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Summary Geometry Related PDB entries

2YL

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C9	C10	doub	1.38Å	1.39Å	Aromatic
C9	C14	sing	1.38Å	1.39Å	Aromatic
C10	C11	sing	1.38Å	1.39Å	Aromatic
C14	C13	doub	1.38Å	1.39Å	Aromatic
C11	C12	doub	1.39Å	1.39Å	Aromatic
C13	C12	sing	1.39Å	1.38Å	Aromatic
C12	C4	sing	1.48Å	1.48Å
C4	N3	doub	1.33Å	1.35Å
C4	N5	sing	1.34Å	1.35Å
N3	C2	sing	1.34Å	1.35Å
N5	C6	doub	1.32Å	1.35Å
C2	O8	doub	1.22Å	1.24Å
C2	N1	sing	1.35Å	1.35Å
C6	N1	sing	1.37Å	1.35Å
C6	N7	sing	1.37Å	1.36Å
N7	H2	sing	0.97Å	1.00Å
N7	H3	sing	0.97Å	1.00Å
C9	H4	sing	1.08Å	1.08Å
C10	H5	sing	1.08Å	1.08Å
C11	H6	sing	1.08Å	1.08Å
C13	H7	sing	1.08Å	1.08Å
C14	H8	sing	1.08Å	1.08Å
N1	H9	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C10	C9	C14	119.8°	120.3°
C9	C10	C11	119.9°	120.1°
C10	C9	H4	120.1°	119.9°
C9	C10	H5	120.0°	120.0°
C9	C14	C13	120.5°	120.1°
C14	C9	H4	120.1°	119.9°
C9	C14	H8	119.7°	119.9°
C10	C11	C12	119.9°	119.9°
C11	C10	H5	120.1°	119.9°
C10	C11	H6	120.0°	120.0°
C14	C13	C12	119.6°	119.9°
C14	C13	H7	120.2°	120.0°
C13	C14	H8	119.7°	119.9°
C11	C12	C13	120.2°	119.7°
C11	C12	C4	120.5°	120.1°
C12	C11	H6	120.0°	120.1°
C13	C12	C4	119.3°	120.1°
C12	C13	H7	120.2°	120.1°
C12	C4	N3	120.5°	119.7°
C12	C4	N5	119.2°	119.7°
N3	C4	N5	120.3°	120.7°
C4	N3	C2	119.3°	120.3°
C4	N5	C6	120.1°	120.3°
N3	C2	O8	119.7°	120.1°
N3	C2	N1	120.6°	119.7°
N5	C6	N1	119.8°	119.7°
N5	C6	N7	120.2°	120.2°
O8	C2	N1	119.7°	120.2°
C2	N1	C6	119.9°	119.4°
C2	N1	H9	120.1°	120.3°
N1	C6	N7	120.0°	120.1°
C6	N1	H9	120.0°	120.3°
C6	N7	H2	120.0°	119.9°
C6	N7	H3	120.0°	120.0°
H2	N7	H3	120.0°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C10	C9	C14	H4	180.0°	179.7°
C9	C10	C11	H5	180.0°	179.9°
C10	C9	C14	C13	0.1°	0.0°
C9	C10	C11	C12	0.1°	0.1°
C9	C10	C11	H6	179.9°	179.9°
C10	C9	C14	H8	179.9°	179.9°
C14	C9	C10	C11	0.1°	0.0°
C9	C14	C13	H8	180.0°	179.9°
C9	C14	C13	C12	0.4°	0.0°
C14	C9	C10	H5	179.9°	180.0°
C9	C14	C13	H7	179.6°	180.0°
C10	C11	C12	H6	180.0°	180.0°
C10	C11	C12	C13	0.4°	0.1°
C10	C11	C12	C4	179.5°	180.0°
C11	C10	C9	H4	179.9°	179.8°
C14	C13	C12	C11	0.6°	0.0°
C14	C13	C12	H7	180.0°	180.0°
C14	C13	C12	C4	179.7°	180.0°
C13	C14	C9	H4	179.9°	179.7°
C11	C12	C13	C4	179.1°	179.9°
C11	C12	C4	N3	36.2°	0.0°
C11	C12	C4	N5	143.0°	180.0°
C12	C11	C10	H5	179.9°	180.0°
C11	C12	C13	H7	179.4°	180.0°
C13	C12	C4	N3	144.8°	180.0°
C13	C12	C4	N5	36.0°	0.0°
C13	C12	C11	H6	179.5°	179.9°
C12	C13	C14	H8	179.6°	179.9°
C12	C4	N3	N5	179.2°	180.0°
C12	C4	N3	C2	179.9°	180.0°
C12	C4	N5	C6	179.4°	179.7°
C4	C12	C11	H6	0.5°	0.0°
C4	C12	C13	H7	0.3°	0.1°
N3	C4	N5	C6	0.2°	0.3°
C4	N3	C2	O8	179.6°	179.9°
C4	N3	C2	N1	0.7°	0.0°
N5	C4	N3	C2	0.7°	0.0°
C4	N5	C6	N1	0.2°	0.5°
C4	N5	C6	N7	179.9°	180.0°
N3	C2	O8	N1	179.6°	179.9°
N3	C2	N1	C6	0.3°	0.3°
N3	C2	N1	H9	179.7°	179.9°
N5	C6	N1	C2	0.1°	0.6°
N5	C6	N1	N7	179.6°	179.5°
N5	C6	N7	H2	0.0°	0.0°
N5	C6	N7	H3	180.0°	180.0°
N5	C6	N1	H9	179.9°	179.8°
O8	C2	N1	C6	180.0°	179.8°
O8	C2	N1	H9	0.0°	0.2°
C2	N1	C6	H9	180.0°	179.6°
C2	N1	C6	N7	179.8°	180.0°
N1	C6	N7	H2	179.6°	179.4°
N1	C6	N7	H3	0.3°	0.6°
C6	N7	H2	H3	180.0°	180.0°
N7	C6	N1	H9	0.2°	0.4°
H4	C9	C10	H5	0.1°	0.3°
H4	C9	C14	H8	0.1°	0.2°
H5	C10	C11	H6	0.1°	0.0°
H7	C13	C14	H8	0.5°	0.0°

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PDB entries from 2026-02-04

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