1.446	1.421
S33	C12	1.757	1.769
S33	N26	1.681	1.672
C12	C8	1.404	1.371
C12	C10	1.401	1.400
C8	C11	1.392	1.392
C11	O32	1.376	1.359
C11	C7	1.401	1.388
O32	C20	1.432	1.428
C7	C6	1.405	1.378
N26	C16	1.409	1.386
C16	N24	1.298	1.297
C16	C14	1.469	1.471
N24	C10	1.413	1.363
C10	C6	1.405	1.400
C14	C15	1.356	1.399
C14	C17	1.491	1.421
C15	O31	1.382	1.352
C15	C13	1.488	1.419
C17	O28	1.230	1.220
C17	N27	1.388	1.345
N27	C22	1.449	1.466
N27	N25	1.370	1.283
C22	C21	1.523	1.530
C21	C23	1.532	1.530
C23	C19	1.529	1.529
C23	C18	1.527	1.530
N25	C13	1.297	1.311
C13	C9	1.488	1.483
C9	C4	1.395	1.394
C9	C5	1.394	1.393
C4	C2	1.394	1.380
C2	C1	1.393	1.383
C5	C3	1.392	1.380
C3	C1	1.392	1.383
C8	H8	1.080	1.080
C20	H20	1.100	1.091
C20	H20A	1.100	1.090
C20	H20B	1.100	1.091
C7	H7	1.080	1.080
N26	HN26	1.000	0.970
C6	H6	1.080	1.080
O31	HO31	0.950	0.967
C22	H22	1.099	1.090
C22	H22A	1.100	1.090
C21	H21	1.100	1.090
C21	H21A	1.100	1.090
C23	H23	1.099	1.090
C19	H19	1.100	1.090
C19	H19A	1.100	1.090
C19	H19B	1.100	1.090
C18	H18	1.100	1.090
C18	H18A	1.100	1.090
C18	H18B	1.100	1.090
C4	H4	1.080	1.080
C2	H2	1.080	1.080
C5	H5	1.080	1.080
C3	H3	1.080	1.080
C1	H1	1.080	1.080

Bond Angles for 2PD

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
O30	S33	O29	122.6	123.7
O30	S33	C12	107.7	107.0
O30	S33	N26	107.0	107.0
O29	S33	C12	107.1	107.0
O29	S33	N26	108.4	107.0
C12	S33	N26	102.2	103.5
S33	C12	C8	117.1	121.3
S33	C12	C10	120.5	117.5
S33	N26	C16	124.6	116.4
S33	N26	HN26	117.7	121.8
C8	C12	C10	122.5	121.2
C12	C8	C11	120.1	119.6
C12	C8	H8	119.9	120.2
C12	C10	N24	125.6	121.0
C12	C10	C6	116.7	118.7
C8	C11	O32	119.5	120.1
C8	C11	C7	118.5	119.9
C11	C8	H8	119.9	120.2
O32	C11	C7	122.0	120.1
C11	O32	C20	120.4	117.0
C11	C7	C6	120.9	120.6
C11	C7	H7	119.6	119.7
O32	C20	H20	109.5	109.4
O32	C20	H20A	109.4	109.5
O32	C20	H20B	109.5	109.5
C7	C6	C10	121.4	120.0
C6	C7	H7	119.6	119.7
C7	C6	H6	119.3	120.0
N26	C16	N24	125.5	123.3
N26	C16	C14	110.6	118.3
C16	N26	HN26	117.7	121.8
N24	C16	C14	123.7	118.4
C16	N24	C10	121.5	127.4
C16	C14	C15	120.3	121.3
C16	C14	C17	120.9	121.3
N24	C10	C6	117.7	120.4
C10	C6	H6	119.3	119.9
C15	C14	C17	118.7	117.4
C14	C15	O31	123.0	121.2
