PDB Chemical Component MMD

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 MMD

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C1	C2	1.530	1.531
C1	N6	1.476	1.470
C2	O3	1.438	1.430
O3	C4	1.447	1.430
C4	C5	1.528	1.532
C5	N6	1.476	1.471
N6	C7	1.390	1.384
C7	N8	1.341	1.324
C7	N9	1.341	1.322
N8	C19	1.348	1.335
N9	C10	1.342	1.337
C10	N11	1.332	1.382
C10	C18	1.393	1.389
N11	S12	1.639	1.656
N11	C16	1.468	1.467
S12	C13	1.774	1.814
S12	O14	1.495	1.420
S12	O15	1.493	1.421
C16	C17	1.527	1.539
C17	C18	1.519	1.510
C18	C19	1.396	1.391
C19	C20	1.408	1.482
C20	C21	1.398	1.398
C20	C28	1.392	1.398
C21	N22	1.324	1.321
N22	C23	1.345	1.326
C23	N24	1.332	1.383
C23	N27	1.347	1.325
N27	C28	1.329	1.321
C1	H1	1.100	1.091
C1	H1A	1.100	1.091
C2	H2	1.100	1.091
C2	H2A	1.100	1.090
C4	H4	1.100	1.091
C4	H4A	1.100	1.090
C5	H5	1.100	1.089
C5	H5A	1.100	1.090
C13	H13	1.100	1.090
C13	H13A	1.100	1.090
C13	H13B	1.100	1.090
C16	H16	1.100	1.089
C16	H16A	1.100	1.091
C17	H17	1.100	1.089
C17	H17A	1.099	1.090
C21	H21	1.080	1.080
N24	HN24	1.000	0.970
N24	HN2A	1.001	0.970
C28	H28	1.080	1.080

Bond Angles for MMD

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	C1	N6	110.7	109.3
C1	C2	O3	107.7	109.2
C2	C1	H1	109.1	109.5
C2	C1	H1A	109.0	109.5
C1	C2	H2	110.1	109.5
C1	C2	H2A	110.1	109.5
C1	N6	C5	120.9	110.8
C1	N6	C7	120.0	111.0
N6	C1	H1	109.1	109.5
N6	C1	H1A	109.1	109.5
C2	O3	C4	108.4	113.8
O3	C2	H2	110.1	109.5
O3	C2	H2A	110.0	109.5
O3	C4	C5	110.4	109.3
O3	C4	H4	109.2	109.5
O3	C4	H4A	109.2	109.5
C4	C5	N6	111.8	109.2
C5	C4	H4	109.2	109.5
C5	C4	H4A	109.2	109.5
C4	C5	H5	108.7	109.5
C4	C5	H5A	108.7	109.5
C5	N6	C7	119.1	111.0
N6	C5	H5	108.7	109.5
N6	C5	H5A	108.7	109.5
N6	C7	N8	119.2	118.9
N6	C7	N9	119.7	119.0
N8	C7	N9	121.1	122.1
C7	N8	C19	122.0	120.4
C7	N9	C10	120.4	121.1
N8	C19	C18	117.3	118.9
N8	C19	C20	118.2	120.6
N9	C10	N11	130.6	130.1
N9	C10	C18	119.2	118.2
N11	C10	C18	110.2	111.8
C10	N11	S12	123.2	124.9
C10	N11	C16	112.9	110.3
C10	C18	C17	109.4	108.6
C10	C18	C19	120.1	119.3
S12	N11	C16	123.3	124.8
N11	S12	C13	106.4	104.4
N11	S12	O14	112.6	104.3
N11	S12	O15	109.3	104.3
N11	C16	C17	104.2	105.1
N11	C16	H16	111.2	110.3
N11	C16	H16A	111.2	110.3
C13	S12	O14	109.6	110.5
C13	S12	O15	109.9	110.5
S12	C13	H13	109.5	109.5
S12	C13	H13A	109.5	109.5
