PDB Chemical Component SPD

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 SPD

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
N1	C2	1.570	1.468
N1	HN11	1.020	1.009
N1	HN12	1.020	1.008
C2	C3	1.558	1.529
C2	H21	1.115	1.089
C2	H22	1.115	1.090
C3	C4	1.555	1.529
C3	H31	1.116	1.090
C3	H32	1.114	1.089
C4	C5	1.595	1.529
C4	H41	1.116	1.089
C4	H42	1.116	1.090
C5	N6	1.509	1.468
C5	H51	1.114	1.089
C5	H52	1.115	1.089
N6	C7	1.553	1.469
N6	HN6	1.020	1.008
C7	C8	1.565	1.529
C7	H71	1.116	1.090
C7	H72	1.115	1.089
C8	C9	1.576	1.530
C8	H81	1.115	1.090
C8	H82	1.115	1.089
C9	N10	1.578	1.468
C9	H91	1.115	1.090
C9	H92	1.115	1.089
N10	H101	1.021	1.008
N10	H102	1.021	1.009

Bond Angles for SPD

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	N1	HN11	123.0	106.7
C2	N1	HN12	107.3	106.8
N1	C2	C3	123.1	109.6
N1	C2	H21	107.4	109.5
N1	C2	H22	107.4	109.4
HN11	N1	HN12	107.4	106.7
C3	C2	H21	107.3	109.4
C3	C2	H22	107.3	109.4
C2	C3	C4	119.9	109.6
C2	C3	H31	108.5	109.5
C2	C3	H32	108.5	109.4
H21	C2	H22	102.4	109.5
C4	C3	H31	108.4	109.5
C4	C3	H32	108.5	109.4
C3	C4	C5	111.1	109.5
C3	C4	H41	111.6	109.4
C3	C4	H42	111.6	109.4
H31	C3	H32	101.5	109.4
C5	C4	H41	111.6	109.5
C5	C4	H42	111.6	109.5
C4	C5	N6	122.5	109.5
C4	C5	H51	107.5	109.5
C4	C5	H52	107.5	109.5
H41	C4	H42	98.7	109.5
N6	C5	H51	107.6	109.5
N6	C5	H52	107.6	109.5
C5	N6	C7	122.6	106.7
C5	N6	HN6	107.6	106.7
H51	C5	H52	102.3	109.4
C7	N6	HN6	107.5	106.7
N6	C7	C8	119.7	109.5
N6	C7	H71	108.5	109.5
N6	C7	H72	108.5	109.4
C8	C7	H71	108.5	109.5
C8	C7	H72	108.5	109.5
C7	C8	C9	117.1	109.5
C7	C8	H81	109.5	109.5
C7	C8	H82	109.5	109.5
H71	C7	H72	101.5	109.4
C9	C8	H81	109.4	109.5
C9	C8	H82	109.4	109.4
C8	C9	N10	117.9	109.6
C8	C9	H91	109.2	109.5
C8	C9	H92	109.2	109.4
H81	C8	H82	100.7	109.4
N10	C9	H91	109.1	109.5
N10	C9	H92	109.2	109.5
C9	N10	H101	117.9	106.8
C9	N10	H102	109.2	106.7
H91	C9	H92	100.9	109.4
H101	N10	H102	109.1	106.7