C14	C15	C13	117.7	117.8
C14	C17	O28	120.3	120.3
C14	C17	N27	117.1	119.4
O31	C15	C13	119.4	121.1
C15	O31	HO31	109.5	114.0
C15	C13	N25	124.1	120.2
C15	C13	C9	115.5	119.9
O28	C17	N27	122.6	120.3
C17	N27	C22	121.4	118.9
C17	N27	N25	124.3	122.3
C22	N27	N25	114.3	118.8
N27	C22	C21	110.3	109.5
N27	C22	H22	109.2	109.5
N27	C22	H22A	109.0	109.4
N27	N25	C13	118.0	122.9
C22	C21	C23	113.1	109.4
C21	C22	H22	109.2	109.5
C21	C22	H22A	109.0	109.5
C22	C21	H21	108.3	109.4
C22	C21	H21A	107.4	109.5
C21	C23	C19	111.8	109.5
C21	C23	C18	109.0	109.4
C23	C21	H21	108.3	109.5
C23	C21	H21A	107.4	109.5
C21	C23	H23	108.5	109.5
C19	C23	C18	110.3	109.5
C19	C23	H23	107.1	109.5
C23	C19	H19	109.5	109.5
C23	C19	H19A	109.5	109.5
C23	C19	H19B	109.4	109.5
C18	C23	H23	110.1	109.5
C23	C18	H18	109.5	109.5
C23	C18	H18A	109.5	109.5
C23	C18	H18B	109.4	109.5
N25	C13	C9	120.3	119.9
C13	C9	C4	121.9	120.1
C13	C9	C5	118.3	120.1
C4	C9	C5	119.7	119.8
C9	C4	C2	119.5	119.8
C9	C4	H4	120.2	120.1
C9	C5	C3	120.7	119.9
C9	C5	H5	119.6	120.0
C4	C2	C1	120.6	120.1
C2	C4	H4	120.2	120.1
C4	C2	H2	119.7	119.9
C2	C1	C3	119.9	120.2
C1	C2	H2	119.7	119.9
C2	C1	H1	120.0	119.9
C5	C3	C1	119.6	120.1
C3	C5	H5	119.7	120.1
C5	C3	H3	120.2	119.9
C1	C3	H3	120.2	119.9
C3	C1	H1	120.1	119.9
H20	C20	H20A	109.5	109.5
H20	C20	H20B	109.4	109.4
H20A	C20	H20B	109.5	109.5
H22	C22	H22A	110.1	109.4
H21	C21	H21A	112.4	109.5
H19	C19	H19A	109.4	109.5
H19	C19	H19B	109.5	109.5
H19A	C19	H19B	109.5	109.4
H18	C18	H18A	109.5	109.4
H18	C18	H18B	109.5	109.5
H18A	C18	H18B	109.5	109.5

Torsion Angles for 2PD

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
O29	S33	O30	C12	124.7	124.8
O29	S33	O30	N26	234.0	235.2
C12	S33	O30	N26	109.3	110.5
O30	S33	C12	C8	67.2	44.6
O30	S33	C12	C10	247.2	224.6
O30	S33	N26	C16	112.4	148.9
O30	S33	N26	HN26	292.3	328.9
O30	S33	O29	C12	235.0	235.2
O30	S33	O29	N26	125.4	124.8
C12	S33	O29	N26	250.4	249.6
O29	S33	C12	C8	293.7	270.2
O29	S33	C12	C10	113.6	90.2
O29	S33	N26	C16	246.4	283.3
O29	S33	N26	HN26	66.4	103.3
O30	S33	C12	O29	133.6	134.4
O30	S33	C12	N26	247.4	247.1
O29	S33	C12	N26	113.9	112.8
C12	S33	N26	C16	359.3	36.1
C12	S33	N26	HN26	179.3	216.0
C8	C12	S33	C10	180.0	180.0
