Summary Geometry PCM/PTM Related PDB entries

Y3H

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C18	C17	sing	1.53Å	1.53Å
C19	C17	sing	1.53Å	1.52Å
C17	C20	sing	1.53Å	1.52Å
C17	O3	sing	1.45Å	1.44Å
C7	C4	sing	1.53Å	1.52Å
O4	C1	doub	1.21Å	1.22Å
O3	C16	sing	1.34Å	1.47Å
C1	C2	sing	1.51Å	1.50Å
C1	C6	sing	1.51Å	1.52Å
C2	C16	sing	1.51Å	1.51Å
C2	C3	sing	1.53Å	1.52Å
C6	C5	sing	1.53Å	1.53Å
C16	O2	doub	1.21Å	1.22Å
C4	C5	sing	1.53Å	1.53Å
C4	C3	sing	1.53Å	1.51Å
C4	C21	sing	1.51Å	1.51Å
O1	C21	doub	1.21Å	1.22Å
C21	O	sing	1.34Å	1.46Å
C24	C23	trip	1.17Å	1.27Å
O	C22	sing	1.45Å	1.43Å
C23	C22	sing	1.47Å	1.47Å
C18	H1	sing	1.09Å	1.10Å
C18	H2	sing	1.09Å	1.10Å
C18	H3	sing	1.09Å	1.10Å
C19	H4	sing	1.09Å	1.10Å
C19	H5	sing	1.09Å	1.10Å
C19	H6	sing	1.09Å	1.10Å
C2	H7	sing	1.09Å	1.10Å
C20	H8	sing	1.09Å	1.10Å
C20	H9	sing	1.09Å	1.10Å
C20	H10	sing	1.09Å	1.10Å
C22	H11	sing	1.09Å	1.10Å
C22	H12	sing	1.09Å	1.10Å
C24	H13	sing	1.05Å	1.06Å
C3	H14	sing	1.09Å	1.10Å
C3	H15	sing	1.09Å	1.10Å
C5	H16	sing	1.09Å	1.10Å
C5	H17	sing	1.09Å	1.10Å
C6	H18	sing	1.09Å	1.10Å
C6	H19	sing	1.09Å	1.10Å
C7	H20	sing	1.09Å	1.10Å
C7	H21	sing	1.09Å	1.10Å
C7	H22	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C18	C17	C19	107.9°	109.5°
C18	C17	C20	110.0°	109.4°
C18	C17	O3	112.5°	109.5°
C17	C18	H1	109.5°	109.4°
C17	C18	H2	109.5°	109.5°
C17	C18	H3	109.5°	109.5°
C19	C17	C20	109.4°	109.5°
C19	C17	O3	109.0°	109.5°
C17	C19	H4	109.5°	109.4°
C17	C19	H5	109.4°	109.5°
C17	C19	H6	109.5°	109.5°
C20	C17	O3	108.0°	109.5°
C17	C20	H8	109.5°	109.4°
C17	C20	H9	109.5°	109.5°
C17	C20	H10	109.5°	109.5°
C17	O3	C16	122.4°	117.0°
C7	C4	C5	110.8°	109.4°
C7	C4	C3	111.3°	109.4°
C7	C4	C21	104.9°	109.4°
C4	C7	H20	109.5°	109.5°
C4	C7	H21	109.5°	109.4°
C4	C7	H22	109.5°	109.5°
O4	C1	C2	117.2°	120.9°
O4	C1	C6	120.3°	120.8°
O3	C16	C2	122.2°	120.0°
O3	C16	O2	117.9°	120.0°
C2	C1	C6	122.6°	118.3°
C1	C2	C16	112.2°	109.7°
C1	C2	C3	110.5°	108.6°
C1	C2	H7	108.2°	109.6°
C1	C6	C5	114.2°	108.5°
C1	C6	H18	108.3°	109.6°
C1	C6	H19	108.3°	109.6°
C16	C2	C3	109.9°	109.6°
C2	C16	O2	119.9°	120.0°
C16	C2	H7	108.0°	109.6°
C2	C3	C4	111.5°	109.4°
C3	C2	H7	107.9°	109.8°
C2	C3	H14	109.0°	109.5°
C2	C3	H15	108.9°	109.4°
C6	C5	C4	112.3°	109.5°
C6	C5	H16	108.8°	109.5°
C6	C5	H17	108.8°	109.5°
C5	C6	H18	108.2°	109.7°
C5	C6	H19	108.3°	109.6°
C5	C4	C3	109.1°	109.8°
C5	C4	C21	112.1°	109.4°
C4	C5	H16	108.8°	109.5°
C4	C5	H17	108.8°	109.5°
C3	C4	C21	108.6°	109.4°
C4	C3	H14	108.9°	109.5°
C4	C3	H15	109.0°	109.5°
C4	C21	O1	119.1°	120.0°
C4	C21	O	120.3°	120.0°
O1	C21	O	120.6°	120.0°
