VMX

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
S	C1S	sing	1.81Å	1.66Å
S	O2S	doub	1.42Å	1.44Å
S	O3S	doub	1.42Å	1.44Å
S	N5'	sing	1.66Å	1.60Å
N1	C2	doub	1.32Å	1.34Å	Aromatic
N1	C6	sing	1.33Å	1.35Å	Aromatic
C2	N3	sing	1.32Å	1.34Å	Aromatic
N3	C4	doub	1.33Å	1.36Å	Aromatic
C4	C5	sing	1.41Å	1.38Å	Aromatic
C4	N9	sing	1.37Å	1.32Å	Aromatic
C5	C6	doub	1.40Å	1.49Å	Aromatic
C5	N7	sing	1.35Å	1.36Å	Aromatic
C6	N6	sing	1.38Å	1.35Å
N7	C8	doub	1.30Å	1.36Å	Aromatic
C8	N9	sing	1.36Å	1.33Å	Aromatic
N9	C1'	sing	1.47Å	1.37Å
C1'	C2'	sing	1.55Å	1.50Å
C1'	O4'	sing	1.44Å	1.46Å
C10	C11	sing	1.53Å	1.53Å
C10	C1S	sing	1.53Å	1.53Å
C11	N12	sing	1.47Å	1.45Å
C2'	O2'	sing	1.43Å	1.43Å
C2'	C3'	sing	1.55Å	1.52Å
C3'	O3'	sing	1.43Å	1.43Å
C3'	C4'	sing	1.54Å	1.51Å
C4'	O4'	sing	1.44Å	1.43Å
C4'	C5'	sing	1.53Å	1.52Å
C5'	N5'	sing	1.46Å	1.45Å
C2	H2	sing	1.08Å	1.08Å
N6	HN6	sing	0.97Å	1.00Å
N6	HN6A	sing	0.97Å	1.00Å
C8	H8	sing	1.08Å	1.08Å
C1'	H1'	sing	1.09Å	1.10Å
C10	H10	sing	1.09Å	1.10Å
C10	H10A	sing	1.09Å	1.10Å
C11	H11	sing	1.09Å	1.10Å
C11	H11A	sing	1.09Å	1.10Å
N12	HN12	sing	1.01Å	1.00Å
N12	HN1A	sing	1.01Å	1.00Å
C1S	H1S	sing	1.09Å	1.10Å
C1S	H1SA	sing	1.09Å	1.10Å
C2'	H2'	sing	1.09Å	1.10Å
O2'	HO2'	sing	0.97Å	0.95Å
C3'	H3'	sing	1.09Å	1.10Å
O3'	HO3'	sing	0.97Å	0.95Å
C4'	H4'	sing	1.09Å	1.10Å
C5'	H5'	sing	1.09Å	1.10Å
C5'	H5'A	sing	1.09Å	1.10Å
N5'	HN5'	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1S	S	O2S	110.7°	110.5°
C1S	S	O3S	109.6°	110.5°
C1S	S	N5'	108.0°	104.4°
S	C1S	C10	111.6°	109.5°
S	C1S	H1S	108.8°	109.5°
S	C1S	H1SA	108.8°	109.5°
O2S	S	O3S	109.8°	121.0°
O2S	S	N5'	108.9°	104.3°
O3S	S	N5'	109.9°	104.3°
S	N5'	C5'	120.0°	120.0°
S	N5'	HN5'	106.1°	120.0°
C2	N1	C6	120.9°	121.2°
N1	C2	N3	122.4°	122.4°
N1	C2	H2	118.8°	118.8°
N1	C6	C5	118.3°	118.5°
N1	C6	N6	120.7°	120.7°
C2	N3	C4	120.6°	120.6°
N3	C2	H2	118.8°	118.7°
N3	C4	C5	120.7°	119.1°
N3	C4	N9	135.6°	134.9°
C5	C4	N9	103.7°	106.0°
C4	C5	C6	117.1°	118.2°
C4	C5	N7	108.6°	107.2°
C4	N9	C8	114.3°	107.4°
C4	N9	C1'	122.5°	126.3°
C6	C5	N7	134.3°	134.7°
C5	C6	N6	121.0°	120.8°
C5	N7	C8	108.6°	109.4°
C6	N6	HN6	109.5°	120.0°
C6	N6	HN6A	109.5°	120.0°
N7	C8	N9	104.9°	110.0°
N7	C8	H8	127.6°	125.0°
C8	N9	C1'	123.2°	126.3°