S33	C12	C8	C11	179.8	179.8
S33	C12	C8	H8	359.8	359.8
S33	C12	C10	N24	359.7	0.7
S33	C12	C10	C6	180.1	180.4
O30	S33	N26	O29	226.0	225.6
O30	S33	N26	C12	113.1	112.9
O29	S33	N26	C12	247.1	247.2
N26	S33	C12	C8	179.8	157.4
N26	S33	C12	C10	359.8	337.4
S33	N26	C16	N24	2.5	329.7
S33	N26	C16	C14	177.6	149.6
C16	N26	S33	HN26	180.0	180.0
C8	C12	S33	N26	179.8	157.4
S33	C12	C8	C10	180.0	180.0
C8	C12	C10	N24	179.7	180.7
C8	C12	C10	C6	0.1	0.4
C12	C8	C11	O32	179.5	180.0
C12	C8	C11	C7	0.2	359.9
C11	C8	C12	H8	180.0	180.0
C10	C12	S33	N26	359.8	337.4
S33	C12	C10	C8	180.0	180.0
C10	C12	C8	C11	359.8	359.8
C10	C12	C8	H8	179.8	179.8
C7	C6	C10	C12	360.0	359.8
C16	N24	C10	C12	1.9	13.4
N24	C10	C12	C6	179.6	180.4
C12	C10	C6	H6	180.0	179.7
C11	C8	C12	C10	359.8	359.8
C12	C8	C11	H8	180.0	180.0
O32	C11	C8	C7	179.2	180.0
C8	C11	O32	C20	125.1	180.0
C8	C11	C7	C6	359.8	0.2
C8	C11	C7	H7	179.8	180.1
C8	C11	O32	C7	180.8	180.0
O32	C11	C8	H8	359.5	360.0
O32	C11	C7	C6	180.6	180.2
O32	C11	C7	H7	0.6	0.1
C11	O32	C20	H20	189.1	300.0
C11	O32	C20	H20A	309.1	60.0
C11	O32	C20	H20B	69.2	180.0
C8	C11	C7	O32	179.2	180.0
C7	C11	C8	H8	180.2	179.9
C7	C11	O32	C20	304.3	0.1
C11	C7	C6	C10	0.1	360.0
C6	C7	C11	H7	180.0	180.1
C11	C7	C6	H6	180.1	180.0
C20	O32	C11	C7	304.3	0.1
H20	C20	O32	H20A	240.0	240.0
H20	C20	O32	H20B	120.0	119.9
H20A	C20	O32	H20B	240.0	239.9
C12	C10	C6	C7	360.0	359.8
C11	C7	C6	H7	180.0	179.9
N24	C10	C6	C7	180.3	179.4
C10	C6	C7	H6	180.0	180.0
S33	N26	C16	HN26	180.0	180.0
N24	C16	N26	C14	184.9	180.0
N26	C16	N24	C10	357.0	2.5
N26	C16	C14	C15	336.5	180.0
N26	C16	C14	C17	160.9	359.7
C12	C10	N24	C16	1.9	13.4
N26	C16	N24	C14	174.5	180.0
N24	C16	N26	HN26	182.5	149.7
N24	C16	C14	C15	151.7	360.0
N24	C16	C14	C17	336.1	179.7
C16	N24	C10	C6	181.5	193.7
N26	C16	C14	N24	184.8	180.0
C14	C16	N26	HN26	357.6	329.7
C14	C16	N24	C10	182.5	182.6
C15	C14	C16	C17	175.6	180.3
C16	C14	C15	O31	3.4	360.0
C16	C14	C15	C13	182.0	180.0
C16	C14	C17	O28	356.5	0.0
C16	C14	C17	N27	177.5	180.0
C12	C10	N24	C6	180.4	179.6
C7	C6	C10	N24	180.3	179.4
C10	N24	C16	C14	182.5	182.6
N24	C10	C6	H6	0.3	359.3
C12	C10	C6	N24	179.6	180.4
C10	C6	C7	H7	180.1	180.1
C7	C6	C10	H6	180.0	180.0
C16	C14	C15	C17	184.3	179.7
