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Summary Geometry Related PDB entries

PTU

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N1	C	sing	1.37Å	1.48Å
N1	HN11	sing	0.97Å	1.02Å
N1	HN12	sing	0.97Å	1.02Å
C	S	sing	1.76Å	1.80Å
C	N2	doub	1.31Å	1.35Å
S	C1'	sing	1.81Å	1.81Å
N2	C1	sing	1.37Å	1.36Å
C1	C2	doub	1.40Å	1.43Å	Aromatic
C1	C6	sing	1.40Å	1.43Å	Aromatic
C2	C3	sing	1.38Å	1.42Å	Aromatic
C2	H21	sing	1.08Å	1.10Å
C3	C4	doub	1.38Å	1.42Å	Aromatic
C3	H31	sing	1.08Å	1.10Å
C4	C5	sing	1.38Å	1.42Å	Aromatic
C4	H41	sing	1.08Å	1.10Å
C5	C6	doub	1.38Å	1.42Å	Aromatic
C5	H51	sing	1.08Å	1.10Å
C6	H61	sing	1.08Å	1.10Å
C1'	C2'	sing	1.53Å	1.52Å
C1'	H1'1	sing	1.09Å	1.11Å
C1'	H1'2	sing	1.09Å	1.12Å
C2'	H2'1	sing	1.09Å	1.12Å
C2'	H2'2	sing	1.09Å	1.12Å
C2'	H2'3	sing	1.09Å	1.11Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C	N1	HN11	118.8°	120.0°
C	N1	HN12	108.9°	120.0°
N1	C	S	118.8°	120.0°
N1	C	N2	116.7°	120.0°
HN11	N1	HN12	108.8°	120.0°
S	C	N2	124.5°	120.0°
C	S	C1'	109.9°	100.0°
C	N2	C1	138.2°	120.0°
S	C1'	C2'	109.3°	109.5°
S	C1'	H1'1	112.3°	109.5°
S	C1'	H1'2	112.2°	109.5°
N2	C1	C2	117.1°	120.2°
N2	C1	C6	124.4°	120.1°
C2	C1	C6	118.5°	119.7°
C1	C2	C3	120.7°	119.9°
C1	C2	H21	120.0°	120.0°
C1	C6	C5	120.6°	119.9°
C1	C6	H61	120.3°	120.0°
C3	C2	H21	119.4°	120.1°
C2	C3	C4	119.9°	120.2°
C2	C3	H31	120.2°	119.9°
C4	C3	H31	119.9°	119.9°
C3	C4	C5	120.0°	120.2°
C3	C4	H41	120.1°	119.9°
C5	C4	H41	119.9°	119.8°
C4	C5	C6	120.3°	120.2°
C4	C5	H51	119.8°	119.9°
C6	C5	H51	120.0°	119.9°
C5	C6	H61	119.2°	120.1°
C2'	C1'	H1'1	112.3°	109.5°
C2'	C1'	H1'2	112.3°	109.5°
C1'	C2'	H2'1	109.3°	109.5°
C1'	C2'	H2'2	112.2°	109.5°
C1'	C2'	H2'3	112.3°	109.5°
H1'1	C1'	H1'2	98.2°	109.4°
H2'1	C2'	H2'2	112.2°	109.4°
H2'1	C2'	H2'3	112.3°	109.5°
H2'2	C2'	H2'3	98.2°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C	N1	HN11	HN12	125.2°	180.0°
N1	C	S	N2	180.0°	180.0°
N1	C	S	C1'	138.5°	180.0°
N1	C	N2	C1	159.3°	6.2°
HN11	N1	C	S	180.0°	8.0°
HN11	N1	C	N2	0.1°	171.9°
HN12	N1	C	S	54.8°	172.0°
HN12	N1	C	N2	125.3°	8.1°
S	C	N2	C1	20.7°	173.8°
C	S	C1'	C2'	136.4°	180.0°
C	S	C1'	H1'1	98.3°	59.9°
C	S	C1'	H1'2	11.2°	60.0°
N2	C	S	C1'	41.4°	0.0°
C	N2	C1	C2	151.7°	123.5°
C	N2	C1	C6	28.2°	56.9°
S	C1'	C2'	H1'1	125.3°	120.1°
S	C1'	C2'	H1'2	125.2°	120.0°
S	C1'	H1'1	H1'2	118.2°	120.0°
S	C1'	C2'	H2'1	180.0°	180.0°
S	C1'	C2'	H2'2	54.8°	60.0°
S	C1'	C2'	H2'3	54.7°	60.0°
N2	C1	C2	C6	179.9°	179.6°
N2	C1	C2	C3	179.7°	179.9°
N2	C1	C2	H21	0.3°	0.1°
N2	C1	C6	C5	179.7°	179.8°
N2	C1	C6	H61	0.3°	0.4°
C1	C2	C3	H21	180.0°	180.0°
C1	C2	C3	C4	0.3°	0.0°
C1	C2	C3	H31	179.7°	180.0°
C2	C1	C6	C5	0.4°	0.5°
C2	C1	C6	H61	179.6°	180.0°
C6	C1	C2	C3	0.4°	0.3°
C6	C1	C2	H21	179.6°	179.7°
C1	C6	C5	C4	0.2°	0.5°
C1	C6	C5	H61	180.0°	179.5°
C1	C6	C5	H51	179.8°	179.7°
C2	C3	C4	H31	180.0°	180.0°
C2	C3	C4	C5	0.1°	0.1°
C2	C3	C4	H41	180.0°	180.0°
H21	C2	C3	C4	179.8°	180.0°
H21	C2	C3	H31	0.3°	0.0°
C3	C4	C5	H41	180.0°	179.9°
C3	C4	C5	C6	0.0°	0.2°
C3	C4	C5	H51	179.9°	180.0°
H31	C3	C4	C5	179.9°	180.0°
H31	C3	C4	H41	0.1°	0.0°
C4	C5	C6	H51	180.0°	179.8°
C4	C5	C6	H61	179.8°	180.0°
H41	C4	C5	C6	180.0°	179.8°
H41	C4	C5	H51	0.0°	0.1°
H51	C5	C6	H61	0.2°	0.2°
C2'	C1'	H1'1	H1'2	118.2°	120.0°
C1'	C2'	H2'1	H2'2	125.2°	120.0°
C1'	C2'	H2'1	H2'3	125.3°	120.0°
C1'	C2'	H2'2	H2'3	118.2°	120.0°
H1'1	C1'	C2'	H2'1	54.8°	59.9°
H1'1	C1'	C2'	H2'2	180.0°	60.1°
H1'1	C1'	C2'	H2'3	70.5°	180.0°
H1'2	C1'	C2'	H2'1	54.7°	60.0°
H1'2	C1'	C2'	H2'2	70.4°	180.0°
H1'2	C1'	C2'	H2'3	180.0°	60.0°
H2'1	C2'	H2'2	H2'3	118.2°	120.0°

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PDB entries from 2026-01-21

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