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Summary Geometry Related PDB entries

4UD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C3	N1	doub	1.28Å	1.29Å
C3	C5	sing	1.52Å	1.49Å
N1	O2	sing	1.41Å	1.34Å
C5	C4	sing	1.55Å	1.52Å
O2	C4	sing	1.44Å	1.43Å
C4	C6	sing	1.53Å	1.54Å
C6	C8	sing	1.51Å	1.51Å
C6	N7	sing	1.47Å	1.47Å
O10	C8	doub	1.21Å	1.35Å
C8	O9	sing	1.34Å	1.21Å
C3	H1	sing	1.08Å	1.08Å
C4	H3	sing	1.09Å	1.10Å
C5	H4	sing	1.09Å	1.10Å
C5	H5	sing	1.09Å	1.10Å
C6	H6	sing	1.09Å	1.10Å
O9	H7	sing	0.97Å	0.95Å
N7	H8	sing	1.01Å	1.00Å
N7	H9	sing	1.01Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N1	C3	C5	110.3°	108.5°
C3	N1	O2	113.5°	113.2°
N1	C3	H1	124.9°	125.7°
C3	C5	C4	95.2°	102.4°
C5	C3	H1	124.9°	125.8°
C3	C5	H4	112.9°	110.8°
C3	C5	H5	112.9°	110.8°
N1	O2	C4	102.3°	107.5°
C5	C4	O2	105.6°	101.6°
C5	C4	C6	115.6°	111.0°
C5	C4	H3	109.0°	111.0°
C4	C5	H4	112.9°	110.8°
C4	C5	H5	112.9°	110.8°
O2	C4	C6	107.5°	111.0°
O2	C4	H3	110.3°	111.1°
C4	C6	C8	106.5°	109.4°
C4	C6	N7	110.7°	109.5°
C6	C4	H3	108.8°	110.9°
C4	C6	H6	110.0°	109.4°
C8	C6	N7	108.3°	109.5°
C6	C8	O10	120.3°	120.0°
C6	C8	O9	121.1°	120.0°
C8	C6	H6	110.3°	109.5°
N7	C6	H6	110.9°	109.5°
C6	N7	H8	109.5°	111.0°
C6	N7	H9	109.5°	111.0°
O10	C8	O9	118.6°	120.0°
C8	O9	H7	109.5°	117.0°
H4	C5	H5	109.5°	110.9°
H8	N7	H9	109.4°	111.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N1	C3	C5	H1	180.0°	179.7°
N1	C3	C5	C4	20.6°	15.3°
C3	N1	O2	C4	22.4°	17.4°
N1	C3	C5	H4	138.2°	133.5°
N1	C3	C5	H5	96.9°	102.9°
C5	C3	N1	O2	0.0°	0.3°
C3	C5	C4	H4	117.6°	118.2°
C3	C5	C4	H5	117.6°	118.3°
C3	C5	C4	O2	33.2°	24.0°
C3	C5	C4	C6	151.9°	142.0°
C3	C5	C4	H3	85.3°	94.2°
C3	C5	H4	H5	126.7°	123.5°
N1	O2	C4	C5	35.4°	25.2°
N1	O2	C4	C6	159.3°	143.2°
O2	N1	C3	H1	180.0°	179.4°
N1	O2	C4	H3	82.2°	93.0°
C5	C4	O2	C6	124.0°	118.0°
C5	C4	O2	H3	117.6°	118.1°
C5	C4	C6	H3	122.9°	123.9°
C5	C4	C6	C8	176.2°	176.8°
C5	C4	C6	N7	58.7°	63.2°
C4	C5	C3	H1	159.4°	165.0°
C4	C5	H4	H5	126.7°	123.5°
C5	C4	C6	H6	64.2°	56.8°
O2	C4	C6	H3	119.4°	124.0°
O2	C4	C6	C8	66.1°	64.6°
O2	C4	C6	N7	176.4°	175.4°
O2	C4	C5	H4	150.8°	142.2°
O2	C4	C5	H5	84.4°	94.3°
O2	C4	C6	H6	53.5°	55.3°
C4	C6	C8	N7	119.0°	120.0°
C4	C6	C8	H6	119.4°	119.9°
C4	C6	N7	H6	122.4°	120.0°
C4	C6	C8	O10	97.7°	100.0°
C4	C6	C8	O9	81.9°	80.0°
C6	C4	C5	H4	90.5°	99.8°
C6	C4	C5	H5	34.3°	23.8°
C4	C6	N7	H8	180.0°	176.0°
C4	C6	N7	H9	60.0°	60.0°
C8	C6	N7	H6	121.2°	120.1°
C6	C8	O10	O9	179.6°	180.0°
C8	C6	C4	H3	53.3°	59.3°
C6	C8	O9	H7	179.6°	180.0°
C8	C6	N7	H8	63.6°	64.0°
C8	C6	N7	H9	56.4°	60.0°
N7	C6	C8	O10	143.3°	20.0°
N7	C6	C8	O9	37.1°	160.0°
N7	C6	C4	H3	64.2°	60.7°
C6	N7	H8	H9	120.0°	124.0°
O10	C8	C6	H6	21.7°	140.0°
O10	C8	O9	H7	0.0°	0.0°
O9	C8	C6	H6	158.7°	39.9°
H1	C3	C5	H4	41.8°	46.8°
H1	C3	C5	H5	83.1°	76.8°
H3	C4	C5	H4	32.3°	24.0°
H3	C4	C5	H5	157.2°	147.6°
H3	C4	C6	H6	172.9°	179.3°
H6	C6	N7	H8	57.6°	56.1°
H6	C6	N7	H9	177.6°	180.0°

248636

PDB entries from 2026-02-04

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