S12	C13	H13B	109.5	109.5
O14	S12	O15	109.0	121.1
C16	C17	C18	103.2	104.3
C17	C16	H16	111.3	110.3
C17	C16	H16A	111.3	110.3
C16	C17	H17	111.7	110.5
C16	C17	H17A	111.6	110.5
C17	C18	C19	130.5	132.1
C18	C17	H17	111.6	110.5
C18	C17	H17A	111.6	110.4
C18	C19	C20	124.5	120.6
C19	C20	C21	119.8	120.9
C19	C20	C28	123.0	120.8
C21	C20	C28	117.2	118.3
C20	C21	N22	121.2	119.1
C20	C21	H21	119.4	120.4
C20	C28	N27	119.5	119.0
C20	C28	H28	120.3	120.5
C21	N22	C23	120.2	120.8
N22	C21	H21	119.4	120.5
N22	C23	N24	120.0	119.0
N22	C23	N27	120.1	121.9
N24	C23	N27	119.9	119.1
C23	N24	HN24	109.5	120.0
C23	N24	HN2A	109.5	120.0
C23	N27	C28	121.8	120.9
N27	C28	H28	120.3	120.4
H1	C1	H1A	109.9	109.5
H2	C2	H2A	108.9	109.6
H4	C4	H4A	109.8	109.6
H5	C5	H5A	110.2	109.6
H13	C13	H13A	109.4	109.5
H13	C13	H13B	109.5	109.5
H13A	C13	H13B	109.5	109.5
H16	C16	H16A	107.6	110.4
H17	C17	H17A	107.2	110.6
HN24	N24	HN2A	109.5	120.0

Torsion Angles for MMD

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
C2	C1	N6	C5	33.9	58.6
C2	C1	N6	C7	214.4	182.4
N6	C1	C2	H1	240.0	240.0
N6	C1	C2	H1A	120.0	119.9
C1	C2	O3	C4	72.0	58.7
O3	C2	C1	H2	240.0	240.1
O3	C2	C1	H2A	120.0	120.0
H1	C1	C2	H1A	240.0	239.9
H2	C2	C1	H2A	240.0	239.9
N6	C1	C2	O3	307.1	303.2
C2	C1	N6	H1	120.0	120.0
C2	C1	N6	H1A	240.0	240.1
N6	C1	C2	H2	67.1	63.1
N6	C1	C2	H2A	187.1	183.2
C4	C5	N6	C1	330.6	301.4
C5	N6	C1	C7	179.5	236.3
C1	N6	C5	H5	210.6	181.5
C1	N6	C5	H5A	90.6	61.3
C1	N6	C7	N8	187.5	0.1
C1	N6	C7	N9	7.5	179.7
H1	C1	N6	H1A	120.0	120.1
O3	C2	C1	N6	307.1	303.2
O3	C2	C1	H1	67.1	63.1
O3	C2	C1	H1A	187.1	183.2
C1	C2	O3	H2	120.0	119.9
C1	C2	O3	H2A	240.0	240.0
C2	O3	C4	C5	292.3	301.3
C2	O3	C4	H4	52.3	61.3
C2	O3	C4	H4A	172.3	181.4
H2	C2	O3	H2A	120.0	120.2
C4	O3	C2	H2	312.0	298.8
C4	O3	C2	H2A	192.0	178.6
O3	C4	C5	N6	43.9	56.9
C5	C4	O3	H4	240.0	240.0
C5	C4	O3	H4A	120.0	119.9
O3	C4	C5	H5	164.0	176.8
O3	C4	C5	H5A	284.0	296.9
H4	C4	O3	H4A	240.0	239.8
C1	N6	C5	C4	330.6	301.4
O3	C4	C5	H4	120.0	120.0
O3	C4	C5	H4A	240.0	240.1
C4	C5	N6	C7	150.1	177.6
N6	C5	C4	H5	240.0	240.1
N6	C5	C4	H5A	120.0	119.9
H4	C4	C5	H4A	120.0	120.1
H5	C5	C4	H5A	240.0	239.8
C1	N6	C5	C7	180.5	123.8
C5	N6	C1	H1	273.9	298.7
C5	N6	C1	H1A	153.9	178.6
N6	C5	C4	H4	283.9	296.9
N6	C5	C4	H4A	163.9	176.8
C4	C5	N6	H5	120.0	119.9