C15	C14	C17	O28	180.8	179.7
C15	C14	C17	N27	1.8	359.8
O31	C15	C14	C13	181.4	180.0
C14	C15	O31	HO31	7.4	174.4
C14	C15	C13	N25	2.1	360.0
C14	C15	C13	C9	179.4	180.0
C16	C14	C17	C15	175.7	180.3
C17	C14	C15	O31	179.1	180.3
C17	C14	C15	C13	357.7	0.3
O28	C17	C14	N27	179.0	180.0
C14	C17	N27	C22	178.9	180.0
C14	C17	N27	N25	359.1	360.0
O31	C15	C14	C17	179.1	180.3
C14	C15	O31	C13	178.6	180.0
O31	C15	C13	N25	180.7	179.9
O31	C15	C13	C9	358.0	359.9
C13	C15	C14	C17	357.7	0.3
C14	C15	C13	O31	181.4	180.0
C13	C15	O31	HO31	188.8	354.4
N27	N25	C13	C15	358.8	359.8
N25	C13	C15	C9	182.7	180.0
C15	C13	C9	C4	42.7	139.1
C15	C13	C9	C5	226.4	318.8
C14	C17	O28	N27	181.0	180.0
O28	C17	N27	C22	359.9	0.1
O28	C17	N27	N25	180.1	180.0
C14	C17	N27	O28	179.0	180.0
C22	N27	C17	N25	179.7	180.0
C17	N27	C22	C21	243.4	90.0
C17	N27	C22	H22	3.4	210.0
C17	N27	C22	H22A	123.7	330.0
C17	N27	N25	C13	0.6	0.3
C17	N27	C22	N25	180.2	180.0
C22	N27	N25	C13	180.8	180.2
N27	C22	C21	C23	69.0	180.0
C21	C22	N27	H22	240.0	240.0
C21	C22	N27	H22A	119.7	120.0
N27	C22	C21	H21	189.0	300.0
N27	C22	C21	H21A	310.6	60.0
H22	C22	N27	H22A	239.7	240.1
C15	C13	N25	N27	358.8	359.8
C17	N27	N25	C22	179.8	180.0
N25	N27	C22	C21	63.2	270.0
N25	N27	C22	H22	183.2	30.1
N25	N27	C22	H22A	303.5	150.0
N27	N25	C13	C9	181.7	179.8
C21	C22	N27	N25	63.2	270.0
N27	C22	C21	H22	120.0	120.0
N27	C22	C21	H22A	240.3	240.0
C22	C21	C23	C19	43.2	65.0
C22	C21	C23	C18	165.4	185.0
C23	C21	C22	H21	240.0	240.0
C23	C21	C22	H21A	118.4	120.1
C22	C21	C23	H23	285.2	305.0
H22	C22	C21	H22A	120.3	120.0
H21	C21	C22	H21A	238.4	240.0
C23	C21	C22	H22	309.0	60.0
C23	C21	C22	H22A	188.7	300.0
C22	C21	C23	H21	120.0	120.0
C22	C21	C23	H21A	241.6	240.0
C19	C23	C21	C18	237.8	240.0
C19	C23	C21	H23	117.9	120.0
C21	C23	C19	H19	214.8	60.0
C21	C23	C19	H19A	334.8	180.0
C21	C23	C19	H19B	94.8	300.0
C18	C23	C21	H23	240.2	240.0
C21	C23	C18	H18	34.5	60.0
C21	C23	C18	H18A	154.5	180.0
C21	C23	C18	H18B	274.5	300.0
H21	C21	C23	H21A	121.6	120.0
C21	C23	C19	C18	121.5	119.9
C19	C23	C21	H21	283.2	305.0
C19	C23	C21	H21A	161.5	185.0
C21	C23	C19	H23	241.3	240.0
C18	C23	C19	H23	119.8	120.0
C19	C23	C18	H18	157.6	180.0
C19	C23	C18	H18A	277.6	299.9
