Summary Geometry PCM/PTM Related PDB entries

VG1

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	sing	1.54Å	1.55Å
C1	O1	sing	1.40Å	1.44Å
C1	O5	sing	1.43Å	1.43Å
C1	H1	sing	0.98Å	1.11Å
C2	C3	sing	1.54Å	1.56Å
C2	O2	sing	1.43Å	1.45Å
C2	H2	sing	0.99Å	1.11Å
C3	C4	sing	1.53Å	1.54Å
C3	O3	sing	1.43Å	1.46Å
C3	H3	sing	0.99Å	1.11Å
C4	C5	sing	1.54Å	1.54Å
C4	O4	sing	1.43Å	1.44Å
C4	H4	sing	1.00Å	1.12Å
C5	C6	sing	1.53Å	1.47Å
C5	O5	sing	1.45Å	1.50Å
C5	H5	sing	1.00Å	1.11Å
C6	O6	sing	1.43Å	1.39Å
C6	H61	sing	0.99Å	1.12Å
C6	H62	sing	0.99Å	1.12Å
O1	P	sing	1.57Å	1.50Å
O2	HO2	sing	0.84Å	0.95Å
O3	HO3	sing	0.84Å	0.95Å
O4	HO4	sing	0.84Å	0.95Å
O6	V	sing	2.01Å	1.88Å
P	OP1	sing	1.55Å	1.50Å
P	OP2	sing	1.55Å	1.50Å
P	OP3	doub	1.49Å	1.50Å
OP1	HOP1	sing	0.89Å	0.95Å
OP2	HOP2	sing	0.89Å	0.95Å
V	OV1	sing	1.64Å	1.73Å
V	OV2	doub	1.64Å	1.71Å
V	OV3	doub	1.64Å	1.74Å
OV1	HTV	sing	0.87Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	C1	O1	110.1°	110.0°
C2	C1	O5	106.2°	111.2°
C2	C1	H1	111.1°	108.2°
C1	C2	C3	109.1°	111.9°
C1	C2	O2	105.6°	108.9°
C1	C2	H2	112.2°	108.2°
O1	C1	O5	109.1°	110.9°
O1	C1	H1	108.3°	108.6°
C1	O1	P	116.2°	123.7°
O5	C1	H1	112.0°	107.9°
C1	O5	C5	110.1°	119.2°
C3	C2	O2	109.4°	111.8°
C3	C2	H2	108.5°	108.1°
C2	C3	C4	107.4°	113.4°
C2	C3	O3	107.4°	106.9°
C2	C3	H3	111.5°	108.3°
O2	C2	H2	111.9°	107.8°
C2	O2	HO2	105.6°	111.5°
C4	C3	O3	107.5°	111.5°
C4	C3	H3	111.4°	108.3°
C3	C4	C5	111.8°	111.6°
C3	C4	O4	114.1°	106.0°
C3	C4	H4	105.0°	108.6°
O3	C3	H3	111.5°	108.2°
C3	O3	HO3	107.3°	111.4°
C5	C4	O4	110.7°	112.6°
C5	C4	H4	108.7°	109.4°
C4	C5	C6	109.0°	114.9°
C4	C5	O5	106.0°	111.2°
C4	C5	H5	113.5°	108.3°
O4	C4	H4	106.1°	108.4°
C4	O4	HO4	114.1°	112.8°
C6	C5	O5	113.5°	104.9°
C6	C5	H5	105.9°	108.4°
C5	C6	O6	106.1°	111.7°
C5	C6	H61	113.5°	109.4°
C5	C6	H62	113.5°	109.3°
O5	C5	H5	109.0°	109.0°
O6	C6	H61	113.5°	109.2°
O6	C6	H62	113.5°	109.1°
C6	O6	V	131.4°	114.6°
H61	C6	H62	96.9°	108.1°
O1	P	OP1	109.9°	105.8°
O1	P	OP2	107.9°	107.8°
O1	P	OP3	109.5°	115.1°
O6	V	OV1	102.0°	90.1°
O6	V	OV2	83.8°	95.7°
O6	V	OV3	87.2°	94.6°
OP1	P	OP2	110.7°	106.1°
OP1	P	OP3	108.8°	110.6°
P	OP1	HOP1	109.9°	113.2°
OP2	P	OP3	110.0°	110.9°
P	OP2	HOP2	107.9°	113.8°
OV1	V	OV2	118.8°	117.1°
OV1	V	OV3	119.7°	118.8°
V	OV1	HTV	102.0°	109.5°
OV2	V	OV3	121.5°	122.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	C1	O1	O5	116.3°	123.5°
C2	C1	O1	H1	121.6°	118.2°
C2	C1	O5	H1	121.4°	118.5°
C1	C2	C3	O2	115.2°	122.5°
C1	C2	C3	H2	122.5°	119.0°
C1	C2	O2	H2	122.3°	117.2°
C1	C2	C3	C4	56.1°	49.0°
C1	C2	C3	O3	171.4°	172.2°
C1	C2	C3	H3	66.2°	71.3°
C2	C1	O5	C5	70.6°	52.4°
C2	C1	O1	P	133.5°	170.2°
C1	C2	O2	HO2	180.0°	172.9°
O1	C1	O5	H1	119.9°	118.8°
O1	C1	C2	C3	53.7°	75.1°
