Summary Geometry PCM/PTM Related PDB entries

Y6K

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C18	C17	sing	1.53Å	1.52Å
C20	C17	sing	1.53Å	1.51Å
C17	O3	sing	1.45Å	1.49Å
C17	C19	sing	1.53Å	1.51Å
O3	C16	sing	1.34Å	1.34Å
C16	O2	doub	1.21Å	1.20Å
C16	C2	sing	1.51Å	1.50Å
C7	C8	sing	1.52Å	1.51Å
C7	C4	sing	1.54Å	1.54Å
C9	C8	doub	1.31Å	1.32Å
C8	C6	sing	1.53Å	1.51Å
O1	C14	doub	1.21Å	1.19Å
C2	C3	sing	1.53Å	1.51Å
C2	C1	sing	1.51Å	1.52Å
C3	C4	sing	1.53Å	1.50Å
C4	C14	sing	1.51Å	1.52Å
C4	C5	sing	1.55Å	1.56Å
O4	C1	doub	1.21Å	1.22Å
C1	C6	sing	1.53Å	1.52Å
C14	O	sing	1.34Å	1.32Å
C6	C5	sing	1.55Å	1.53Å
O	C15	sing	1.45Å	1.45Å
C2	H1	sing	1.09Å	1.10Å
C3	H2	sing	1.09Å	1.10Å
C3	H3	sing	1.09Å	1.10Å
C15	H4	sing	1.09Å	1.10Å
C15	H5	sing	1.09Å	1.10Å
C15	H6	sing	1.09Å	1.10Å
C19	H7	sing	1.09Å	1.10Å
C19	H8	sing	1.09Å	1.10Å
C19	H9	sing	1.09Å	1.10Å
C20	H10	sing	1.09Å	1.10Å
C20	H11	sing	1.09Å	1.10Å
C20	H12	sing	1.09Å	1.10Å
C18	H13	sing	1.09Å	1.10Å
C18	H14	sing	1.09Å	1.10Å
C18	H15	sing	1.09Å	1.10Å
C7	H16	sing	1.09Å	1.10Å
C7	H17	sing	1.09Å	1.10Å
C5	H18	sing	1.09Å	1.10Å
C5	H19	sing	1.09Å	1.10Å
C6	H20	sing	1.09Å	1.10Å
C9	H21	sing	1.08Å	1.08Å
C9	H22	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C18	C17	C20	112.3°	109.5°
C18	C17	O3	107.9°	109.5°
C18	C17	C19	111.3°	109.4°
C17	C18	H13	109.5°	109.5°
C17	C18	H14	109.5°	109.5°
C17	C18	H15	109.5°	109.5°
C20	C17	O3	107.7°	109.5°
C20	C17	C19	108.9°	109.5°
C17	C20	H10	109.5°	109.5°
C17	C20	H11	109.4°	109.5°
C17	C20	H12	109.5°	109.5°
O3	C17	C19	108.5°	109.4°
C17	O3	C16	124.8°	117.1°
C17	C19	H7	109.5°	109.5°
C17	C19	H8	109.5°	109.4°
C17	C19	H9	109.5°	109.4°
O3	C16	O2	127.5°	119.9°
O3	C16	C2	110.8°	120.0°
O2	C16	C2	120.4°	120.0°
C16	C2	C3	125.3°	109.5°
C16	C2	C1	112.8°	109.5°
C16	C2	H1	97.2°	109.5°
C8	C7	C4	105.3°	106.7°
C7	C8	C9	127.1°	126.7°
C7	C8	C6	108.4°	106.6°
C8	C7	H16	110.5°	110.0°
C8	C7	H17	110.5°	110.1°
C7	C4	C3	114.7°	108.6°
C7	C4	C14	115.2°	112.1°
C7	C4	C5	103.4°	103.4°
C4	C7	H16	110.5°	110.0°
C4	C7	H17	110.5°	110.0°