Torsion Angles for SPD

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
HN11	N1	C2	HN12	125.3	113.7
C3	C2	N1	H21	234.8	240.0
C3	C2	N1	H22	125.2	120.0
N1	C2	C3	C4	70.5	180.0
N1	C2	C3	H31	195.7	300.1
N1	C2	C3	H32	305.2	60.0
H21	C2	N1	H22	250.5	240.0
C2	N1	HN11	HN12	234.8	246.2
HN11	N1	C2	C3	180.0	293.8
HN11	N1	C2	H21	305.2	53.8
HN11	N1	C2	H22	54.7	173.8
C2	N1	HN12	HN11	134.2	113.7
HN12	N1	C2	C3	54.7	180.0
HN12	N1	C2	H21	180.0	300.0
HN12	N1	C2	H22	289.5	60.0
C3	C2	N1	HN11	180.0	293.8
C3	C2	N1	HN12	54.7	180.0
N1	C2	C3	H21	125.3	120.1
N1	C2	C3	H22	234.7	240.0
H21	C2	C3	H22	109.5	119.9
C4	C3	C2	H31	234.8	239.9
C4	C3	C2	H32	125.3	120.0
C2	C3	C4	C5	316.2	180.0
C2	C3	C4	H41	81.5	300.1
C2	C3	C4	H42	190.9	60.0
H31	C3	C2	H32	250.5	240.1
H21	C2	N1	HN11	305.2	53.8
H21	C2	N1	HN12	180.0	300.0
N1	C2	H21	C3	225.8	239.9
N1	C2	H21	H22	112.9	120.0
C3	C2	H21	H22	247.1	240.1
H21	C2	C3	C4	305.2	59.9
H21	C2	C3	H31	70.5	180.0
H21	C2	C3	H32	180.0	299.9
H22	C2	N1	HN11	54.7	173.8
H22	C2	N1	HN12	289.5	60.0
N1	C2	H22	C3	134.2	120.1
N1	C2	H22	H21	247.0	240.0
C3	C2	H22	H21	112.9	119.9
H22	C2	C3	C4	195.8	300.0
H22	C2	C3	H31	321.0	60.1
H22	C2	C3	H32	70.5	180.0
C4	C3	C2	H21	305.2	59.9
C4	C3	C2	H22	195.8	300.0
C2	C3	C4	H31	125.3	120.1
C2	C3	C4	H32	234.7	240.0
H31	C3	C4	H32	109.4	119.9
C5	C4	C3	H41	234.7	239.9
C5	C4	C3	H42	125.3	120.0
C3	C4	C5	N6	260.4	180.0
C3	C4	C5	H51	25.7	300.0
C3	C4	C5	H52	135.1	60.0
H41	C4	C3	H42	250.6	240.0
H31	C3	C2	H21	70.5	180.0
H31	C3	C2	H22	321.0	60.1
C2	C3	H31	C4	228.3	239.9
C2	C3	H31	H32	114.2	119.9
C4	C3	H31	H32	245.9	240.1
H31	C3	C4	C5	191.0	59.9
H31	C3	C4	H41	316.3	180.0
H31	C3	C4	H42	65.6	299.9
H32	C3	C2	H21	180.0	299.9
H32	C3	C2	H22	70.5	180.0
C2	C3	H32	C4	131.7	120.1
C2	C3	H32	H31	245.8	240.1
C4	C3	H32	H31	114.1	120.0
H32	C3	C4	C5	81.5	300.0
H32	C3	C4	H41	206.8	60.1
H32	C3	C4	H42	316.2	180.0
C5	C4	C3	H31	191.0	59.9
C5	C4	C3	H32	81.5	300.0
C3	C4	C5	H41	125.3	120.0
C3	C4	C5	H42	234.7	240.0
H41	C4	C5	H42	109.4	120.0
N6	C5	C4	H51	234.7	240.0
N6	C5	C4	H52	125.2	120.0
C4	C5	N6	C7	3.9	180.0
C4	C5	N6	HN6	238.7	293.8
H51	C5	C4	H52	250.5	240.0
H41	C4	C3	H31	316.3	180.0
H41	C4	C3	H32	206.8	60.1
C3	C4	H41	C5	235.0	239.9
C3	C4	H41	H42	117.5	119.9
C5	C4	H41	H42	242.5	240.0
H41	C4	C5	N6	135.1	60.0
H41	C4	C5	H51	260.4	180.0
H41	C4	C5	H52	9.8	300.0
H42	C4	C3	H31	65.6	299.9
H42	C4	C3	H32	316.2	180.0
C3	C4	H42	C5	125.0	120.0
C3	C4	H42	H41	242.5	240.1
C5	C4	H42	H41	117.5	120.0
H42	C4	C5	N6	25.7	300.0
H42	C4	C5	H51	151.0	60.0
H42	C4	C5	H52	260.4	180.0
N6	C5	C4	H41	135.1	60.0
N6	C5	C4	H42	25.7	300.0
C4	C5	N6	H51	125.3	120.0
C4	C5	N6	H52	234.8	240.0
H51	C5	N6	H52	109.5	120.0
C7	N6	C5	HN6	125.2	246.2
C5	N6	C7	C8	215.0	180.0
C5	N6	C7	H71	340.2	300.1
C5	N6	C7	H72	89.7	60.0
