VY6

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O	C1	sing	1.34Å	1.36Å	Aromatic
O	C2	sing	1.34Å	1.35Å	Aromatic
C8	C9	sing	1.53Å	1.54Å
C8	O3	sing	1.43Å	1.39Å
C5	C2	sing	1.51Å	1.46Å
C5	N	sing	1.47Å	1.53Å
C1	C	doub	1.34Å	1.36Å	Aromatic
C2	C3	doub	1.37Å	1.38Å	Aromatic
C9	N	sing	1.47Å	1.52Å
O3	C7	sing	1.43Å	1.39Å
N	C6	sing	1.47Å	1.51Å
C	C3	sing	1.47Å	1.42Å	Aromatic
C7	C6	sing	1.53Å	1.54Å
C3	C4	sing	1.47Å	1.49Å
C4	O2	doub	1.22Å	1.22Å
C4	O1	sing	1.35Å	1.27Å
C7	H1	sing	1.09Å	1.10Å
C7	H2	sing	1.09Å	1.10Å
C8	H3	sing	1.09Å	1.10Å
C8	H4	sing	1.09Å	1.10Å
C9	H5	sing	1.09Å	1.10Å
C9	H6	sing	1.09Å	1.10Å
O1	H7	sing	0.97Å	0.95Å
C1	H8	sing	1.08Å	1.08Å
C5	H9	sing	1.09Å	1.10Å
C5	H10	sing	1.09Å	1.10Å
C6	H11	sing	1.09Å	1.10Å
C6	H12	sing	1.09Å	1.10Å
C	H13	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	O	C2	105.8°	110.9°
O	C1	C	111.3°	109.1°
O	C1	H8	124.4°	125.5°
O	C2	C5	116.0°	125.8°
O	C2	C3	111.1°	108.4°
C9	C8	O3	110.1°	109.3°
C8	C9	N	107.6°	109.2°
C9	C8	H3	109.3°	109.5°
C9	C8	H4	109.3°	109.5°
C8	C9	H5	109.9°	109.5°
C8	C9	H6	109.9°	109.5°
C8	O3	C7	112.9°	113.7°
O3	C8	H3	109.3°	109.5°
O3	C8	H4	109.3°	109.5°
C2	C5	N	106.2°	109.5°
C5	C2	C3	132.8°	125.8°
C2	C5	H9	110.3°	109.5°
C2	C5	H10	110.3°	109.5°
C5	N	C9	110.6°	111.0°
C5	N	C6	109.3°	111.0°
N	C5	H9	110.3°	109.5°
N	C5	H10	110.3°	109.4°
C1	C	C3	106.1°	106.0°
C	C1	H8	124.4°	125.4°
C1	C	H13	127.0°	127.0°
C2	C3	C	105.7°	105.6°
C2	C3	C4	131.0°	127.2°
C9	N	C6	107.8°	110.7°
N	C9	H5	109.9°	109.4°
N	C9	H6	109.9°	109.5°
O3	C7	C6	108.9°	109.3°
O3	C7	H1	109.6°	109.5°
O3	C7	H2	109.6°	109.5°
N	C6	C7	106.7°	109.3°
N	C6	H11	110.2°	109.5°
N	C6	H12	110.2°	109.5°
C	C3	C4	123.2°	127.2°
C3	C	H13	126.9°	127.0°
C6	C7	H1	109.6°	109.5°
C6	C7	H2	109.6°	109.5°
C7	C6	H11	110.2°	109.6°
C7	C6	H12	110.2°	109.5°
C3	C4	O2	120.9°	120.0°
C3	C4	O1	116.8°	120.0°
O2	C4	O1	122.3°	120.0°
C4	O1	H7	109.5°	117.0°
H1	C7	H2	109.5°	109.5°
H3	C8	H4	109.5°	109.5°
H5	C9	H6	109.5°	109.6°
H9	C5	H10	109.5°	109.5°
H11	C6	H12	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	O	C2	C5	177.9°	179.7°
O	C1	C	H8	180.0°	179.8°
C1	O	C2	C3	0.7°	0.3°
O	C1	C	C3	0.1°	0.2°
O	C1	C	H13	179.9°	179.7°
O	C2	C5	C3	178.2°	179.9°
O	C2	C5	N	167.8°	90.0°
C2	O	C1	C	0.5°	0.0°
O	C2	C3	C	0.6°	0.4°
O	C2	C3	C4	179.3°	180.0°
C2	O	C1	H8	179.5°	179.8°