C21	O	C22	123.8°	117.0°
C24	C23	C22	178.0°	179.9°
C23	C24	H13	180.0°	179.9°
O	C22	C23	115.0°	109.5°
O	C22	H11	108.1°	109.5°
O	C22	H12	108.1°	109.5°
C23	C22	H11	108.1°	109.4°
C23	C22	H12	108.0°	109.5°
H1	C18	H2	109.5°	109.5°
H1	C18	H3	109.4°	109.5°
H2	C18	H3	109.5°	109.5°
H4	C19	H5	109.4°	109.5°
H4	C19	H6	109.4°	109.5°
H5	C19	H6	109.5°	109.5°
H8	C20	H9	109.5°	109.5°
H8	C20	H10	109.5°	109.4°
H9	C20	H10	109.4°	109.5°
H11	C22	H12	109.5°	109.5°
H14	C3	H15	109.5°	109.5°
H16	C5	H17	109.5°	109.4°
H18	C6	H19	109.5°	109.8°
H20	C7	H21	109.5°	109.5°
H20	C7	H22	109.4°	109.5°
H21	C7	H22	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C18	C17	C19	C20	119.6°	119.9°
C18	C17	C19	O3	122.5°	120.0°
C18	C17	C20	O3	123.1°	120.0°
C18	C17	O3	C16	53.4°	60.0°
C17	C18	H1	H2	120.0°	120.0°
C17	C18	H1	H3	120.0°	120.0°
C17	C18	H2	H3	120.0°	120.0°
C18	C17	C19	H4	180.0°	180.0°
C18	C17	C19	H5	60.0°	60.0°
C18	C17	C19	H6	60.0°	60.0°
C18	C17	C20	H8	180.0°	180.0°
C18	C17	C20	H9	60.0°	60.0°
C18	C17	C20	H10	60.0°	60.1°
C19	C17	C20	O3	118.5°	120.0°
C19	C17	O3	C16	173.1°	180.0°
C19	C17	C18	H1	180.0°	60.0°
C19	C17	C18	H2	60.0°	60.0°
C19	C17	C18	H3	60.0°	180.0°
C17	C19	H4	H5	120.0°	120.0°
C17	C19	H4	H6	120.0°	120.0°
C17	C19	H5	H6	120.0°	120.0°
C19	C17	C20	H8	61.7°	60.0°
C19	C17	C20	H9	58.4°	60.0°
C19	C17	C20	H10	178.3°	180.0°
C20	C17	O3	C16	68.2°	60.0°
C20	C17	C18	H1	60.8°	60.0°
C20	C17	C18	H2	59.2°	180.0°
C20	C17	C18	H3	179.3°	60.0°
C20	C17	C19	H4	60.4°	60.0°
C20	C17	C19	H5	179.7°	179.9°
C20	C17	C19	H6	59.6°	60.0°
C17	C20	H8	H9	120.0°	120.0°
C17	C20	H8	H10	120.0°	120.0°
C17	C20	H9	H10	120.0°	120.0°
C17	O3	C16	C2	91.4°	179.9°
C17	O3	C16	O2	89.6°	0.1°
O3	C17	C18	H1	59.6°	180.0°
O3	C17	C18	H2	179.7°	60.0°
O3	C17	C18	H3	60.3°	60.0°
O3	C17	C19	H4	57.5°	60.0°
O3	C17	C19	H5	62.5°	60.0°
O3	C17	C19	H6	177.5°	180.0°
O3	C17	C20	H8	56.8°	60.0°
O3	C17	C20	H9	176.9°	180.0°
O3	C17	C20	H10	63.2°	59.9°
C7	C4	C3	C2	55.9°	56.5°
C7	C4	C5	C6	65.0°	56.5°
C7	C4	C5	C3	122.9°	120.1°
C7	C4	C5	C21	116.9°	119.8°
C7	C4	C3	C21	115.0°	119.9°
C7	C4	C21	O1	12.9°	120.1°
C7	C4	C21	O	166.1°	59.8°
C7	C4	C3	H14	64.4°	63.5°
C7	C4	C3	H15	176.2°	176.5°
C7	C4	C5	H16	174.6°	63.5°
C7	C4	C5	H17	55.4°	176.5°
C4	C7	H20	H21	120.0°	120.0°
C4	C7	H20	H22	120.0°	120.0°
C4	C7	H21	H22	120.0°	120.0°
O4	C1	C2	C6	178.3°	179.7°
O4	C1	C2	C16	27.7°	8.6°
O4	C1	C2	C3	150.7°	128.4°
O4	C1	C6	C5	157.5°	128.4°
O4	C1	C2	H7	91.4°	111.7°
O4	C1	C6	H18	36.8°	8.6°
O4	C1	C6	H19	81.8°	111.9°
O3	C16	C2	C1	129.6°	59.9°
O3	C16	C2	O2	179.0°	179.9°
