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Summary Geometry Related PDB entries

PHD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N	CA	sing	1.47Å	1.44Å
N	H2	sing	1.01Å	1.02Å
N	H	sing	1.01Å	1.02Å
CA	C	sing	1.51Å	1.54Å
CA	CB	sing	1.53Å	1.54Å
CA	HA	sing	1.09Å	1.11Å
C	O	doub	1.21Å	1.24Å
C	OXT	sing	1.34Å	1.32Å
CB	CG	sing	1.51Å	1.60Å
CB	HB2	sing	1.09Å	1.12Å
CB	HB3	sing	1.09Å	1.11Å
CG	OD1	sing	1.34Å	1.33Å
CG	OD2	doub	1.21Å	1.21Å
OD1	P	sing	1.61Å	1.65Å
P	OP1	doub	1.48Å	1.51Å
P	OP2	sing	1.61Å	1.46Å
P	OP3	sing	1.61Å	1.51Å
OP2	H2O	sing	0.97Å	0.95Å
OP3	H3O	sing	0.97Å	0.95Å
OXT	HXT	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
CA	N	H2	107.9°	106.7°
CA	N	H	112.9°	106.7°
N	CA	C	107.8°	109.5°
N	CA	CB	103.7°	109.5°
N	CA	HA	114.3°	109.4°
H2	N	H	112.7°	106.7°
C	CA	CB	109.9°	109.6°
C	CA	HA	108.6°	109.4°
CA	C	O	118.0°	120.0°
CA	C	OXT	118.9°	120.0°
CB	CA	HA	112.4°	109.5°
CA	CB	CG	111.4°	109.5°
CA	CB	HB2	111.5°	109.5°
CA	CB	HB3	111.5°	109.5°
O	C	OXT	123.1°	120.0°
C	OXT	HXT	118.9°	120.0°
CG	CB	HB2	111.5°	109.5°
CG	CB	HB3	111.5°	109.5°
CB	CG	OD1	116.8°	120.1°
CB	CG	OD2	116.0°	120.0°
HB2	CB	HB3	98.8°	109.4°
OD1	CG	OD2	126.3°	119.9°
CG	OD1	P	132.1°	120.0°
OD1	P	OP1	104.3°	109.5°
OD1	P	OP2	112.8°	109.5°
OD1	P	OP3	104.9°	109.5°
OP1	P	OP2	110.3°	109.4°
OP1	P	OP3	114.4°	109.5°
OP2	P	OP3	110.0°	109.5°
P	OP2	H2O	112.8°	106.8°
P	OP3	H3O	104.9°	106.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
CA	N	H2	H	125.3°	113.8°
N	CA	C	CB	112.4°	120.1°
N	CA	C	HA	124.4°	119.9°
N	CA	CB	HA	123.9°	119.9°
N	CA	C	O	22.1°	30.1°
N	CA	C	OXT	156.2°	150.0°
N	CA	CB	CG	179.9°	59.9°
N	CA	CB	HB2	54.8°	60.1°
N	CA	CB	HB3	54.6°	180.0°
H2	N	CA	C	180.0°	173.9°
H2	N	CA	CB	63.4°	53.7°
H2	N	CA	HA	59.2°	66.2°
H	N	CA	C	54.7°	60.1°
H	N	CA	CB	61.8°	60.1°
H	N	CA	HA	175.6°	180.0°
C	CA	CB	HA	121.0°	120.0°
CA	C	O	OXT	178.2°	179.8°
C	CA	CB	CG	64.9°	180.0°
C	CA	CB	HB2	169.9°	60.0°
C	CA	CB	HB3	60.4°	59.9°
CA	C	OXT	HXT	179.9°	179.9°
CB	CA	C	O	90.3°	89.9°
CB	CA	C	OXT	91.4°	89.9°
CA	CB	CG	HB2	125.3°	120.0°
CA	CB	CG	HB3	125.3°	120.1°
CA	CB	HB2	HB3	117.4°	120.0°
CA	CB	CG	OD1	38.7°	180.0°
CA	CB	CG	OD2	151.6°	0.1°
HA	CA	C	O	146.5°	150.1°
HA	CA	C	OXT	31.9°	30.1°
HA	CA	CB	CG	56.1°	60.0°
HA	CA	CB	HB2	69.1°	180.0°
HA	CA	CB	HB3	178.6°	60.1°
O	C	OXT	HXT	1.7°	0.1°
CG	CB	HB2	HB3	117.4°	120.0°
CB	CG	OD1	OD2	168.5°	180.0°
CB	CG	OD1	P	156.5°	179.9°
HB2	CB	CG	OD1	86.6°	60.0°
HB2	CB	CG	OD2	83.1°	120.1°
HB3	CB	CG	OD1	164.0°	59.9°
HB3	CB	CG	OD2	26.3°	120.0°
CG	OD1	P	OP1	142.7°	60.1°
CG	OD1	P	OP2	23.0°	180.0°
CG	OD1	P	OP3	96.7°	60.0°
OD2	CG	OD1	P	35.0°	0.0°
OD1	P	OP1	OP2	121.4°	120.0°
OD1	P	OP1	OP3	114.0°	120.0°
OD1	P	OP2	OP3	116.7°	120.1°
OD1	P	OP2	H2O	180.0°	180.0°
OD1	P	OP3	H3O	180.0°	60.0°
OP1	P	OP2	OP3	127.1°	120.0°
OP1	P	OP2	H2O	63.8°	60.0°
OP1	P	OP3	H3O	66.3°	180.0°
OP2	P	OP3	H3O	58.4°	60.0°
OP3	P	OP2	H2O	63.3°	60.0°

222415

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