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Summary Geometry Related PDB entries

5XB

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O22	C2A	doub	1.21Å	1.18Å
O21	C2A	sing	1.34Å	1.22Å
C2A	C2	sing	1.51Å	1.55Å
N3	C2	sing	1.48Å	1.47Å
N3	C4	sing	1.47Å	1.44Å
C2	S1	sing	1.83Å	1.80Å
O42	C4A	doub	1.21Å	1.20Å
C4	C4A	sing	1.51Å	1.54Å
C4	C5	sing	1.55Å	1.54Å
C4A	O41	sing	1.34Å	1.22Å
S1	C5	sing	1.84Å	1.82Å
C2	H1	sing	1.09Å	1.10Å
C4	H2	sing	1.09Å	1.10Å
C5	H3	sing	1.09Å	1.10Å
C5	H4	sing	1.09Å	1.10Å
O41	H5	sing	0.97Å	0.95Å
O21	H6	sing	0.97Å	0.95Å
N3	H7	sing	1.01Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O22	C2A	O21	121.6°	120.0°
O22	C2A	C2	119.9°	120.0°
O21	C2A	C2	118.5°	120.0°
C2A	O21	H6	109.5°	117.0°
C2A	C2	N3	116.2°	110.6°
C2A	C2	S1	111.9°	110.4°
C2A	C2	H1	110.1°	110.4°
C2	N3	C4	114.6°	110.9°
N3	C2	S1	99.3°	104.5°
N3	C2	H1	111.3°	110.4°
C2	N3	H7	108.2°	111.0°
N3	C4	C4A	117.5°	109.9°
N3	C4	C5	105.5°	107.4°
N3	C4	H2	108.7°	110.0°
C4	N3	H7	108.2°	111.0°
C2	S1	C5	98.6°	96.3°
S1	C2	H1	107.2°	110.5°
O42	C4A	C4	118.3°	120.0°
O42	C4A	O41	124.3°	120.0°
C4A	C4	C5	109.9°	109.9°
C4	C4A	O41	117.4°	120.0°
C4A	C4	H2	107.4°	109.9°
C4	C5	S1	102.0°	101.0°
C5	C4	H2	107.5°	109.8°
C4	C5	H3	111.3°	111.1°
C4	C5	H4	111.3°	111.1°
C4A	O41	H5	109.5°	117.0°
S1	C5	H3	111.3°	111.1°
S1	C5	H4	111.3°	111.2°
H3	C5	H4	109.5°	110.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O22	C2A	O21	C2	180.0°	179.9°
O22	C2A	C2	N3	17.8°	106.6°
O22	C2A	C2	S1	95.3°	8.6°
O22	C2A	C2	H1	145.5°	131.0°
O22	C2A	O21	H6	0.0°	0.1°
O21	C2A	C2	N3	162.3°	73.3°
O21	C2A	C2	S1	84.7°	171.5°
O21	C2A	C2	H1	34.5°	49.1°
C2A	C2	N3	S1	120.1°	118.8°
C2A	C2	N3	H1	127.2°	122.4°
C2A	C2	N3	C4	160.0°	148.3°
C2A	C2	S1	H1	120.9°	122.4°
C2A	C2	S1	C5	137.5°	121.9°
C2	C2A	O21	H6	180.0°	180.0°
C2A	C2	N3	H7	39.2°	24.4°
C2	N3	C4	H7	120.7°	123.9°
N3	C2	S1	H1	115.9°	118.7°
C2	N3	C4	C4A	173.7°	168.0°
C2	N3	C4	C5	51.0°	48.5°
N3	C2	S1	C5	14.3°	3.0°
C2	N3	C4	H2	64.1°	71.0°
C4	N3	C2	S1	39.9°	29.5°
N3	C4	C4A	O42	16.3°	17.9°
N3	C4	C4A	C5	120.5°	117.9°
N3	C4	C4A	H2	122.8°	121.1°
N3	C4	C5	H2	115.8°	119.5°
N3	C4	C4A	O41	161.1°	162.1°
N3	C4	C5	S1	32.8°	41.3°
C4	N3	C2	H1	72.9°	89.3°
N3	C4	C5	H3	86.0°	76.6°
N3	C4	C5	H4	151.6°	159.4°
C2	S1	C5	C4	10.4°	21.4°
C2	S1	C5	H3	108.4°	96.5°
C2	S1	C5	H4	129.2°	139.4°
S1	C2	N3	H7	80.9°	94.4°
O42	C4A	C4	O41	177.4°	180.0°
O42	C4A	C4	C5	104.3°	100.1°
O42	C4A	C4	H2	139.1°	139.0°
O42	C4A	O41	H5	0.0°	0.0°
C4A	C4	C5	H2	116.6°	121.0°
C4A	C4	C5	S1	160.3°	160.8°
C4A	C4	C5	H3	41.5°	42.9°
C4A	C4	C5	H4	80.9°	81.1°
C4	C4A	O41	H5	177.3°	180.0°
C4A	C4	N3	H7	53.0°	44.1°
C5	C4	C4A	O41	78.3°	80.0°
C4	C5	S1	H3	118.8°	117.9°
C4	C5	S1	H4	118.8°	118.0°
C4	C5	H3	H4	123.5°	124.1°
C5	C4	N3	H7	69.8°	75.4°
O41	C4A	C4	H2	38.3°	40.9°
C5	S1	C2	H1	101.6°	115.7°
S1	C5	C4	H2	83.0°	78.2°
S1	C5	H3	H4	123.4°	124.3°
H1	C2	N3	H7	166.4°	146.8°
H2	C4	C5	H3	158.1°	163.9°
H2	C4	C5	H4	35.7°	39.9°
H2	C4	N3	H7	175.2°	165.2°

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