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Summary Geometry Related PDB entries

VJ0

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C8	O	sing	1.43Å	1.37Å
C4	C3	doub	1.38Å	1.36Å	Aromatic
C4	C5	sing	1.39Å	1.49Å	Aromatic
O	C5	sing	1.36Å	1.30Å
C3	C2	sing	1.38Å	1.31Å	Aromatic
C5	C6	doub	1.39Å	1.35Å	Aromatic
C	C1	sing	1.53Å	1.51Å
C2	C7	doub	1.38Å	1.43Å	Aromatic
C2	C1	sing	1.51Å	1.46Å
C6	C7	sing	1.38Å	1.36Å	Aromatic
C6	F	sing	1.35Å	1.21Å
C1	N	sing	1.47Å	1.55Å
C7	H1	sing	1.08Å	1.08Å
C8	H2	sing	1.09Å	1.10Å
C8	H3	sing	1.09Å	1.10Å
C8	H4	sing	1.09Å	1.10Å
C1	H5	sing	1.09Å	1.10Å
C4	H6	sing	1.08Å	1.08Å
C3	H7	sing	1.08Å	1.08Å
C	H8	sing	1.09Å	1.10Å
C	H9	sing	1.09Å	1.10Å
C	H10	sing	1.09Å	1.10Å
N	H11	sing	1.01Å	1.00Å
N	H12	sing	1.01Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C8	O	C5	119.0°	117.0°
O	C8	H2	109.5°	109.4°
O	C8	H3	109.5°	109.5°
O	C8	H4	109.4°	109.5°
C3	C4	C5	121.7°	120.0°
C4	C3	C2	119.3°	120.1°
C3	C4	H6	119.2°	120.0°
C4	C3	H7	120.3°	120.0°
C4	C5	O	116.1°	120.1°
C4	C5	C6	116.8°	119.9°
C5	C4	H6	119.2°	120.0°
O	C5	C6	126.8°	120.0°
C3	C2	C7	120.3°	120.1°
C3	C2	C1	129.9°	119.9°
C2	C3	H7	120.4°	120.0°
C5	C6	C7	119.9°	119.9°
C5	C6	F	120.7°	120.0°
C	C1	C2	113.8°	109.4°
C	C1	N	111.4°	109.5°
C	C1	H5	105.4°	109.5°
C1	C	H8	109.5°	109.5°
C1	C	H9	109.5°	109.5°
C1	C	H10	109.5°	109.5°
C7	C2	C1	109.4°	119.9°
C2	C7	C6	122.0°	120.0°
C2	C7	H1	119.0°	120.0°
C2	C1	N	114.3°	109.5°
C2	C1	H5	105.9°	109.4°
C7	C6	F	119.4°	120.1°
C6	C7	H1	119.0°	120.0°
N	C1	H5	105.0°	109.5°
C1	N	H11	109.5°	111.0°
C1	N	H12	109.5°	111.0°
H2	C8	H3	109.4°	109.5°
H2	C8	H4	109.5°	109.5°
H3	C8	H4	109.5°	109.5°
H8	C	H9	109.5°	109.4°
H8	C	H10	109.5°	109.5°
H9	C	H10	109.5°	109.5°
H11	N	H12	109.5°	111.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C8	O	C5	C4	1.9°	0.0°
C8	O	C5	C6	170.9°	179.9°
O	C8	H2	H3	120.0°	120.0°
O	C8	H2	H4	120.0°	120.0°
O	C8	H3	H4	120.0°	120.0°
C3	C4	C5	H6	180.0°	179.7°
C3	C4	C5	O	171.8°	179.7°
C4	C3	C2	H7	180.0°	179.7°
C3	C4	C5	C6	1.8°	0.3°
C4	C3	C2	C7	1.1°	0.0°
C4	C3	C2	C1	172.1°	180.0°
C4	C5	O	C6	172.8°	179.9°
C5	C4	C3	C2	0.4°	0.3°
C4	C5	C6	C7	1.5°	0.1°
C4	C5	C6	F	178.9°	180.0°
C5	C4	C3	H7	179.6°	180.0°
O	C5	C6	C7	171.3°	180.0°
O	C5	C6	F	8.3°	0.0°
C5	O	C8	H2	180.0°	60.0°
C5	O	C8	H3	60.0°	60.0°
C5	O	C8	H4	60.0°	180.0°
O	C5	C4	H6	8.2°	0.1°
C3	C2	C1	C	86.5°	100.0°
C3	C2	C7	C1	174.5°	180.0°
C3	C2	C7	C6	1.4°	0.2°
C3	C2	C1	N	43.2°	140.0°
C3	C2	C7	H1	178.5°	180.0°
C3	C2	C1	H5	158.2°	20.0°
C2	C3	C4	H6	179.6°	180.0°
C5	C6	C7	C2	0.0°	0.2°
C5	C6	C7	F	179.6°	180.0°
C5	C6	C7	H1	180.0°	180.0°
C6	C5	C4	H6	178.2°	180.0°
C	C1	C2	C7	99.7°	80.0°
C	C1	C2	N	129.6°	120.0°
C	C1	C2	H5	115.3°	120.0°
C	C1	N	H5	113.6°	120.0°
C1	C	H8	H9	120.0°	120.0°
C1	C	H8	H10	120.0°	120.0°
C1	C	H9	H10	120.0°	120.1°
C	C1	N	H11	180.0°	63.9°
C	C1	N	H12	60.0°	60.1°
C2	C7	C6	H1	180.0°	179.7°
C2	C7	C6	F	179.6°	179.7°
C7	C2	C1	N	130.7°	40.0°
C7	C2	C1	H5	15.6°	160.0°
C7	C2	C3	H7	178.8°	179.7°
C1	C2	C7	C6	173.1°	179.7°
C2	C1	N	H5	115.6°	120.0°
C1	C2	C7	H1	6.9°	0.0°
C1	C2	C3	H7	7.9°	0.3°
C2	C1	C	H8	180.0°	60.0°
C2	C1	C	H9	60.0°	180.0°
C2	C1	C	H10	60.0°	60.0°
C2	C1	N	H11	49.2°	56.0°
C2	C1	N	H12	70.8°	180.0°
F	C6	C7	H1	0.4°	0.0°
N	C1	C	H8	48.9°	180.0°
N	C1	C	H9	71.1°	60.1°
N	C1	C	H10	168.9°	60.0°
C1	N	H11	H12	120.0°	124.0°
H2	C8	H3	H4	120.0°	120.0°
H5	C1	C	H8	64.4°	59.9°
H5	C1	C	H9	175.6°	60.0°
H5	C1	C	H10	55.6°	179.9°
H5	C1	N	H11	66.4°	176.0°
H5	C1	N	H12	173.6°	60.0°
H6	C4	C3	H7	0.4°	0.3°
H8	C	H9	H10	120.0°	120.0°

248335

PDB entries from 2026-01-28

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