N9	C8	H8	127.6°	125.0°
N9	C1'	C2'	110.9°	110.6°
N9	C1'	O4'	128.3°	110.6°
N9	C1'	H1'	91.8°	110.5°
C2'	C1'	O4'	105.2°	103.5°
C1'	C2'	O2'	110.3°	110.8°
C1'	C2'	C3'	107.1°	102.1°
C2'	C1'	H1'	121.9°	110.7°
C1'	C2'	H2'	111.1°	110.9°
C1'	O4'	C4'	112.0°	107.0°
O4'	C1'	H1'	99.4°	110.8°
C11	C10	C1S	109.4°	109.5°
C10	C11	N12	107.9°	109.5°
C11	C10	H10	109.5°	109.5°
C11	C10	H10A	109.5°	109.4°
C10	C11	H11	110.0°	109.4°
C10	C11	H11A	110.0°	109.5°
C1S	C10	H10	109.5°	109.5°
C1S	C10	H10A	109.5°	109.5°
C10	C1S	H1S	108.8°	109.4°
C10	C1S	H1SA	108.8°	109.5°
N12	C11	H11	110.0°	109.5°
N12	C11	H11A	110.0°	109.5°
C11	N12	HN12	109.5°	111.0°
C11	N12	HN1A	109.5°	111.0°
O2'	C2'	C3'	111.2°	110.9°
O2'	C2'	H2'	107.0°	110.8°
C2'	O2'	HO2'	109.5°	114.0°
C2'	C3'	O3'	111.1°	110.5°
C2'	C3'	C4'	105.9°	104.2°
C3'	C2'	H2'	110.2°	111.0°
C2'	C3'	H3'	110.7°	110.5°
O3'	C3'	C4'	109.4°	110.5°
O3'	C3'	H3'	107.4°	110.4°
C3'	O3'	HO3'	109.5°	114.0°
C3'	C4'	O4'	107.2°	107.3°
C3'	C4'	C5'	111.0°	109.9°
C4'	C3'	H3'	112.4°	110.6°
C3'	C4'	H4'	109.9°	109.9°
O4'	C4'	C5'	109.1°	109.9°
O4'	C4'	H4'	111.7°	109.9°
C4'	C5'	N5'	109.5°	109.5°
C5'	C4'	H4'	108.0°	110.0°
C4'	C5'	H5'	109.5°	109.4°
C4'	C5'	H5'A	109.5°	109.4°
N5'	C5'	H5'	109.5°	109.5°
N5'	C5'	H5'A	109.5°	109.5°
C5'	N5'	HN5'	106.1°	120.0°
HN6	N6	HN6A	109.4°	120.0°
H10	C10	H10A	109.5°	109.4°
H11	C11	H11A	109.0°	109.4°
HN12	N12	HN1A	109.4°	111.0°
H1S	C1S	H1SA	110.2°	109.5°
H5'	C5'	H5'A	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1S	S	O2S	O3S	121.1°	131.5°
C1S	S	O2S	N5'	118.5°	111.7°
C1S	S	O3S	N5'	118.4°	111.7°
S	C1S	C10	C11	136.3°	180.0°
S	C1S	C10	H1S	120.0°	120.0°
S	C1S	C10	H1SA	120.0°	120.0°
C1S	S	N5'	C5'	77.9°	65.0°
S	C1S	C10	H10	103.7°	60.0°
S	C1S	C10	H10A	16.3°	60.0°
S	C1S	H1S	H1SA	119.1°	120.0°
C1S	S	N5'	HN5'	162.1°	115.1°
O2S	S	O3S	N5'	119.8°	116.8°
O2S	S	C1S	C10	64.6°	68.4°
O2S	S	N5'	C5'	42.3°	51.0°
O2S	S	C1S	H1S	55.4°	51.6°
O2S	S	C1S	H1SA	175.4°	171.6°
O2S	S	N5'	HN5'	77.7°	128.8°
O3S	S	C1S	C10	56.7°	68.4°
O3S	S	N5'	C5'	162.6°	178.9°
O3S	S	C1S	H1S	176.7°	171.7°
O3S	S	C1S	H1SA	63.3°	51.6°
O3S	S	N5'	HN5'	42.7°	1.0°
N5'	S	C1S	C10	176.3°	180.0°
S	N5'	C5'	C4'	144.4°	165.0°
S	N5'	C5'	HN5'	120.0°	179.9°
N5'	S	C1S	H1S	63.7°	60.0°