C4	C5	N6	H5A	240.0	240.1
C5	N6	C7	N8	8.0	123.7
C5	N6	C7	N9	188.0	303.4
H5	C5	N6	H5A	120.0	120.2
C1	N6	C7	C5	179.5	236.4
C7	N6	C1	H1	94.4	62.4
C7	N6	C1	H1A	334.4	302.3
C7	N6	C5	H5	30.1	57.7
C7	N6	C5	H5A	270.1	297.5
N8	C7	N6	N9	180.0	180.3
N6	C7	N8	C19	179.8	180.0
N6	C7	N9	C10	180.2	180.0
N6	C7	N8	N9	180.0	179.7
N8	C7	N9	C10	0.3	359.7
C7	N8	C19	C18	0.6	359.9
C7	N8	C19	C20	180.4	180.0
N6	C7	N9	N8	180.0	180.3
N9	C7	N8	C19	359.8	0.3
C7	N9	C10	N11	181.3	180.0
C7	N9	C10	C18	359.3	360.0
C19	N8	C7	N9	359.8	0.3
C10	C18	C19	N8	358.9	359.8
C17	C18	C19	N8	179.8	180.1
C18	C19	N8	C20	180.2	180.0
N8	C19	C20	C21	344.2	325.0
N8	C19	C20	C28	163.4	144.7
N11	C10	N9	C18	182.1	180.0
N9	C10	N11	S12	9.0	0.0
N9	C10	N11	C16	180.6	180.0
N9	C10	C18	C17	180.4	180.0
N9	C10	C18	C19	1.2	0.2
N9	C10	N11	C18	178.1	180.0
N11	C10	C18	C17	358.8	360.0
N11	C10	C18	C19	179.5	180.2
S12	N11	C10	C16	188.4	180.0
C10	N11	S12	C13	72.3	89.9
C10	N11	S12	O14	312.3	206.0
C10	N11	S12	O15	190.9	333.9
C10	N11	C16	C17	357.3	0.0
C10	N11	C16	H16	117.3	118.9
C10	N11	C16	H16A	237.3	241.1
N8	C19	C18	C10	358.9	359.8
N9	C10	C18	N11	181.7	180.0
C18	C10	N11	S12	190.9	180.0
C18	C10	N11	C16	2.5	360.0
C16	C17	C18	C10	359.5	0.0
C17	C18	C10	C19	179.3	179.7
C10	C18	C17	H17	239.5	241.3
C10	C18	C17	H17A	119.5	118.7
C10	C18	C19	C20	179.1	179.8
S12	N11	C10	C18	190.9	180.0
C10	N11	S12	C16	170.7	180.0
S12	N11	C16	C17	168.9	180.0
S12	N11	C16	H16	288.9	298.9
S12	N11	C16	H16A	48.9	61.1
C13	S12	N11	O14	120.0	243.9
C13	S12	N11	O15	241.4	116.0
N11	S12	C13	H13	180.0	60.0
N11	S12	C13	H13A	300.0	180.0
N11	S12	C13	H13B	60.0	300.0
O14	S12	N11	O15	121.4	232.1
C16	N11	C10	C18	2.5	360.0
C10	N11	C16	S12	188.4	180.0
C16	N11	S12	C13	261.6	270.0
C16	N11	S12	O14	141.5	26.0
C16	N11	S12	O15	20.2	153.9
N11	C16	C17	C18	1.8	360.0
C17	C16	N11	H16	240.0	241.1
C17	C16	N11	H16A	120.0	118.9
N11	C16	C17	H17	121.8	118.7
N11	C16	C17	H17A	241.8	241.3
H16	C16	N11	H16A	240.0	237.8
C13	S12	N11	C16	261.6	270.0
N11	S12	C13	O14	238.0	111.6
N11	S12	C13	O15	118.2	248.4
O14	S12	C13	O15	240.2	136.8
H13	C13	S12	H13A	240.0	240.0
H13	C13	S12	H13B	120.0	120.0
H13A	C13	S12	H13B	240.0	240.0
O14	S12	N11	C16	141.5	26.0
N11	S12	O14	C13	118.2	248.3
N11	S12	O14	O15	238.5	116.8
C13	S12	O14	O15	120.3	228.5
O14	S12	C13	H13	302.0	308.4