H51	C5	C4	H41	260.4	180.0
H51	C5	C4	H42	151.0	60.0
C4	C5	H51	N6	226.2	240.0
C4	C5	H51	H52	113.1	120.0
N6	C5	H51	H52	246.9	240.0
H51	C5	N6	C7	238.6	60.0
H51	C5	N6	HN6	113.4	173.7
H52	C5	C4	H41	9.8	300.0
H52	C5	C4	H42	260.4	180.0
C4	C5	H52	N6	133.8	120.0
C4	C5	H52	H51	246.9	240.0
N6	C5	H52	H51	113.2	120.0
H52	C5	N6	C7	129.1	300.0
H52	C5	N6	HN6	3.9	53.8
C7	N6	C5	H51	238.6	60.0
C7	N6	C5	H52	129.1	300.0
C5	N6	C7	HN6	234.8	113.8
C8	C7	N6	H71	234.8	240.0
C8	C7	N6	H72	125.3	120.0
N6	C7	C8	C9	79.8	180.0
N6	C7	C8	H81	205.1	300.0
N6	C7	C8	H82	314.6	60.0
H71	C7	N6	H72	250.5	240.1
HN6	N6	C5	H51	113.4	173.7
HN6	N6	C5	H52	3.9	53.8
C5	N6	HN6	C7	133.8	246.2
HN6	N6	C7	C8	340.2	66.2
HN6	N6	C7	H71	105.4	186.2
HN6	N6	C7	H72	214.9	306.2
C8	C7	N6	HN6	340.2	66.2
N6	C7	C8	H71	125.3	120.0
N6	C7	C8	H72	234.7	240.0
H71	C7	C8	H72	109.5	120.0
C9	C8	C7	H81	234.8	240.0
C9	C8	C7	H82	125.3	120.0
C7	C8	C9	N10	77.7	180.0
C7	C8	C9	H91	202.9	300.0
C7	C8	C9	H92	312.4	60.0
H81	C8	C7	H82	250.5	240.0
H71	C7	N6	HN6	105.4	186.2
N6	C7	H71	C8	228.4	239.9
N6	C7	H71	H72	114.2	119.9
C8	C7	H71	H72	245.8	240.0
H71	C7	C8	C9	314.6	60.0
H71	C7	C8	H81	79.8	180.0
H71	C7	C8	H82	189.3	300.0
H72	C7	N6	HN6	214.9	306.2
N6	C7	H72	C8	131.6	120.1
N6	C7	H72	H71	245.8	240.0
C8	C7	H72	H71	114.2	120.0
H72	C7	C8	C9	205.1	300.0
H72	C7	C8	H81	330.3	60.0
H72	C7	C8	H82	79.9	180.0
C9	C8	C7	H71	314.6	60.0
C9	C8	C7	H72	205.1	300.0
C7	C8	C9	H81	125.2	120.0
C7	C8	C9	H82	234.7	240.0
H81	C8	C9	H82	109.5	119.9
N10	C9	C8	H91	234.7	240.0
N10	C9	C8	H92	125.3	120.0
C8	C9	N10	H101	180.0	180.0
C8	C9	N10	H102	54.8	293.8
H91	C9	C8	H92	250.5	240.1
H81	C8	C7	H71	79.8	180.0
H81	C8	C7	H72	330.3	60.0
C7	C8	H81	C9	230.5	239.9
C7	C8	H81	H82	115.3	120.0
C9	C8	H81	H82	244.8	240.1
H81	C8	C9	N10	312.4	60.0
H81	C8	C9	H91	77.7	180.0
H81	C8	C9	H92	187.2	299.9
H82	C8	C7	H71	189.3	300.0
H82	C8	C7	H72	79.9	180.0
C7	C8	H82	C9	129.6	120.1
C7	C8	H82	H81	244.7	240.0
C9	C8	H82	H81	115.2	119.9
H82	C8	C9	N10	203.0	300.0
H82	C8	C9	H91	328.2	60.1
H82	C8	C9	H92	77.7	180.0
N10	C9	C8	H81	312.4	60.0
N10	C9	C8	H82	203.0	300.0
C8	C9	N10	H91	125.3	120.0
C8	C9	N10	H92	234.7	240.0
H91	C9	N10	H92	109.4	119.9
H101	N10	C9	H102	125.3	246.2
H91	C9	C8	H81	77.7	180.0
H91	C9	C8	H82	328.2	60.1
C8	C9	H91	N10	229.8	239.9
C8	C9	H91	H92	114.9	119.9
N10	C9	H91	H92	245.1	240.0
H91	C9	N10	H101	54.7	60.0
H91	C9	N10	H102	289.5	173.8
H92	C9	C8	H81	187.2	299.9
H92	C9	C8	H82	77.7	180.0
C8	C9	H92	N10	130.2	120.1
C8	C9	H92	H91	245.0	240.1
N10	C9	H92	H91	114.9	120.0
H92	C9	N10	H101	305.3	300.0
H92	C9	N10	H102	180.0	53.9
H101	N10	C9	H91	54.7	60.0
H101	N10	C9	H92	305.3	300.0
C9	N10	H101	H102	234.7	113.8
H102	N10	C9	H91	289.5	173.8
H102	N10	C9	H92	180.0	53.9
C9	N10	H102	H101	130.2	246.1