N5'	S	C1S	H1SA	56.3°	60.0°
S	N5'	C5'	H5'	24.4°	45.0°
S	N5'	C5'	H5'A	95.6°	75.0°
N1	C2	N3	H2	180.0°	180.0°
N1	C2	N3	C4	0.2°	0.1°
C2	N1	C6	C5	0.2°	0.0°
C2	N1	C6	N6	179.8°	180.0°
C6	N1	C2	N3	0.2°	0.0°
N1	C6	C5	C4	0.1°	0.0°
N1	C6	C5	N6	179.6°	180.0°
N1	C6	C5	N7	179.9°	180.0°
C6	N1	C2	H2	179.8°	180.0°
N1	C6	N6	HN6	0.0°	0.0°
N1	C6	N6	HN6A	120.0°	180.0°
C2	N3	C4	C5	0.1°	0.1°
C2	N3	C4	N9	179.7°	179.9°
N3	C4	C5	N9	179.9°	180.0°
N3	C4	C5	C6	0.0°	0.0°
N3	C4	C5	N7	180.0°	180.0°
N3	C4	N9	C8	179.9°	180.0°
N3	C4	N9	C1'	0.4°	0.0°
C4	N3	C2	H2	179.8°	180.0°
C4	C5	C6	N7	180.0°	180.0°
C4	C5	C6	N6	179.7°	180.0°
C4	C5	N7	C8	0.2°	0.0°
C5	C4	N9	C8	0.1°	0.1°
C5	C4	N9	C1'	179.8°	180.0°
N9	C4	C5	C6	179.8°	180.0°
N9	C4	C5	N7	0.2°	0.1°
C4	N9	C8	N7	0.0°	0.0°
C4	N9	C8	C1'	179.7°	179.9°
C4	N9	C1'	C2'	110.8°	85.0°
C4	N9	C1'	O4'	117.9°	161.0°
C4	N9	C8	H8	180.0°	180.0°
C4	N9	C1'	H1'	14.5°	37.9°
C6	C5	N7	C8	179.8°	180.0°
C5	C6	N6	HN6	179.6°	180.0°
C5	C6	N6	HN6A	60.4°	0.0°
N7	C5	C6	N6	0.3°	0.0°
C5	N7	C8	N9	0.1°	0.0°
C5	N7	C8	H8	179.9°	180.0°
C6	N6	HN6	HN6A	120.0°	180.0°
N7	C8	N9	H8	180.0°	180.0°
N7	C8	N9	C1'	179.7°	180.0°
C8	N9	C1'	C2'	68.9°	94.9°
C8	N9	C1'	O4'	62.4°	19.1°
C8	N9	C1'	H1'	165.8°	142.1°
N9	C1'	C2'	O4'	142.3°	118.5°
N9	C1'	C2'	H1'	106.1°	122.8°
N9	C1'	O4'	H1'	99.9°	122.9°
N9	C1'	C2'	O2'	80.7°	86.3°
N9	C1'	C2'	C3'	158.2°	155.6°
N9	C1'	O4'	C4'	148.6°	158.6°
C1'	N9	C8	H8	0.3°	0.0°
N9	C1'	C2'	H2'	37.8°	37.3°
C2'	C1'	O4'	H1'	126.8°	118.6°
C1'	C2'	O2'	C3'	118.7°	112.6°
C1'	C2'	O2'	H2'	120.9°	123.6°
C1'	C2'	C3'	H2'	121.0°	118.2°
C1'	C2'	C3'	O3'	107.6°	97.8°
C1'	C2'	C3'	C4'	11.1°	20.9°
C2'	C1'	O4'	C4'	15.3°	40.1°
C1'	C2'	O2'	HO2'	180.0°	180.0°
C1'	C2'	C3'	H3'	133.2°	139.7°
O4'	C1'	C2'	O2'	136.9°	155.2°
O4'	C1'	C2'	C3'	15.8°	37.1°
C1'	O4'	C4'	C3'	8.4°	26.5°
C1'	O4'	C4'	C5'	128.6°	146.0°
O4'	C1'	C2'	H2'	104.6°	81.2°
C1'	O4'	C4'	H4'	112.0°	92.9°
C11	C10	C1S	H10	120.0°	120.0°
C11	C10	C1S	H10A	120.0°	120.0°
C10	C11	N12	H11	120.0°	120.0°
C10	C11	N12	H11A	120.0°	120.0°
C11	C10	H10	H10A	120.1°	119.9°
C10	C11	H11	H11A	120.6°	119.9°
C10	C11	N12	HN12	180.0°	180.0°
C10	C11	N12	HN1A	60.0°	56.1°
C11	C10	C1S	H1S	103.7°	60.0°
C11	C10	C1S	H1SA	16.3°	60.0°
C1S	C10	C11	N12	84.0°	180.0°