C19	C23	C18	H18B	37.6	60.0
H19	C19	C23	H19A	240.0	240.0
H19	C19	C23	H19B	120.0	120.0
H19A	C19	C23	H19B	240.0	240.0
C21	C23	C18	C19	236.8	240.0
C18	C23	C21	H21	45.4	65.0
C18	C23	C21	H21A	283.8	305.0
C21	C23	C18	H23	118.8	120.0
C19	C23	C18	H23	242.0	240.0
C18	C23	C19	H19	93.3	300.0
C18	C23	C19	H19A	213.3	60.1
C18	C23	C19	H19B	333.3	180.0
H18	C18	C23	H18A	240.0	240.1
H18	C18	C23	H18B	120.0	120.0
H18A	C18	C23	H18B	240.0	240.0
C15	C13	N25	C9	177.1	180.0
N25	C13	C9	C4	220.1	319.1
N25	C13	C9	C5	43.8	138.8
C15	C13	C9	N25	182.6	180.0
C4	C9	C13	C5	176.3	180.3
C13	C9	C4	C2	181.9	180.0
C13	C9	C4	H4	1.8	360.0
C13	C9	C5	C3	178.3	180.0
C13	C9	C5	H5	358.3	359.9
C13	C9	C4	C5	183.7	179.7
C4	C9	C5	C3	1.9	359.7
C4	C9	C5	H5	181.9	179.7
C9	C4	C2	C1	1.0	360.0
C2	C4	C9	H4	180.0	180.0
C9	C4	C2	H2	181.0	179.9
C13	C9	C5	C4	176.4	180.3
C5	C9	C4	C2	358.2	0.3
C5	C9	C4	H4	178.1	180.2
C9	C5	C3	C1	358.9	0.0
C3	C5	C9	H5	180.0	180.1
C9	C5	C3	H3	178.9	180.0
C2	C4	C9	C5	358.2	0.3
C9	C4	C2	H4	180.0	180.0
C4	C2	C1	C3	359.9	359.8
C1	C2	C4	H2	180.0	180.0
C4	C2	C1	H1	179.9	180.0
C1	C2	C4	H4	181.0	180.0
C4	C2	C1	H2	180.0	180.0
C5	C3	C1	C2	0.2	0.3
C2	C1	C3	H3	180.2	180.3
C3	C1	C2	H1	180.0	179.8
C9	C5	C3	H5	180.0	179.9
C2	C1	C3	C5	0.2	0.3
C1	C3	C5	H3	180.0	180.0
C5	C3	C1	H1	180.2	180.0
C3	C1	C2	H2	179.8	179.8
C2	C1	C3	H1	180.0	180.2
C1	C3	C5	H5	178.9	180.1
C5	C3	C1	H3	180.0	180.0
H8	C8	C12	C10	179.8	179.8
C12	C8	H8	C11	180.0	180.0
H8	C8	C11	O32	359.5	360.0
H8	C8	C11	C7	180.2	179.9
O32	C20	H20	H20A	120.0	120.0
O32	C20	H20	H20B	240.0	240.0
H20A	C20	H20	H20B	120.0	120.0
O32	C20	H20A	H20	240.0	240.0
O32	C20	H20A	H20B	120.0	120.1
H20	C20	H20A	H20B	240.0	240.1
O32	C20	H20B	H20	120.0	119.9
O32	C20	H20B	H20A	240.0	239.9
H20	C20	H20B	H20A	120.0	120.0
C11	C7	H7	C6	180.0	180.1
H7	C7	C6	C10	180.1	180.1
H7	C7	C6	H6	0.1	0.1
S33	N26	HN26	C16	180.0	180.0
HN26	N26	C16	N24	182.5	149.7
HN26	N26	C16	C14	357.6	329.7
C7	C6	H6	C10	180.0	180.0
H6	C6	C7	H7	0.1	0.1
HO31	O31	C15	C13	188.8	354.4
H22	C22	N27	N25	183.2	30.1
N27	C22	H22	C21	239.3	240.0
N27	C22	H22	H22A	119.7	119.9
H22	C22	C21	C23	309.0	60.0
C21	C22	H22	H22A	240.3	239.9
H22	C22	C21	H21	69.0	180.0
H22	C22	C21	H21A	190.6	300.0