C9	C8	C6	124.5°	126.7°
C8	C9	H21	120.0°	120.0°
C8	C9	H22	120.0°	120.0°
C8	C6	C1	107.2°	105.8°
C8	C6	C5	101.2°	103.4°
C8	C6	H20	112.9°	113.6°
O1	C14	C4	124.7°	120.0°
O1	C14	O	122.8°	120.1°
C3	C2	C1	117.2°	109.4°
C2	C3	C4	118.2°	109.8°
C3	C2	H1	97.2°	109.5°
C2	C3	H2	107.2°	109.4°
C2	C3	H3	107.3°	109.4°
C2	C1	O4	121.3°	121.7°
C2	C1	C6	116.5°	116.6°
C1	C2	H1	97.2°	109.5°
C3	C4	C14	108.1°	112.0°
C3	C4	C5	100.6°	107.5°
C4	C3	H2	107.2°	109.4°
C4	C3	H3	107.2°	109.4°
C14	C4	C5	114.0°	112.6°
C4	C14	O	112.3°	120.0°
C4	C5	C6	102.7°	101.1°
C4	C5	H18	111.1°	111.1°
C4	C5	H19	111.1°	111.1°
O4	C1	C6	122.0°	121.7°
C1	C6	C5	109.6°	105.2°
C1	C6	H20	112.8°	113.5°
C14	O	C15	114.5°	117.0°
C6	C5	H18	111.1°	111.1°
C6	C5	H19	111.1°	111.1°
C5	C6	H20	112.5°	114.4°
O	C15	H4	109.5°	109.5°
O	C15	H5	109.5°	109.5°
O	C15	H6	109.4°	109.5°
H2	C3	H3	109.4°	109.3°
H4	C15	H5	109.5°	109.4°
H4	C15	H6	109.5°	109.4°
H5	C15	H6	109.5°	109.4°
H7	C19	H8	109.4°	109.5°
H7	C19	H9	109.4°	109.5°
H8	C19	H9	109.5°	109.4°
H10	C20	H11	109.5°	109.4°
H10	C20	H12	109.5°	109.5°
H11	C20	H12	109.5°	109.5°
H13	C18	H14	109.5°	109.4°
H13	C18	H15	109.4°	109.5°
H14	C18	H15	109.5°	109.5°
H16	C7	H17	109.5°	110.0°
H18	C5	H19	109.5°	111.0°
H21	C9	H22	120.0°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C18	C17	C20	O3	118.7°	120.0°
C18	C17	C20	C19	123.8°	120.0°
C18	C17	O3	C19	120.8°	119.9°
C18	C17	O3	C16	58.7°	177.9°
C18	C17	C19	H7	180.0°	56.0°
C18	C17	C19	H8	60.0°	64.0°
C18	C17	C19	H9	60.0°	176.1°
C18	C17	C20	H10	180.0°	180.0°
C18	C17	C20	H11	60.0°	60.0°
C18	C17	C20	H12	60.0°	60.0°
C17	C18	H13	H14	120.0°	120.0°
C17	C18	H13	H15	120.0°	120.1°
C17	C18	H14	H15	120.0°	120.1°
C20	C17	O3	C19	117.7°	120.0°
C20	C17	O3	C16	179.9°	62.0°
C20	C17	C19	H7	55.6°	176.1°
C20	C17	C19	H8	64.4°	56.0°
C20	C17	C19	H9	175.6°	63.9°
C17	C20	H10	H11	120.0°	120.0°
C17	C20	H10	H12	120.0°	120.1°
C17	C20	H11	H12	120.0°	120.0°
C20	C17	C18	H13	180.0°	59.9°
C20	C17	C18	H14	60.0°	60.0°
C20	C17	C18	H15	60.0°	180.0°
C17	O3	C16	O2	0.4°	5.3°
