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Summary Geometry Related PDB entries

PEP

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	O1	doub	1.21Å	1.29Å
C1	O2'	sing	1.35Å	1.21Å
C1	C2	sing	1.47Å	1.52Å
O2'	HO2	sing	0.97Å	0.95Å
C2	C3	doub	1.33Å	1.36Å
C2	O2	sing	1.36Å	1.38Å
C3	H31	sing	1.08Å	1.10Å
C3	H32	sing	1.08Å	1.10Å
O2	P	sing	1.61Å	1.58Å
P	O1P	doub	1.48Å	1.54Å
P	O2P	sing	1.61Å	1.50Å
P	O3P	sing	1.61Å	1.48Å
O2P	HOP2	sing	0.97Å	0.95Å
O3P	HOP3	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C1	O2'	122.8°	120.0°
O1	C1	C2	114.0°	120.0°
O2'	C1	C2	123.0°	120.0°
C1	O2'	HO2	122.8°	120.1°
C1	C2	C3	129.5°	120.0°
C1	C2	O2	114.1°	120.0°
C3	C2	O2	116.0°	120.1°
C2	C3	H31	116.0°	120.0°
C2	C3	H32	129.5°	120.0°
C2	O2	P	124.9°	106.8°
H31	C3	H32	114.1°	119.9°
O2	P	O1P	104.8°	109.4°
O2	P	O2P	104.0°	109.5°
O2	P	O3P	107.9°	109.5°
O1P	P	O2P	114.3°	109.4°
O1P	P	O3P	108.2°	109.5°
O2P	P	O3P	116.7°	109.4°
P	O2P	HOP2	104.1°	106.9°
P	O3P	HOP3	107.9°	106.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C1	O2'	C2	174.8°	180.0°
O1	C1	O2'	HO2	179.9°	0.0°
O1	C1	C2	C3	5.8°	180.0°
O1	C1	C2	O2	178.0°	0.0°
O2'	C1	C2	C3	179.1°	0.0°
O2'	C1	C2	O2	6.8°	180.0°
C2	C1	O2'	HO2	5.2°	180.0°
C1	C2	C3	O2	172.1°	180.0°
C1	C2	C3	H31	7.9°	174.8°
C1	C2	C3	H32	180.0°	5.2°
C1	C2	O2	P	94.6°	93.6°
C2	C3	H31	H32	173.4°	180.0°
C3	C2	O2	P	78.8°	86.3°
O2	C2	C3	H31	180.0°	5.2°
O2	C2	C3	H32	7.9°	174.8°
C2	O2	P	O1P	72.5°	55.3°
C2	O2	P	O2P	167.2°	175.3°
C2	O2	P	O3P	42.7°	64.7°
O2	P	O1P	O2P	113.2°	120.0°
O2	P	O1P	O3P	114.9°	120.0°
O2	P	O2P	O3P	118.6°	120.1°
O2	P	O2P	HOP2	180.0°	180.0°
O2	P	O3P	HOP3	179.9°	60.0°
O1P	P	O2P	O3P	127.7°	120.0°
O1P	P	O2P	HOP2	66.3°	60.0°
O1P	P	O3P	HOP3	67.2°	180.0°
O2P	P	O3P	HOP3	63.4°	60.1°
O3P	P	O2P	HOP2	61.3°	59.9°

219140

PDB entries from 2024-05-01

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