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Summary Geometry Related PDB entries

XR9

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	B2	sing	0.00Å	1.48Å
B2	O3	sing	0.00Å	1.50Å
O3	C4	sing	0.00Å	1.42Å
C4	C5	sing	0.00Å	1.48Å
C5	N6	trip	0.00Å	1.14Å
C4	C7	sing	0.00Å	1.51Å
C7	C8	doub	0.00Å	1.39Å	Aromatic
C8	C9	sing	0.00Å	1.39Å	Aromatic
C9	C10	doub	0.00Å	1.39Å	Aromatic
C10	C11	sing	0.00Å	1.38Å	Aromatic
C11	C12	doub	0.00Å	1.40Å	Aromatic
C12	B2	sing	0.00Å	1.56Å
C12	C7	sing	0.00Å	1.39Å	Aromatic
C11	H11	sing	0.00Å	1.08Å
C9	H9	sing	0.00Å	1.08Å
C4	H4	sing	0.00Å	1.10Å
C10	H10	sing	0.00Å	1.08Å
C8	H8	sing	0.00Å	1.08Å
O1	H1	sing	0.00Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	B2	O3	111.2°	90.0°
O1	B2	C12	111.9°	90.0°
B2	O1	H1	109.5°	90.0°
B2	O3	C4	112.2°	90.0°
O3	B2	C12	103.5°	90.0°
O3	C4	C5	110.0°	90.0°
O3	C4	C7	105.0°	90.0°
O3	C4	H4	111.5°	90.0°
C4	C5	N6	178.0°	90.0°
C5	C4	C7	109.4°	90.0°
C5	C4	H4	110.6°	90.0°
C4	C7	C8	126.6°	90.0°
C4	C7	C12	111.8°	90.0°
C7	C4	H4	110.1°	90.0°
C7	C8	C9	119.5°	90.0°
C8	C7	C12	121.6°	90.0°
C7	C8	H8	120.3°	90.0°
C8	C9	C10	120.1°	90.0°
C8	C9	H9	120.0°	90.0°
C9	C8	H8	120.3°	90.0°
C9	C10	C11	120.0°	90.0°
C10	C9	H9	120.0°	90.0°
C9	C10	H10	120.0°	90.0°
C10	C11	C12	121.2°	90.0°
C10	C11	H11	119.4°	90.0°
C11	C10	H10	120.0°	90.0°
C11	C12	B2	135.0°	90.0°
C11	C12	C7	117.7°	90.0°
C12	C11	H11	119.4°	90.0°
B2	C12	C7	107.3°	90.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	B2	O3	C12	120.4°	90.0°
O1	B2	O3	C4	120.4°	90.0°
O1	B2	C12	C11	58.8°	90.0°
O1	B2	C12	C7	120.0°	90.0°
B2	O3	C4	C5	117.5°	90.0°
B2	O3	C4	C7	0.1°	90.0°
O3	B2	C12	C11	178.7°	90.0°
O3	B2	C12	C7	0.1°	90.0°
B2	O3	C4	H4	119.4°	90.0°
O3	B2	O1	H1	0.0°	90.0°
O3	C4	C5	C7	114.9°	90.0°
O3	C4	C5	H4	123.6°	90.0°
O3	C4	C5	N6	168.8°	90.0°
O3	C4	C7	H4	120.2°	90.0°
O3	C4	C7	C8	179.0°	90.0°
C4	O3	B2	C12	0.0°	90.0°
O3	C4	C7	C12	0.2°	90.0°
C5	C4	C7	H4	121.7°	90.0°
C5	C4	C7	C8	61.0°	90.0°
C5	C4	C7	C12	117.9°	90.0°
N6	C5	C4	C7	76.3°	90.0°
N6	C5	C4	H4	45.2°	90.0°
C4	C7	C8	C12	178.7°	90.0°
C4	C7	C8	C9	178.7°	90.0°
C4	C7	C12	C11	178.8°	90.0°
C4	C7	C12	B2	0.2°	90.0°
C4	C7	C8	H8	1.3°	90.0°
C7	C8	C9	H8	180.0°	90.0°
C7	C8	C9	C10	0.1°	90.0°
C8	C7	C12	C11	0.0°	90.0°
C8	C7	C12	B2	179.1°	90.0°
C7	C8	C9	H9	179.9°	90.0°
C8	C7	C4	H4	60.8°	90.0°
C8	C9	C10	H9	180.0°	90.0°
C8	C9	C10	C11	0.1°	90.0°
C9	C8	C7	C12	0.0°	90.0°
C8	C9	C10	H10	179.9°	90.0°
C9	C10	C11	H10	180.0°	90.0°
C9	C10	C11	C12	0.1°	90.0°
C9	C10	C11	H11	179.8°	90.0°
C10	C9	C8	H8	180.0°	90.0°
C10	C11	C12	H11	180.0°	90.0°
C10	C11	C12	B2	178.7°	90.0°
C10	C11	C12	C7	0.0°	90.0°
C11	C10	C9	H9	179.8°	90.0°
C11	C12	B2	C7	178.8°	90.0°
C12	C11	C10	H10	179.9°	90.0°
B2	C12	C11	H11	1.4°	90.0°
C12	B2	O1	H1	115.3°	90.0°
C7	C12	C11	H11	179.9°	90.0°
C12	C7	C4	H4	120.4°	90.0°
C12	C7	C8	H8	179.9°	90.0°
H11	C11	C10	H10	0.2°	90.0°
H9	C9	C10	H10	0.2°	90.0°
H9	C9	C8	H8	0.1°	90.0°

250835

PDB entries from 2026-03-18

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