C17	O3	C16	C2	167.5°	174.7°
O3	C17	C19	H7	61.3°	63.9°
O3	C17	C19	H8	178.7°	176.0°
O3	C17	C19	H9	58.7°	56.1°
O3	C17	C20	H10	61.3°	60.0°
O3	C17	C20	H11	58.7°	180.0°
O3	C17	C20	H12	178.7°	60.1°
O3	C17	C18	H13	61.5°	60.1°
O3	C17	C18	H14	178.5°	180.0°
O3	C17	C18	H15	58.5°	60.0°
C19	C17	O3	C16	62.1°	58.0°
C17	C19	H7	H8	120.0°	120.0°
C17	C19	H7	H9	120.0°	120.0°
C17	C19	H8	H9	120.0°	119.9°
C19	C17	C20	H10	56.2°	59.9°
C19	C17	C20	H11	176.2°	60.0°
C19	C17	C20	H12	63.8°	180.0°
C19	C17	C18	H13	57.6°	180.0°
C19	C17	C18	H14	62.5°	60.1°
C19	C17	C18	H15	177.5°	59.9°
O3	C16	O2	C2	166.1°	179.9°
O3	C16	C2	C3	12.2°	42.4°
O3	C16	C2	C1	167.1°	162.3°
O3	C16	C2	H1	91.9°	77.7°
O2	C16	C2	C3	179.6°	137.6°
O2	C16	C2	C1	24.7°	17.7°
O2	C16	C2	H1	76.3°	102.4°
C16	C2	C3	C1	153.9°	120.0°
C16	C2	C3	H1	104.2°	120.0°
C16	C2	C1	H1	101.0°	120.0°
C16	C2	C3	C4	145.4°	71.1°
C16	C2	C1	O4	22.1°	108.9°
C16	C2	C1	C6	162.9°	71.5°
C16	C2	C3	H2	24.1°	49.0°
C16	C2	C3	H3	93.3°	168.8°
C8	C7	C4	H16	119.4°	119.3°
C8	C7	C4	H17	119.4°	119.4°
C7	C8	C9	C6	179.1°	179.9°
C8	C7	C4	C3	90.4°	90.8°
C8	C7	C4	C14	143.2°	144.9°
C8	C7	C4	C5	18.1°	23.2°
C7	C8	C6	C1	82.2°	82.0°
C7	C8	C6	C5	32.5°	28.3°
C8	C7	H16	H17	121.9°	121.4°
C7	C8	C6	H20	153.0°	152.9°
C7	C8	C9	H21	179.1°	174.6°
C7	C8	C9	H22	0.9°	5.3°
C4	C7	C8	C9	170.3°	176.9°
C4	C7	C8	C6	8.9°	3.2°
C7	C4	C14	O1	65.8°	116.9°
C7	C4	C3	C2	60.1°	45.5°
C7	C4	C3	C14	130.0°	124.4°
C7	C4	C3	C5	110.2°	111.3°
C7	C4	C14	C5	119.4°	116.2°
C7	C4	C14	O	120.0°	63.1°
C7	C4	C5	C6	38.2°	39.8°
C7	C4	C3	H2	61.2°	74.6°
C7	C4	C3	H3	178.6°	165.6°
C4	C7	H16	H17	121.9°	121.3°
C7	C4	C5	H18	80.7°	157.8°
C7	C4	C5	H19	157.1°	78.1°
C9	C8	C6	C1	98.5°	97.9°
C9	C8	C6	C5	146.7°	151.8°
C9	C8	C7	H16	50.9°	57.6°
C9	C8	C7	H17	70.4°	63.7°
C9	C8	C6	H20	26.2°	27.2°
C8	C9	H21	H22	179.9°	179.9°
C8	C6	C1	C2	83.6°	49.0°
C8	C6	C5	C4	43.0°	42.0°
C8	C6	C1	O4	101.5°	131.4°
C8	C6	C1	C5	109.0°	109.0°
C8	C6	C1	H20	124.8°	125.2°
C8	C6	C5	H20	120.7°	124.0°
C6	C8	C7	H16	128.3°	122.5°
C6	C8	C7	H17	110.4°	116.2°