O3	C16	C2	C3	107.0°	179.1°
O3	C16	C2	H7	10.5°	60.4°
C1	C2	C16	C3	123.3°	119.1°
C1	C2	C16	H7	119.2°	120.4°
C1	C2	C3	H7	118.0°	119.8°
C2	C1	C6	C5	24.2°	51.3°
C1	C2	C16	O2	51.4°	119.9°
C1	C2	C3	C4	51.2°	54.6°
C1	C2	C3	H14	171.5°	174.6°
C1	C2	C3	H15	69.1°	65.4°
C2	C1	C6	H18	144.9°	171.1°
C2	C1	C6	H19	96.5°	68.4°
C6	C1	C2	C16	154.0°	171.1°
C6	C1	C2	C3	31.0°	51.3°
C1	C6	C5	H18	120.7°	119.8°
C1	C6	C5	H19	120.7°	119.6°
C1	C6	C5	C4	36.4°	54.6°
C6	C1	C2	H7	86.9°	68.6°
C1	C6	C5	H16	84.1°	174.6°
C1	C6	C5	H17	156.8°	65.5°
C1	C6	H18	H19	117.9°	120.4°
C16	C2	C3	H7	117.6°	120.4°
C16	C2	C3	C4	175.6°	174.4°
C16	C2	C3	H14	64.1°	65.6°
C16	C2	C3	H15	55.3°	54.4°
C3	C2	C16	O2	71.9°	0.8°
C2	C3	C4	C5	66.7°	63.5°
C2	C3	C4	H14	120.3°	120.0°
C2	C3	C4	H15	120.3°	120.0°
C2	C3	C4	C21	170.9°	176.4°
C2	C3	H14	H15	119.1°	120.0°
C6	C5	C4	H16	120.4°	120.0°
C6	C5	C4	H17	120.4°	120.1°
C6	C5	C4	C3	57.9°	63.6°
C6	C5	C4	C21	178.2°	176.3°
C6	C5	H16	H17	118.7°	120.0°
C5	C6	H18	H19	117.8°	120.5°
O2	C16	C2	H7	170.6°	119.7°
C5	C4	C3	C21	122.4°	120.1°
C5	C4	C21	O1	107.4°	120.0°
C5	C4	C21	O	73.5°	60.0°
C5	C4	C3	H14	173.0°	176.5°
C5	C4	C3	H15	53.6°	56.4°
C4	C5	H16	H17	118.7°	120.0°
C4	C5	C6	H18	157.1°	174.4°
C4	C5	C6	H19	84.3°	65.0°
C5	C4	C7	H20	180.0°	60.0°
C5	C4	C7	H21	60.0°	180.0°
C5	C4	C7	H22	60.0°	60.1°
C3	C4	C21	O1	131.9°	0.3°
C3	C4	C21	O	47.1°	179.6°
C4	C3	C2	H7	66.8°	65.2°
C4	C3	H14	H15	119.1°	120.1°
C3	C4	C5	H16	62.5°	176.4°
C3	C4	C5	H17	178.3°	56.5°
C3	C4	C7	H20	58.4°	60.3°
C3	C4	C7	H21	178.4°	59.7°
C3	C4	C7	H22	61.6°	179.6°
C4	C21	O1	O	179.1°	179.9°
C4	C21	O	C22	175.9°	180.0°
C21	C4	C3	H14	50.6°	56.4°
C21	C4	C3	H15	68.9°	63.7°
C21	C4	C5	H16	57.7°	56.3°
C21	C4	C5	H17	61.4°	63.6°
C21	C4	C7	H20	58.8°	179.8°
C21	C4	C7	H21	61.2°	60.2°
C21	C4	C7	H22	178.8°	59.8°
O1	C21	O	C22	3.1°	0.0°
C21	O	C22	C23	51.4°	180.0°
C21	O	C22	H11	172.2°	60.0°
C21	O	C22	H12	69.4°	60.0°
C24	C23	C22	O	179.5°	108.0°
C24	C23	C22	H11	59.7°	132.1°
C24	C23	C22	H12	58.7°	12.1°
O	C22	C23	H11	120.8°	120.0°
O	C22	C23	H12	120.8°	120.0°
O	C22	H11	H12	117.5°	120.0°
C23	C22	H11	H12	117.5°	120.0°
C22	C23	C24	H13	160.2°	169.8°
H1	C18	H2	H3	119.9°	120.0°
H4	C19	H5	H6	120.0°	120.0°
H7	C2	C3	H14	53.5°	54.8°
H7	C2	C3	H15	172.9°	174.8°
H8	C20	H9	H10	120.0°	120.0°
H16	C5	C6	H18	36.7°	65.6°
H16	C5	C6	H19	155.2°	55.0°
H17	C5	C6	H18	82.5°	54.3°
H17	C5	C6	H19	36.1°	174.9°
H20	C7	H21	H22	120.0°	120.0°

Release date:	2024-11-27
Definition date:	2023-11-16
Last modified:	2024-11-22
Release status:	REL
Processing site:	PDBE
Derived from:	8R5F