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Summary Geometry Related PDB entries

Obsolete: 3MD

3MD was replaced with 2AS on

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N	CA	sing	1.47Å	1.48Å
N	H	sing	1.01Å	1.02Å
N	H2	sing	1.01Å	1.02Å
CB	CG	sing	1.51Å	1.51Å
CB	CA	sing	1.53Å	1.56Å
CB	CB1	sing	1.53Å	1.53Å
CB	HB	sing	1.09Å	1.11Å
CG	OD1	doub	1.21Å	1.22Å
CG	OD2	sing	1.34Å	1.23Å
OD2	HD2	sing	0.97Å	0.95Å
CA	C	sing	1.51Å	1.54Å
CA	HA	sing	1.09Å	1.12Å
CB1	HB11	sing	1.09Å	1.12Å
CB1	HB12	sing	1.09Å	1.12Å
CB1	HB13	sing	1.09Å	1.12Å
C	O	doub	1.21Å	1.23Å
C	OXT	sing	1.34Å	1.23Å
OXT	HXT	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
CA	N	H	110.4°	106.6°
CA	N	H2	114.3°	106.8°
N	CA	CB	114.3°	109.5°
N	CA	C	113.7°	109.5°
N	CA	HA	103.0°	109.5°
H	N	H2	110.5°	106.7°
CG	CB	CA	111.7°	109.5°
CG	CB	CB1	106.5°	109.5°
CG	CB	HB	113.2°	109.5°
CB	CG	OD1	117.3°	119.9°
CB	CG	OD2	122.7°	120.1°
CA	CB	CB1	117.5°	109.4°
CA	CB	HB	101.1°	109.5°
CB	CA	C	109.9°	109.5°
CB	CA	HA	107.4°	109.4°
CB1	CB	HB	106.9°	109.4°
CB	CB1	HB11	113.3°	109.4°
CB	CB1	HB12	106.5°	109.5°
CB	CB1	HB13	113.3°	109.5°
OD1	CG	OD2	119.9°	120.0°
CG	OD2	HD2	122.7°	120.0°
C	CA	HA	108.1°	109.4°
CA	C	O	119.8°	120.0°
CA	C	OXT	121.9°	120.0°
HB11	CB1	HB12	113.4°	109.5°
HB11	CB1	HB13	97.1°	109.5°
HB12	CB1	HB13	113.3°	109.5°
O	C	OXT	118.2°	120.0°
C	OXT	HXT	122.0°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
CA	N	H	H2	127.4°	113.8°
N	CA	CB	CG	59.5°	59.9°
N	CA	CB	C	129.2°	120.1°
N	CA	CB	HA	113.5°	120.0°
N	CA	CB	CB1	64.0°	60.1°
N	CA	CB	HB	179.8°	180.0°
N	CA	C	HA	113.6°	120.0°
N	CA	C	O	156.0°	29.9°
N	CA	C	OXT	24.6°	149.9°
H	N	CA	CB	54.7°	60.1°
H	N	CA	C	178.1°	60.0°
H	N	CA	HA	61.4°	180.0°
H2	N	CA	CB	180.0°	53.7°
H2	N	CA	C	52.8°	173.8°
H2	N	CA	HA	63.9°	66.2°
CG	CB	CA	CB1	123.5°	120.0°
CG	CB	CA	HB	120.7°	120.0°
CG	CB	CB1	HB	121.3°	120.0°
CB	CG	OD1	OD2	177.6°	179.9°
CB	CG	OD2	HD2	180.0°	180.0°
CG	CB	CA	C	171.4°	180.0°
CG	CB	CA	HA	54.0°	60.1°
CG	CB	CB1	HB11	54.7°	60.0°
CG	CB	CB1	HB12	180.0°	179.9°
CG	CB	CB1	HB13	54.7°	60.0°
CA	CB	CB1	HB	112.6°	120.0°
CA	CB	CG	OD1	16.0°	0.0°
CA	CB	CG	OD2	161.5°	180.0°
CB	CA	C	HA	116.9°	119.9°
CA	CB	CB1	HB11	71.4°	60.0°
CA	CB	CB1	HB12	53.9°	60.0°
CA	CB	CB1	HB13	179.2°	180.0°
CB	CA	C	O	74.5°	90.1°
CB	CA	C	OXT	104.9°	90.0°
CB1	CB	CG	OD1	113.5°	120.0°
CB1	CB	CG	OD2	68.9°	60.0°
CB1	CB	CA	C	65.1°	60.0°
CB1	CB	CA	HA	177.5°	179.9°
CB	CB1	HB11	HB12	121.5°	120.0°
CB	CB1	HB11	HB13	119.2°	120.0°
CB	CB1	HB12	HB13	125.3°	120.0°
HB	CB	CG	OD1	129.3°	120.0°
HB	CB	CG	OD2	48.2°	59.9°
HB	CB	CA	C	50.7°	60.0°
HB	CB	CA	HA	66.7°	60.0°
HB	CB	CB1	HB11	176.0°	180.0°
HB	CB	CB1	HB12	58.7°	60.0°
HB	CB	CB1	HB13	66.6°	60.0°
OD1	CG	OD2	HD2	2.5°	0.1°
CA	C	O	OXT	179.5°	179.9°
CA	C	OXT	HXT	180.0°	180.0°
HA	CA	C	O	42.4°	149.9°
HA	CA	C	OXT	138.2°	29.9°
HB11	CB1	HB12	HB13	109.5°	120.0°
O	C	OXT	HXT	0.5°	0.1°

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PDB entries from 2025-06-11

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