H22A	C22	N27	N25	303.5	150.0
N27	C22	H22A	C21	120.5	120.0
N27	C22	H22A	H22	240.2	240.0
H22A	C22	C21	C23	188.7	300.0
C21	C22	H22A	H22	119.8	120.0
H22A	C22	C21	H21	308.7	60.0
H22A	C22	C21	H21A	70.3	179.9
C22	C21	H21	C23	237.0	240.0
H21	C21	C22	H22	69.0	180.0
H21	C21	C22	H22A	308.7	60.0
C22	C21	H21	H21A	118.5	120.0
H21	C21	C23	C19	283.2	305.0
H21	C21	C23	C18	45.4	65.0
C23	C21	H21	H21A	241.5	240.0
H21	C21	C23	H23	165.2	185.0
C22	C21	H21A	C23	122.0	120.0
H21A	C21	C22	H22	190.6	300.0
H21A	C21	C22	H22A	70.3	179.9
C22	C21	H21A	H21	241.0	240.0
H21A	C21	C23	C19	161.5	185.0
H21A	C21	C23	C18	283.8	305.0
C23	C21	H21A	H21	119.0	120.0
H21A	C21	C23	H23	43.6	65.0
C21	C23	H23	C19	120.9	120.0
C21	C23	H23	C18	240.8	240.0
H23	C23	C21	H21	165.2	185.0
H23	C23	C21	H21A	43.6	65.0
C19	C23	H23	C18	119.9	120.0
H23	C23	C19	H19	333.5	180.0
H23	C23	C19	H19A	93.5	300.0
H23	C23	C19	H19B	213.5	60.0
H23	C23	C18	H18	275.6	300.0
H23	C23	C18	H18A	35.6	60.0
H23	C23	C18	H18B	155.6	180.0
H19	C19	C23	C18	93.3	300.0
H19	C19	C23	H23	333.5	180.0
C23	C19	H19	H19A	120.0	120.0
C23	C19	H19	H19B	240.0	240.0
H19A	C19	H19	H19B	120.0	119.9
H19A	C19	C23	C18	213.3	60.1
H19A	C19	C23	H23	93.5	300.0
C23	C19	H19A	H19	240.0	240.0
C23	C19	H19A	H19B	120.0	120.0
H19	C19	H19A	H19B	240.0	240.1
H19B	C19	C23	C18	333.3	180.0
H19B	C19	C23	H23	213.5	60.0
C23	C19	H19B	H19	120.0	120.0
C23	C19	H19B	H19A	240.0	240.0
H19	C19	H19B	H19A	120.0	119.9
H18	C18	C23	H23	275.6	300.0
C23	C18	H18	H18A	120.0	120.0
C23	C18	H18	H18B	240.0	240.0
H18A	C18	H18	H18B	120.0	120.0
H18A	C18	C23	H23	35.6	60.0
C23	C18	H18A	H18	240.0	240.0
C23	C18	H18A	H18B	120.0	120.0
H18	C18	H18A	H18B	240.0	240.0
H18B	C18	C23	H23	155.6	180.0
C23	C18	H18B	H18	120.0	120.0
C23	C18	H18B	H18A	240.0	240.0
H18	C18	H18B	H18A	120.0	119.9
H4	C4	C9	C5	178.1	180.2
C9	C4	H4	C2	180.0	180.0
H4	C4	C2	C1	181.0	180.0
H4	C4	C2	H2	1.0	360.0
C4	C2	H2	C1	180.0	180.0
H2	C2	C4	H4	1.0	360.0
H2	C2	C1	C3	179.8	179.8
H2	C2	C1	H1	359.8	360.0
C9	C5	H5	C3	180.0	180.1
H5	C5	C3	C1	178.9	180.1
H5	C5	C3	H3	358.9	0.0
C5	C3	H3	C1	180.0	180.0
H3	C3	C5	H5	358.9	0.0
H3	C3	C1	H1	0.2	0.1
C2	C1	H1	C3	180.0	179.8
H1	C1	C2	H2	359.8	360.0
H1	C1	C3	H3	0.2	0.1