C1S	C10	H10	H10A	120.1°	120.0°
C1S	C10	C11	H11	36.0°	60.0°
C1S	C10	C11	H11A	156.0°	59.9°
C10	C1S	H1S	H1SA	119.1°	120.0°
N12	C11	C10	H10	36.0°	60.0°
N12	C11	C10	H10A	156.0°	60.0°
N12	C11	H11	H11A	120.6°	120.0°
C11	N12	HN12	HN1A	120.0°	124.0°
O2'	C2'	C3'	H2'	118.5°	123.6°
O2'	C2'	C3'	O3'	13.0°	20.4°
O2'	C2'	C3'	C4'	131.6°	139.1°
O2'	C2'	C1'	H1'	25.4°	36.5°
O2'	C2'	C3'	H3'	106.2°	102.2°
C2'	C3'	O3'	C4'	116.5°	114.8°
C2'	C3'	O3'	H3'	121.2°	122.6°
C2'	C3'	C4'	H3'	121.0°	118.7°
C2'	C3'	C4'	O4'	2.0°	2.0°
C2'	C3'	C4'	C5'	117.0°	121.4°
C3'	C2'	C1'	H1'	95.7°	81.6°
C3'	C2'	O2'	HO2'	61.3°	67.3°
C2'	C3'	O3'	HO3'	180.0°	61.4°
C2'	C3'	C4'	H4'	123.6°	117.4°
O3'	C3'	C4'	H3'	119.2°	122.5°
O3'	C3'	C4'	O4'	117.8°	120.7°
O3'	C3'	C4'	C5'	123.2°	119.8°
O3'	C3'	C2'	H2'	131.5°	144.0°
O3'	C3'	C4'	H4'	3.8°	1.3°
C3'	C4'	O4'	C5'	120.2°	119.5°
C3'	C4'	O4'	H4'	120.4°	119.4°
C3'	C4'	C5'	H4'	120.5°	121.1°
C3'	C4'	C5'	N5'	150.5°	175.0°
C4'	C3'	C2'	H2'	109.9°	97.3°
C4'	C3'	O3'	HO3'	63.5°	176.2°
C3'	C4'	C5'	H5'	30.5°	55.0°
C3'	C4'	C5'	H5'A	89.5°	64.9°
O4'	C4'	C5'	H4'	121.6°	121.1°
O4'	C4'	C5'	N5'	91.6°	67.2°
C4'	O4'	C1'	H1'	111.5°	78.5°
O4'	C4'	C3'	H3'	123.0°	116.8°
O4'	C4'	C5'	H5'	148.4°	172.8°
O4'	C4'	C5'	H5'A	28.4°	52.9°
C4'	C5'	N5'	H5'	120.0°	120.0°
C4'	C5'	N5'	H5'A	120.0°	120.0°
C5'	C4'	C3'	H3'	4.0°	2.7°
C4'	C5'	H5'	H5'A	120.0°	119.9°
C4'	C5'	N5'	HN5'	24.5°	14.9°
N5'	C5'	C4'	H4'	30.0°	53.9°
N5'	C5'	H5'	H5'A	120.0°	120.0°
H1'	C1'	C2'	H2'	143.9°	160.1°
H10	C10	C11	H11	156.0°	60.1°
H10	C10	C11	H11A	84.0°	180.0°
H10	C10	C1S	H1S	16.3°	60.0°
H10	C10	C1S	H1SA	136.3°	NaN°
H10A	C10	C11	H11	84.0°	180.0°
H10A	C10	C11	H11A	36.0°	60.1°
H10A	C10	C1S	H1S	136.3°	180.0°
H10A	C10	C1S	H1SA	103.7°	60.0°
H11	C11	N12	HN12	60.0°	60.0°
H11	C11	N12	HN1A	180.0°	176.1°
H11A	C11	N12	HN12	60.0°	60.0°
H11A	C11	N12	HN1A	60.0°	64.0°
H2'	C2'	O2'	HO2'	59.1°	56.4°
H2'	C2'	C3'	H3'	12.3°	21.5°
H3'	C3'	O3'	HO3'	58.8°	61.1°
H3'	C3'	C4'	H4'	115.4°	123.9°
H4'	C4'	C5'	H5'	90.0°	66.1°
H4'	C4'	C5'	H5'A	150.0°	174.0°
H5'	C5'	N5'	HN5'	95.5°	134.9°
H5'A	C5'	N5'	HN5'	144.5°	105.1°

Definition date:	2009-12-30
Last modified:	2024-09-27
Release status:	REL
Processing site:	RCSB
Derived from:	3KYD