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Summary Geometry Related PDB entries

DZY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O10	C8	doub	1.21Å	1.24Å
C8	O11	sing	1.34Å	1.25Å
C8	C4	sing	1.51Å	1.50Å
N2	C5	doub	1.29Å	1.36Å	Aromatic
N2	C1	sing	1.32Å	1.37Å	Aromatic
C9	C5	sing	1.51Å	1.50Å
C4	C1	sing	1.51Å	1.50Å
C5	S6	sing	1.71Å	1.73Å	Aromatic
C1	C3	doub	1.34Å	1.49Å	Aromatic
C3	S6	sing	1.76Å	1.75Å	Aromatic
C3	C7	sing	1.51Å	1.50Å
O11	H1	sing	0.97Å	0.95Å
C4	H2	sing	1.09Å	1.10Å
C4	H3	sing	1.09Å	1.10Å
C7	H4	sing	1.09Å	1.10Å
C7	H5	sing	1.09Å	1.10Å
C7	H6	sing	1.09Å	1.10Å
C9	H7	sing	1.09Å	1.10Å
C9	H8	sing	1.09Å	1.10Å
C9	H9	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O10	C8	O11	124.0°	120.0°
O10	C8	C4	116.3°	120.0°
O11	C8	C4	119.7°	120.1°
C8	O11	H1	109.5°	117.1°
C8	C4	C1	110.2°	109.5°
C8	C4	H2	109.3°	109.5°
C8	C4	H3	109.3°	109.5°
C5	N2	C1	115.6°	117.1°
N2	C5	C9	133.2°	125.0°
N2	C5	S6	112.1°	110.2°
N2	C1	C4	125.3°	122.8°
N2	C1	C3	111.5°	114.5°
C9	C5	S6	114.7°	124.9°
C5	C9	H7	109.5°	109.5°
C5	C9	H8	109.5°	109.4°
C5	C9	H9	109.4°	109.4°
C4	C1	C3	123.2°	122.7°
C1	C4	H2	109.3°	109.5°
C1	C4	H3	109.3°	109.4°
C5	S6	C3	92.3°	90.3°
C1	C3	S6	108.5°	107.9°
C1	C3	C7	132.2°	126.1°
S6	C3	C7	119.2°	126.1°
C3	C7	H4	109.5°	109.5°
C3	C7	H5	109.5°	109.5°
C3	C7	H6	109.5°	109.5°
H2	C4	H3	109.5°	109.4°
H4	C7	H5	109.5°	109.5°
H4	C7	H6	109.5°	109.5°
H5	C7	H6	109.4°	109.5°
H7	C9	H8	109.5°	109.5°
H7	C9	H9	109.5°	109.5°
H8	C9	H9	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O10	C8	O11	C4	179.4°	180.0°
O10	C8	C4	C1	146.4°	0.0°
O10	C8	O11	H1	0.0°	0.0°
O10	C8	C4	H2	26.3°	120.1°
O10	C8	C4	H3	93.5°	120.0°
O11	C8	C4	C1	33.0°	180.0°
O11	C8	C4	H2	153.1°	60.0°
O11	C8	C4	H3	87.1°	60.0°
C8	C4	C1	N2	85.7°	90.3°
C8	C4	C1	H2	120.1°	120.0°
C8	C4	C1	H3	120.1°	120.0°
C8	C4	C1	C3	95.3°	90.0°
C4	C8	O11	H1	179.4°	180.0°
C8	C4	H2	H3	119.7°	120.0°
N2	C5	C9	S6	179.2°	179.7°
C5	N2	C1	C4	179.5°	179.7°
C5	N2	C1	C3	0.4°	0.5°
N2	C5	S6	C3	0.7°	0.3°
N2	C5	C9	H7	0.0°	179.7°
N2	C5	C9	H8	120.0°	59.6°
N2	C5	C9	H9	120.0°	60.3°
C1	N2	C5	C9	180.0°	179.7°
N2	C1	C4	C3	179.0°	179.7°
C1	N2	C5	S6	0.8°	0.5°
N2	C1	C3	S6	0.1°	0.3°
N2	C1	C3	C7	179.6°	179.7°
N2	C1	C4	H2	34.4°	149.7°
N2	C1	C4	H3	154.2°	29.7°
C9	C5	S6	C3	180.0°	180.0°
C5	C9	H7	H8	120.0°	120.0°
C5	C9	H7	H9	120.0°	120.0°
C5	C9	H8	H9	120.0°	119.9°
C4	C1	C3	S6	179.0°	180.0°
C4	C1	C3	C7	0.5°	0.0°
C1	C4	H2	H3	119.7°	120.0°
C5	S6	C3	C1	0.4°	0.0°
C5	S6	C3	C7	180.0°	180.0°
S6	C5	C9	H7	179.2°	0.1°
S6	C5	C9	H8	59.2°	120.1°
S6	C5	C9	H9	60.8°	120.0°
C1	C3	S6	C7	179.6°	180.0°
C3	C1	C4	H2	144.6°	30.1°
C3	C1	C4	H3	24.8°	150.0°
C1	C3	C7	H4	179.5°	90.0°
C1	C3	C7	H5	59.5°	150.0°
C1	C3	C7	H6	60.5°	30.0°
S6	C3	C7	H4	0.0°	90.0°
S6	C3	C7	H5	120.0°	30.0°
S6	C3	C7	H6	120.0°	150.0°
C3	C7	H4	H5	120.0°	120.0°
C3	C7	H4	H6	120.0°	120.0°
C3	C7	H5	H6	120.0°	120.0°
H4	C7	H5	H6	120.0°	120.0°
H7	C9	H8	H9	120.0°	120.0°

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PDB entries from 2026-02-04

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