O1	C1	C2	O2	63.9°	49.0°
O1	C1	C2	H2	173.9°	166.0°
O1	C1	O5	C5	48.1°	70.3°
C1	O1	P	OP1	1.6°	172.8°
C1	O1	P	OP2	119.2°	74.0°
C1	O1	P	OP3	121.1°	50.4°
O5	C1	C2	C3	64.3°	48.2°
O5	C1	C2	O2	178.1°	172.3°
O5	C1	C2	H2	55.9°	70.8°
C1	O5	C5	C4	67.6°	52.5°
C1	O5	C5	C6	172.7°	177.3°
C1	O5	C5	H5	54.9°	66.8°
O5	C1	O1	P	110.3°	66.3°
H1	C1	C2	C3	173.6°	166.5°
H1	C1	C2	O2	56.0°	69.4°
H1	C1	C2	H2	66.1°	47.5°
H1	C1	O5	C5	168.0°	170.9°
H1	C1	O1	P	11.9°	52.1°
C3	C2	O2	H2	120.3°	118.6°
C2	C3	C4	O3	115.2°	120.8°
C2	C3	C4	H3	122.4°	120.3°
C2	C3	O3	H3	122.4°	116.5°
C2	C3	C4	C5	55.1°	49.0°
C2	C3	C4	O4	178.4°	172.0°
C2	C3	C4	H4	62.6°	71.7°
C3	C2	O2	HO2	62.6°	62.9°
C2	C3	O3	HO3	179.9°	172.5°
O2	C2	C3	C4	171.3°	171.5°
O2	C2	C3	O3	73.4°	65.3°
O2	C2	C3	H3	49.0°	51.2°
H2	C2	C3	C4	66.4°	70.0°
H2	C2	C3	O3	48.9°	53.2°
H2	C2	C3	H3	171.3°	169.7°
H2	C2	O2	HO2	57.7°	55.7°
C4	C3	O3	H3	122.3°	119.0°
C3	C4	C5	O4	128.4°	119.1°
C3	C4	C5	H4	115.4°	120.3°
C3	C4	O4	H4	115.1°	116.5°
C3	C4	C5	C6	178.5°	167.0°
C3	C4	C5	O5	58.9°	48.1°
C3	C4	C5	H5	60.7°	71.6°
C4	C3	O3	HO3	64.7°	63.0°
C3	C4	O4	HO4	180.0°	171.3°
O3	C3	C4	C5	170.3°	169.8°
O3	C3	C4	O4	63.1°	67.3°
O3	C3	C4	H4	52.6°	49.1°
H3	C3	C4	C5	67.3°	71.3°
H3	C3	C4	O4	59.2°	51.7°
H3	C3	C4	H4	175.0°	168.0°
H3	C3	O3	HO3	57.6°	56.0°
C5	C4	O4	H4	117.8°	121.2°
C4	C5	C6	O5	117.9°	122.4°
C4	C5	C6	H5	122.5°	121.3°
C4	C5	O5	H5	122.5°	119.3°
C4	C5	C6	O6	74.5°	178.4°
C4	C5	C6	H61	160.2°	60.6°
C4	C5	C6	H62	50.8°	57.6°
C5	C4	O4	HO4	52.9°	66.4°
O4	C4	C5	C6	50.1°	73.8°
O4	C4	C5	O5	172.7°	167.2°
O4	C4	C5	H5	67.7°	47.5°
H4	C4	C5	C6	66.1°	46.8°
H4	C4	C5	O5	56.5°	72.1°
H4	C4	C5	H5	176.1°	168.2°
H4	C4	O4	HO4	64.9°	54.8°
C6	C5	O5	H5	117.8°	115.9°
C5	C6	O6	H61	125.3°	121.1°
C5	C6	O6	H62	125.3°	121.0°
C5	C6	H61	H62	119.4°	118.9°
C5	C6	O6	V	174.2°	171.0°
O5	C5	C6	O6	43.4°	59.2°
O5	C5	C6	H61	81.9°	61.8°
O5	C5	C6	H62	168.7°	180.0°
H5	C5	C6	O6	163.0°	57.1°
H5	C5	C6	H61	37.7°	178.1°
H5	C5	C6	H62	71.7°	63.7°
O6	C6	H61	H62	119.4°	118.5°
C6	O6	V	OV1	132.6°	178.8°
C6	O6	V	OV2	109.2°	61.5°
C6	O6	V	OV3	12.9°	62.3°
H61	C6	O6	V	60.4°	67.9°
H62	C6	O6	V	49.0°	50.0°
O1	P	OP1	OP2	119.1°	114.4°
O1	P	OP1	OP3	119.9°	125.3°
O1	P	OP2	OP3	119.4°	126.9°
O1	P	OP1	HOP1	180.0°	176.3°
O1	P	OP2	HOP2	180.0°	66.8°
O6	V	OV1	OV2	89.4°	96.5°
O6	V	OV1	OV3	93.6°	95.4°
O6	V	OV2	OV3	82.8°	99.3°
O6	V	OV1	HTV	180.0°	123.2°
OP1	P	OP2	OP3	120.3°	120.1°
OP1	P	OP2	HOP2	59.8°	179.8°
OP2	P	OP1	HOP1	61.0°	62.0°
OP3	P	OP1	HOP1	60.0°	58.4°
OP3	P	OP2	HOP2	60.5°	60.1°
OV1	V	OV2	OV3	176.9°	167.6°
OV2	V	OV1	HTV	90.6°	140.2°
OV3	V	OV1	HTV	86.4°	27.9°

Definition date:	1999-08-24
Last modified:	2026-07-31
Release status:	REL
Processing site:	EBI
Derived from:	1C4G