C8	C6	C5	H18	75.9°	160.0°
C8	C6	C5	H19	161.9°	76.0°
C6	C8	C9	H21	0.0°	5.2°
C6	C8	C9	H22	180.0°	174.8°
O1	C14	C4	C3	63.9°	120.7°
O1	C14	C4	O	174.2°	180.0°
O1	C14	C4	C5	174.8°	0.7°
O1	C14	O	C15	3.8°	0.0°
C3	C2	C1	H1	101.9°	119.9°
C2	C3	C4	H2	121.3°	120.1°
C2	C3	C4	H3	121.3°	120.1°
C2	C3	C4	C14	169.9°	169.9°
C2	C3	C4	C5	50.2°	65.9°
C3	C2	C1	O4	179.2°	131.1°
C3	C2	C1	C6	5.8°	48.5°
C2	C3	H2	H3	116.0°	119.8°
C1	C2	C3	C4	8.5°	48.9°
C2	C1	O4	C6	174.7°	179.7°
C2	C1	C6	C5	25.4°	60.0°
C1	C2	C3	H2	129.8°	169.0°
C1	C2	C3	H3	112.8°	71.2°
C2	C1	C6	H20	151.6°	174.1°
C3	C4	C14	C5	110.9°	121.4°
C3	C4	C14	O	110.3°	59.3°
C3	C4	C5	C6	80.6°	75.0°
C4	C3	C2	H1	110.4°	168.9°
C4	C3	H2	H3	116.0°	119.8°
C3	C4	C7	H16	150.2°	149.9°
C3	C4	C7	H17	28.9°	28.6°
C3	C4	C5	H18	160.5°	43.0°
C3	C4	C5	H19	38.3°	167.1°
C14	C4	C5	C6	164.0°	161.1°
C4	C14	O	C15	178.1°	180.0°
C14	C4	C3	H2	68.8°	49.8°
C14	C4	C3	H3	48.7°	70.0°
C14	C4	C7	H16	23.8°	25.5°
C14	C4	C7	H17	97.5°	95.8°
C14	C4	C5	H18	45.1°	80.9°
C14	C4	C5	H19	77.1°	43.2°
C4	C5	C6	C1	70.0°	68.7°
C5	C4	C14	O	0.6°	179.3°
C4	C5	C6	H18	118.9°	118.0°
C4	C5	C6	H19	118.9°	118.0°
C5	C4	C3	H2	171.4°	174.0°
C5	C4	C3	H3	71.1°	54.3°
C5	C4	C7	H16	101.3°	96.1°
C5	C4	C7	H17	137.4°	142.6°
C4	C5	H18	H19	123.1°	124.2°
C4	C5	C6	H20	163.7°	166.0°
O4	C1	C6	C5	149.5°	119.6°
O4	C1	C2	H1	78.9°	11.2°
O4	C1	C6	H20	23.3°	6.2°
C1	C6	C5	H20	126.3°	125.2°
C6	C1	C2	H1	96.1°	168.5°
C1	C6	C5	H18	171.1°	49.2°
C1	C6	C5	H19	48.9°	173.3°
C14	O	C15	H4	180.0°	180.0°
C14	O	C15	H5	60.0°	60.0°
C14	O	C15	H6	60.0°	60.0°
C6	C5	H18	H19	123.1°	124.1°
O	C15	H4	H5	120.0°	120.0°
O	C15	H4	H6	120.0°	120.1°
O	C15	H5	H6	120.0°	120.1°
H1	C2	C3	H2	128.3°	71.0°
H1	C2	C3	H3	10.8°	48.7°
H4	C15	H5	H6	120.0°	119.9°
H7	C19	H8	H9	119.9°	120.0°
H10	C20	H11	H12	120.0°	120.0°
H13	C18	H14	H15	120.0°	120.0°
H18	C5	C6	H20	44.8°	76.0°
H19	C5	C6	H20	77.4°	48.0°

Release date:	2024-11-27
Definition date:	2023-11-23
Last modified:	2024-11-22
Release status:	REL
Processing site:	PDBE
Derived from:	8R5E