O14	S12	C13	H13A	62.0	68.4
O14	S12	C13	H13B	182.0	188.4
O15	S12	N11	C16	20.2	153.9
N11	S12	O15	C13	243.6	111.7
N11	S12	O15	O14	123.5	243.2
C13	S12	O15	O14	239.9	131.5
O15	S12	C13	H13	61.8	171.6
O15	S12	C13	H13A	181.8	291.6
O15	S12	C13	H13B	301.8	51.6
C10	C18	C17	C16	359.5	0.0
N11	C16	C17	H16	120.0	118.9
N11	C16	C17	H16A	240.0	241.1
C16	C17	C18	C19	178.7	179.7
C18	C17	C16	H17	240.0	241.3
C18	C17	C16	H17A	120.0	118.7
H16	C16	C17	H16A	120.0	122.2
H17	C17	C16	H17A	240.0	237.3
N8	C19	C18	C17	179.8	180.1
C10	C18	C17	C19	180.8	180.3
C18	C17	C16	H16	241.8	241.1
C18	C17	C16	H16A	121.8	118.9
C16	C17	C18	H17	120.0	118.7
C16	C17	C18	H17A	240.0	241.3
C17	C18	C19	C20	0.0	0.1
H17	C17	C18	H17A	120.0	122.6
N8	C19	C18	C20	179.8	180.0
C10	C18	C19	C17	179.1	179.7
C19	C18	C17	H17	58.7	61.0
C19	C18	C17	H17A	298.7	298.4
C18	C19	C20	C21	164.0	145.0
C18	C19	C20	C28	343.1	324.7
N8	C19	C20	C18	180.2	180.0
C21	C20	C19	C28	180.8	180.3
C19	C20	C21	N22	179.6	180.0
C19	C20	C21	H21	359.6	0.0
C19	C20	C28	N27	180.2	179.7
C19	C20	C28	H28	0.2	0.0
C19	C20	C21	C28	179.2	179.7
C21	C20	C28	N27	359.4	359.4
C21	C20	C28	H28	179.4	179.7
C20	C21	N22	C23	0.0	0.1
N22	C21	C20	H21	180.0	180.0
C19	C20	C28	C21	180.8	180.3
C28	C20	C21	N22	0.4	0.3
C28	C20	C21	H21	180.3	180.3
C23	N27	C28	C20	0.4	0.6
N27	C28	C20	H28	180.0	179.7
N22	C21	C20	C28	0.4	0.3
C20	C21	N22	H21	180.0	180.0
C21	N22	C23	N24	179.6	180.0
C21	N22	C23	N27	359.8	359.9
C23	N22	C21	H21	180.1	180.0
N24	C23	N22	N27	179.9	180.1
N22	C23	N24	HN24	0.0	360.0
N22	C23	N24	HN2A	120.0	179.9
N22	C23	N27	C28	0.0	359.8
N22	C23	N24	N27	180.1	179.9
N24	C23	N27	C28	180.2	179.7
HN24	N24	C23	HN2A	240.0	180.1
C20	C28	N27	C23	0.4	0.6
N22	C23	N27	N24	179.9	180.1
N27	C23	N24	HN24	179.9	180.0
N27	C23	N24	HN2A	299.9	360.0
C23	N27	C28	H28	180.4	180.3
C20	C28	N27	H28	180.0	180.3
C2	C1	H1	N6	239.0	240.2
H1	C1	C2	O3	67.1	63.1
C2	C1	H1	H1A	119.5	120.1
H1	C1	C2	H2	187.1	183.0
H1	C1	C2	H2A	307.1	303.2
H1	C1	N6	C5	273.9	298.7
H1	C1	N6	C7	94.4	62.4
N6	C1	H1	H1A	240.5	239.9
C2	C1	H1A	N6	121.0	119.8
H1A	C1	C2	O3	187.1	183.2
C2	C1	H1A	H1	240.5	239.9
H1A	C1	C2	H2	307.1	303.1
H1A	C1	C2	H2A	67.1	63.3
H1A	C1	N6	C5	153.9	178.6
H1A	C1	N6	C7	334.4	302.3
N6	C1	H1A	H1	119.5	120.1
H2	C2	C1	N6	67.1	63.1
C1	C2	H2	O3	241.4	240.3