O	C2	C5	H9	72.7°	30.0°
O	C2	C5	H10	48.3°	150.0°
C9	C8	O3	H3	120.1°	120.0°
C9	C8	O3	H4	120.1°	119.9°
C8	C9	N	C5	60.4°	177.6°
C8	C9	N	H5	119.7°	119.9°
C8	C9	N	H6	119.7°	120.0°
C9	C8	O3	C7	62.1°	58.6°
C8	C9	N	C6	59.1°	58.6°
C9	C8	H3	H4	119.7°	120.1°
C8	C9	H5	H6	120.8°	120.2°
O3	C8	C9	N	58.3°	56.8°
C8	O3	C7	C6	64.0°	58.6°
C8	O3	C7	H1	176.1°	178.6°
C8	O3	C7	H2	55.9°	61.3°
O3	C8	H3	H4	119.7°	120.1°
O3	C8	C9	H5	178.0°	63.0°
O3	C8	C9	H6	61.4°	176.8°
C2	C5	N	H9	119.5°	120.0°
C2	C5	N	H10	119.5°	120.0°
C2	C5	N	C9	150.2°	170.0°
C2	C5	N	C6	91.2°	66.4°
C5	C2	C3	C	177.7°	179.5°
C5	C2	C3	C4	2.5°	0.1°
C2	C5	H9	H10	121.5°	120.0°
N	C5	C2	C3	10.4°	89.9°
C5	N	C9	C6	119.5°	123.8°
C5	N	C6	C7	59.3°	177.6°
C5	N	C9	H5	59.3°	62.5°
C5	N	C9	H6	179.9°	57.6°
N	C5	H9	H10	121.5°	120.0°
C5	N	C6	H11	60.3°	57.6°
C5	N	C6	H12	178.9°	62.4°
C1	C	C3	C2	0.3°	0.4°
C1	C	C3	H13	180.0°	180.0°
C1	C	C3	C4	179.6°	180.0°
C2	C3	C	C4	179.9°	179.6°
C2	C3	C4	O2	0.4°	0.1°
C2	C3	C4	O1	179.9°	180.0°
C3	C2	C5	H9	109.1°	150.0°
C3	C2	C5	H10	129.9°	30.0°
C2	C3	C	H13	179.7°	179.6°
C9	N	C6	C7	61.0°	58.6°
N	C9	C8	H3	178.3°	63.1°
N	C9	C8	H4	61.8°	176.8°
N	C9	H5	H6	120.9°	120.1°
C9	N	C5	H9	30.7°	50.0°
C9	N	C5	H10	90.3°	70.0°
C9	N	C6	H11	179.4°	178.6°
C9	N	C6	H12	58.5°	61.4°
O3	C7	C6	N	62.3°	56.8°
O3	C7	C6	H1	119.9°	120.0°
O3	C7	C6	H2	119.9°	120.0°
O3	C7	H1	H2	120.3°	120.1°
C7	O3	C8	H3	177.9°	61.3°
C7	O3	C8	H4	58.0°	178.6°
O3	C7	C6	H11	178.1°	176.8°
O3	C7	C6	H12	57.3°	63.1°
N	C6	C7	H11	119.6°	119.9°
N	C6	C7	H12	119.6°	120.0°
N	C6	C7	H1	177.8°	176.8°
N	C6	C7	H2	57.6°	63.1°
C6	N	C9	H5	178.9°	61.3°
C6	N	C9	H6	60.6°	178.6°
C6	N	C5	H9	149.3°	173.6°
C6	N	C5	H10	28.3°	53.6°
N	C6	H11	H12	121.3°	120.1°
C	C3	C4	O2	179.5°	179.5°
C	C3	C4	O1	0.1°	0.5°
C3	C	C1	H8	179.9°	180.0°
C6	C7	H1	H2	120.3°	120.0°
C7	C6	H11	H12	121.3°	120.1°
C3	C4	O2	O1	179.5°	180.0°
C3	C4	O1	H7	179.6°	180.0°
C4	C3	C	H13	0.4°	0.0°
O2	C4	O1	H7	0.0°	0.0°
H1	C7	C6	H11	58.2°	63.3°
H1	C7	C6	H12	62.6°	56.9°
H2	C7	C6	H11	61.9°	56.8°
H2	C7	C6	H12	177.2°	176.9°
H3	C8	C9	H5	62.0°	177.0°
H3	C8	C9	H6	58.6°	56.8°
H4	C8	C9	H5	57.9°	56.9°
H4	C8	C9	H6	178.5°	63.3°
H8	C1	C	H13	0.1°	0.0°

Release date:	2022-11-02
Definition date:	2022-09-02
Last modified:	2022-10-28
Release status:	REL
Processing site:	RCSB
Derived from:	7FNS