YRD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C15	C14	sing	1.53Å	1.53Å
C14	C13	sing	1.53Å	1.53Å
C13	C12	sing	1.53Å	1.53Å
C12	C11	sing	1.53Å	1.54Å
O16	C10	doub	1.21Å	1.23Å
C11	C10	sing	1.51Å	1.54Å
C10	N9	sing	1.35Å	1.35Å
S1	C17	sing	1.77Å	1.76Å
S1	S2	sing	2.07Å	2.07Å
N9	C8	sing	1.41Å	1.35Å
C8	C17	doub	1.41Å	1.36Å
C8	C6	sing	1.38Å	1.33Å
C17	C4	sing	1.39Å	1.38Å
S2	C3	sing	1.71Å	1.67Å
C6	O7	doub	1.22Å	1.23Å
C6	N5	sing	1.34Å	1.31Å
C4	C3	doub	1.36Å	1.36Å
C4	N5	sing	1.43Å	1.33Å
N5	C18	sing	1.47Å	1.44Å
C13	H2	sing	1.09Å	1.10Å
C13	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
C18	H7	sing	1.09Å	1.10Å
C18	H8	sing	1.09Å	1.10Å
C18	H9	sing	1.09Å	1.10Å
C3	H10	sing	1.08Å	1.08Å
N9	H11	sing	0.97Å	1.00Å
C11	H12	sing	1.09Å	1.10Å
C11	H13	sing	1.09Å	1.10Å
C12	H14	sing	1.09Å	1.10Å
C12	H15	sing	1.09Å	1.10Å
C14	H16	sing	1.09Å	1.10Å
C14	H17	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C15	C14	C13	111.1°	109.5°
C14	C15	H4	109.5°	109.5°
C14	C15	H5	109.5°	109.5°
C14	C15	H6	109.5°	109.5°
C15	C14	H16	109.1°	109.5°
C15	C14	H17	109.1°	109.5°
C14	C13	C12	109.0°	109.5°
C14	C13	H2	109.6°	109.5°
C14	C13	H3	109.6°	109.4°
C13	C14	H16	109.1°	109.5°
C13	C14	H17	109.1°	109.4°
C13	C12	C11	111.1°	109.5°
C12	C13	H2	109.6°	109.5°
C12	C13	H3	109.6°	109.5°
C13	C12	H14	109.0°	109.5°
C13	C12	H15	109.0°	109.5°
C12	C11	C10	109.7°	109.5°
C12	C11	H12	109.5°	109.5°
C12	C11	H13	109.4°	109.5°
C11	C12	H14	109.1°	109.5°
C11	C12	H15	109.1°	109.5°
O16	C10	C11	120.3°	120.0°
O16	C10	N9	125.0°	120.0°
C11	C10	N9	114.6°	120.0°
C10	C11	H12	109.4°	109.4°
C10	C11	H13	109.4°	109.4°
C10	N9	C8	122.6°	120.0°
C10	N9	H11	118.7°	120.0°
C17	S1	S2	94.9°	95.3°
S1	C17	C8	140.0°	140.2°
S1	C17	C4	111.9°	111.4°
S1	S2	C3	95.7°	96.0°
N9	C8	C17	131.3°	126.3°
N9	C8	C6	122.0°	126.3°
C8	N9	H11	118.7°	120.0°
C17	C8	C6	106.6°	107.4°
C8	C17	C4	108.1°	108.4°
C8	C6	O7	126.1°	125.4°
C8	C6	N5	109.7°	109.1°
C17	C4	C3	121.3°	122.6°
C17	C4	N5	105.6°	105.5°
S2	C3	C4	116.2°	114.6°
S2	C3	H10	121.9°	122.6°
O7	C6	N5	124.2°	125.4°
C6	N5	C4	110.0°	109.6°
C6	N5	C18	123.9°	125.2°
C3	C4	N5	133.0°	131.9°
C4	C3	H10	121.9°	122.7°
C4	N5	C18	126.1°	125.2°
N5	C18	H7	109.5°	109.5°
N5	C18	H8	109.5°	109.5°
N5	C18	H9	109.5°	109.5°
H2	C13	H3	109.4°	109.5°
H4	C15	H5	109.5°	109.4°
H4	C15	H6	109.4°	109.5°
H5	C15	H6	109.5°	109.4°
H7	C18	H8	109.4°	109.5°
H7	C18	H9	109.5°	109.5°
H8	C18	H9	109.5°	109.5°
H12	C11	H13	109.5°	109.5°
H14	C12	H15	109.5°	109.5°
H16	C14	H17	109.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C15	C14	C13	H16	120.2°	120.0°
C15	C14	C13	H17	120.3°	120.0°
C15	C14	C13	C12	179.6°	180.0°
C15	C14	C13	H2	59.7°	60.0°
C15	C14	C13	H3	60.5°	60.0°
C14	C15	H4	H5	120.0°	120.0°
C14	C15	H4	H6	120.0°	120.1°
C14	C15	H5	H6	120.0°	120.0°
C15	C14	H16	H17	119.3°	120.0°
C14	C13	C12	H2	120.0°	120.0°
C14	C13	C12	H3	119.9°	120.0°
C14	C13	C12	C11	173.2°	180.0°
C14	C13	H2	H3	120.2°	119.9°
C13	C14	C15	H4	180.0°	180.0°
C13	C14	C15	H5	60.0°	60.0°