H2	C2	C1	H1	187.1	183.0
H2	C2	C1	H1A	307.1	303.1
C1	C2	H2	H2A	120.7	120.1
H2	C2	O3	C4	312.0	298.8
O3	C2	H2	H2A	239.3	239.8
H2A	C2	C1	N6	187.1	183.2
C1	C2	H2A	O3	118.5	119.8
H2A	C2	C1	H1	307.1	303.2
H2A	C2	C1	H1A	67.1	63.3
C1	C2	H2A	H2	239.3	239.9
H2A	C2	O3	C4	192.0	178.6
O3	C2	H2A	H2	120.7	120.1
O3	C4	H4	C5	239.3	240.2
O3	C4	H4	H4A	119.6	120.1
H4	C4	C5	N6	283.9	296.9
C5	C4	H4	H4A	240.4	239.9
H4	C4	C5	H5	43.9	56.8
H4	C4	C5	H5A	163.9	177.0
O3	C4	H4A	C5	120.7	119.8
O3	C4	H4A	H4	240.4	239.8
H4A	C4	C5	N6	163.9	176.8
C5	C4	H4A	H4	119.6	120.1
H4A	C4	C5	H5	284.0	296.7
H4A	C4	C5	H5A	44.0	56.8
C4	C5	H5	N6	238.1	240.3
H5	C5	C4	H4	43.9	56.8
H5	C5	C4	H4A	284.0	296.7
C4	C5	H5	H5A	119.0	120.1
H5	C5	N6	C7	30.1	57.7
N6	C5	H5	H5A	240.9	239.9
C4	C5	H5A	N6	121.9	119.7
H5A	C5	C4	H4	163.9	177.0
H5A	C5	C4	H4A	44.0	56.8
C4	C5	H5A	H5	240.9	239.9
H5A	C5	N6	C7	270.1	297.5
N6	C5	H5A	H5	119.1	120.1
H13	C13	S12	O14	302.0	308.4
H13	C13	S12	O15	61.8	171.6
S12	C13	H13	H13A	120.0	120.0
S12	C13	H13	H13B	240.0	240.0
H13A	C13	H13	H13B	120.0	120.0
H13A	C13	S12	O14	62.0	68.4
H13A	C13	S12	O15	181.8	291.6
S12	C13	H13A	H13	240.0	240.0
S12	C13	H13A	H13B	120.0	120.0
H13	C13	H13A	H13B	240.0	240.0
H13B	C13	S12	O14	182.0	188.4
H13B	C13	S12	O15	301.8	51.6
S12	C13	H13B	H13	120.0	120.0
S12	C13	H13B	H13A	240.0	240.0
H13	C13	H13B	H13A	120.0	120.0
N11	C16	H16	C17	244.2	244.3
N11	C16	H16	H16A	122.1	122.2
H16	C16	C17	C18	241.8	241.1
C17	C16	H16	H16A	237.9	237.9
H16	C16	C17	H17	1.8	359.7
H16	C16	C17	H17A	121.8	122.4
N11	C16	H16A	C17	115.8	115.7
N11	C16	H16A	H16	237.9	237.8
H16A	C16	C17	C18	121.8	118.9
C17	C16	H16A	H16	122.2	122.2
H16A	C16	C17	H17	241.8	237.5
H16A	C16	C17	H17A	1.8	0.2
C16	C17	H17	C18	245.1	245.2
H17	C17	C16	H16	1.8	359.7
H17	C17	C16	H16A	241.8	237.5
C16	C17	H17	H17A	122.6	122.6
H17	C17	C18	C19	58.7	61.0
C18	C17	H17	H17A	237.4	237.5
C16	C17	H17A	C18	114.9	114.8
H17A	C17	C16	H16	121.8	122.4
H17A	C17	C16	H16A	1.8	0.2
C16	C17	H17A	H17	237.4	237.4
H17A	C17	C18	C19	298.7	298.4
C18	C17	H17A	H17	122.5	122.6
H21	C21	C20	C28	180.3	180.3
C20	C21	H21	N22	180.0	180.0
H21	C21	N22	C23	180.1	180.0
HN24	N24	C23	N27	179.9	180.0
C23	N24	HN24	HN2A	120.0	179.9
HN2A	N24	C23	N27	299.9	360.0
C23	N24	HN2A	HN24	240.0	180.1
C20	C28	H28	N27	180.0	179.7