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Summary Geometry Related PDB entries

CYX

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	sing	1.46Å	1.55Å
C1	O3	doub	1.21Å	1.24Å
C1	H11	sing	1.08Å	1.10Å
C2	C4	doub	1.33Å	1.35Å
C2	C5	sing	1.51Å	1.54Å
C4	H41	sing	1.08Å	1.10Å
C4	H42	sing	1.08Å	1.10Å
C5	C6	sing	1.53Å	1.56Å
C5	H51	sing	1.09Å	1.12Å
C5	H52	sing	1.09Å	1.11Å
C6	P7	sing	1.82Å	1.75Å
C6	H61	sing	1.09Å	1.12Å
C6	H62	sing	1.09Å	1.12Å
P7	O8	sing	1.61Å	1.60Å
P7	O9	sing	1.61Å	1.61Å
P7	O10	doub	1.48Å	1.61Å
O8	H81	sing	0.97Å	0.95Å
O9	H91	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	C1	O3	122.3°	120.0°
C2	C1	H11	130.5°	120.0°
C1	C2	C4	122.4°	120.0°
C1	C2	C5	118.7°	120.0°
O3	C1	H11	107.2°	120.0°
C4	C2	C5	118.9°	120.0°
C2	C4	H41	118.9°	120.0°
C2	C4	H42	122.4°	120.1°
C2	C5	C6	113.1°	109.5°
C2	C5	H51	110.9°	109.4°
C2	C5	H52	110.9°	109.5°
H41	C4	H42	118.7°	120.0°
C6	C5	H51	110.8°	109.5°
C6	C5	H52	110.9°	109.5°
C5	C6	P7	116.0°	109.5°
C5	C6	H61	109.9°	109.5°
C5	C6	H62	109.8°	109.5°
H51	C5	H52	99.5°	109.5°
P7	C6	H61	109.9°	109.5°
P7	C6	H62	109.9°	109.5°
C6	P7	O8	109.0°	109.5°
C6	P7	O9	109.0°	109.5°
C6	P7	O10	109.9°	109.5°
H61	C6	H62	100.3°	109.4°
O8	P7	O9	109.8°	109.4°
O8	P7	O10	109.8°	109.5°
P7	O8	H81	109.1°	106.8°
O9	P7	O10	109.4°	109.5°
P7	O9	H91	109.0°	106.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	C1	O3	H11	180.0°	179.9°
C1	C2	C4	C5	179.7°	180.0°
C1	C2	C4	H41	0.3°	0.1°
C1	C2	C4	H42	180.0°	179.9°
C1	C2	C5	C6	48.6°	90.0°
C1	C2	C5	H51	76.6°	150.0°
C1	C2	C5	H52	173.9°	30.0°
O3	C1	C2	C4	111.5°	180.0°
O3	C1	C2	C5	68.8°	0.1°
H11	C1	C2	C4	68.5°	0.1°
H11	C1	C2	C5	111.2°	180.0°
C2	C4	H41	H42	179.8°	180.0°
C4	C2	C5	C6	131.7°	90.0°
C4	C2	C5	H51	103.1°	30.0°
C4	C2	C5	H52	6.4°	149.9°
C5	C2	C4	H41	180.0°	180.0°
C5	C2	C4	H42	0.2°	0.0°
C2	C5	C6	H51	125.2°	120.0°
C2	C5	C6	H52	125.2°	120.0°
C2	C5	H51	H52	116.7°	119.9°
C2	C5	C6	P7	156.4°	180.0°
C2	C5	C6	H61	31.1°	60.0°
C2	C5	C6	H62	78.3°	60.0°
C6	C5	H51	H52	116.8°	120.0°
C5	C6	P7	H61	125.3°	120.1°
C5	C6	P7	H62	125.3°	120.0°
C5	C6	H61	H62	115.6°	120.0°
C5	C6	P7	O8	143.7°	180.0°
C5	C6	P7	O9	96.5°	60.1°
C5	C6	P7	O10	23.3°	60.0°
H51	C5	C6	P7	78.4°	60.0°
H51	C5	C6	H61	156.3°	179.9°
H51	C5	C6	H62	47.0°	60.0°
H52	C5	C6	P7	31.1°	60.0°
H52	C5	C6	H61	94.1°	60.0°
H52	C5	C6	H62	156.5°	180.0°
P7	C6	H61	H62	115.7°	119.9°
C6	P7	O8	O9	119.4°	120.0°
C6	P7	O8	O10	120.4°	120.0°
C6	P7	O9	O10	120.1°	120.1°
C6	P7	O8	H81	180.0°	180.0°
C6	P7	O9	H91	179.9°	60.0°
H61	C6	P7	O8	91.0°	59.9°
H61	C6	P7	O9	28.8°	179.9°
H61	C6	P7	O10	148.6°	60.0°
H62	C6	P7	O8	18.4°	59.9°
H62	C6	P7	O9	138.2°	60.0°
H62	C6	P7	O10	102.0°	179.9°
O8	P7	O9	O10	120.5°	120.0°
O8	P7	O9	H91	60.6°	60.0°
O9	P7	O8	H81	60.6°	60.0°
O10	P7	O8	H81	59.6°	60.0°
O10	P7	O9	H91	59.9°	180.0°

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