C13	C14	C15	H6	60.0°	60.0°
C14	C13	C12	H14	52.9°	60.0°
C14	C13	C12	H15	66.6°	60.0°
C13	C14	H16	H17	119.3°	120.0°
C13	C12	C11	H14	120.3°	120.0°
C13	C12	C11	H15	120.2°	120.1°
C13	C12	C11	C10	175.5°	180.0°
C12	C13	H2	H3	120.2°	120.0°
C13	C12	C11	H12	64.5°	60.0°
C13	C12	C11	H13	55.5°	60.1°
C13	C12	H14	H15	119.2°	120.0°
C12	C13	C14	H16	60.1°	60.0°
C12	C13	C14	H17	59.4°	60.0°
C12	C11	C10	O16	7.3°	0.0°
C12	C11	C10	H12	120.1°	120.0°
C12	C11	C10	H13	120.0°	120.0°
C12	C11	C10	N9	169.9°	180.0°
C11	C12	C13	H2	66.9°	60.0°
C11	C12	C13	H3	53.2°	60.0°
C12	C11	H12	H13	119.9°	120.1°
C11	C12	H14	H15	119.3°	120.0°
O16	C10	C11	N9	177.2°	179.9°
O16	C10	N9	C8	5.5°	5.3°
O16	C10	N9	H11	174.5°	174.8°
O16	C10	C11	H12	112.8°	120.0°
O16	C10	C11	H13	127.3°	120.0°
C11	C10	N9	C8	177.4°	174.8°
C11	C10	N9	H11	2.5°	5.2°
C10	C11	H12	H13	119.9°	119.9°
C10	C11	C12	H14	55.2°	60.0°
C10	C11	C12	H15	64.3°	60.0°
C10	N9	C8	H11	180.0°	179.9°
C10	N9	C8	C17	36.2°	6.2°
C10	N9	C8	C6	148.2°	173.6°
N9	C10	C11	H12	70.0°	60.0°
N9	C10	C11	H13	49.9°	60.1°
S1	C17	C8	N9	5.1°	0.0°
S1	C17	C8	C4	177.6°	180.0°
S1	C17	C8	C6	178.8°	179.9°
C17	S1	S2	C3	0.7°	0.3°
S1	C17	C4	C3	0.8°	0.0°
S1	C17	C4	N5	179.2°	179.7°
S2	S1	C17	C8	178.4°	179.7°
S2	S1	C17	C4	0.9°	0.2°
S1	S2	C3	C4	0.4°	0.4°
S1	S2	C3	H10	179.6°	179.6°
N9	C8	C17	C6	176.1°	179.8°
N9	C8	C17	C4	177.4°	180.0°
N9	C8	C6	O7	2.8°	0.0°
N9	C8	C6	N5	177.7°	179.8°
C17	C8	C6	O7	179.4°	179.9°
C17	C8	C6	N5	1.1°	0.0°
C8	C17	C4	C3	179.2°	180.0°
C8	C17	C4	N5	0.9°	0.3°
C17	C8	N9	H11	143.8°	173.8°
C6	C8	C17	C4	1.2°	0.2°
C8	C6	O7	N5	179.4°	179.9°
C8	C6	N5	C4	0.6°	0.2°
C8	C6	N5	C18	178.6°	179.9°
C6	C8	N9	H11	31.8°	6.4°
C17	C4	C3	S2	0.2°	0.3°
C17	C4	N5	C6	0.2°	0.3°
C17	C4	C3	N5	179.9°	179.6°
C17	C4	N5	C18	177.8°	179.8°
C17	C4	C3	H10	179.8°	179.6°
S2	C3	C4	H10	180.0°	180.0°
S2	C3	C4	N5	179.8°	180.0°
O7	C6	N5	C4	180.0°	179.9°
O7	C6	N5	C18	1.9°	0.0°
C6	N5	C4	C3	179.8°	180.0°
C6	N5	C4	C18	178.0°	180.0°
C6	N5	C18	H7	180.0°	90.0°
C6	N5	C18	H8	60.0°	30.0°
C6	N5	C18	H9	60.0°	150.0°
C3	C4	N5	C18	2.1°	0.1°
C4	N5	C18	H7	2.2°	90.1°
C4	N5	C18	H8	117.7°	149.9°
C4	N5	C18	H9	122.3°	29.9°
N5	C4	C3	H10	0.1°	0.0°
N5	C18	H7	H8	120.0°	120.0°
N5	C18	H7	H9	120.0°	120.0°
N5	C18	H8	H9	120.0°	120.0°
H2	C13	C12	H14	172.8°	60.0°
H2	C13	C12	H15	53.4°	180.0°
H2	C13	C14	H16	179.9°	180.0°
H2	C13	C14	H17	60.6°	60.0°
H3	C13	C12	H14	67.0°	180.0°
H3	C13	C12	H15	173.5°	60.0°
H3	C13	C14	H16	59.8°	60.0°
H3	C13	C14	H17	179.3°	180.0°
H4	C15	H5	H6	120.0°	120.0°
H4	C15	C14	H16	59.8°	60.0°
H4	C15	C14	H17	59.7°	60.0°
H5	C15	C14	H16	60.2°	180.0°
H5	C15	C14	H17	179.7°	60.0°
H6	C15	C14	H16	179.8°	60.0°
H6	C15	C14	H17	60.3°	180.0°
H7	C18	H8	H9	120.0°	120.0°
H12	C11	C12	H14	175.3°	60.0°
H12	C11	C12	H15	55.7°	179.9°
H13	C11	C12	H14	64.8°	180.0°
H13	C11	C12	H15	175.7°	60.0°

Release date:	2024-10-16
Definition date:	2023-12-12
Last modified:	2024-10-11
Release status:	REL
Processing site:	PDBE
Derived from:	8RDO