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Summary Geometry Related PDB entries

RD4

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N1	C	doub	1.30Å	1.31Å
C3	C2	doub	1.38Å	1.39Å	Aromatic
C3	C4	sing	1.38Å	1.38Å	Aromatic
C2	C1	sing	1.39Å	1.39Å	Aromatic
C4	C5	doub	1.39Å	1.38Å	Aromatic
C1	C	sing	1.48Å	1.49Å
C1	C6	doub	1.39Å	1.40Å	Aromatic
C	N	sing	1.38Å	1.31Å
C5	C6	sing	1.39Å	1.39Å	Aromatic
C5	O	sing	1.36Å	1.37Å
O	C7	sing	1.43Å	1.43Å
C7	C8	sing	1.53Å	1.46Å
C4	H1	sing	1.08Å	1.08Å
C6	H2	sing	1.08Å	1.08Å
N1	H3	sing	0.97Å	1.00Å
C7	H4	sing	1.09Å	1.10Å
C7	H5	sing	1.09Å	1.10Å
C8	H6	sing	1.09Å	1.10Å
C8	H7	sing	1.09Å	1.10Å
C8	H8	sing	1.09Å	1.10Å
N	H9	sing	0.97Å	1.00Å
N	H10	sing	0.97Å	1.00Å
C3	H11	sing	1.08Å	1.08Å
C2	H12	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N1	C	C1	120.6°	120.0°
N1	C	N	120.3°	120.0°
C	N1	H3	112.0°	120.0°
C2	C3	C4	120.7°	120.2°
C3	C2	C1	120.4°	120.0°
C2	C3	H11	119.7°	120.0°
C3	C2	H12	119.8°	120.0°
C3	C4	C5	119.0°	120.2°
C3	C4	H1	120.5°	119.9°
C4	C3	H11	119.7°	119.9°
C2	C1	C	120.7°	120.1°
C2	C1	C6	119.1°	119.8°
C1	C2	H12	119.8°	120.0°
C4	C5	C6	121.3°	120.0°
C4	C5	O	111.2°	120.0°
C5	C4	H1	120.5°	119.8°
C	C1	C6	120.1°	120.1°
C1	C	N	119.2°	120.0°
C1	C6	C5	119.5°	119.8°
C1	C6	H2	120.2°	120.2°
C	N	H9	120.0°	120.0°
C	N	H10	120.0°	119.9°
C6	C5	O	127.5°	120.0°
C5	C6	H2	120.2°	120.0°
C5	O	C7	118.0°	117.0°
O	C7	C8	107.2°	109.4°
O	C7	H4	110.0°	109.4°
O	C7	H5	110.0°	109.5°
C8	C7	H4	110.0°	109.5°
C8	C7	H5	110.0°	109.5°
C7	C8	H6	109.5°	109.4°
C7	C8	H7	109.5°	109.4°
C7	C8	H8	109.5°	109.5°
H4	C7	H5	109.5°	109.5°
H6	C8	H7	109.5°	109.5°
H6	C8	H8	109.4°	109.6°
H7	C8	H8	109.5°	109.5°
H9	N	H10	120.0°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N1	C	C1	C2	35.3°	180.0°
N1	C	C1	N	179.7°	180.0°
N1	C	C1	C6	148.5°	0.0°
N1	C	N	H9	179.7°	0.1°
N1	C	N	H10	0.3°	180.0°
C2	C3	C4	H11	180.0°	179.4°
C3	C2	C1	H12	180.0°	179.4°
C2	C3	C4	C5	1.8°	0.7°
C3	C2	C1	C	178.3°	179.7°
C3	C2	C1	C6	2.1°	0.3°
C2	C3	C4	H1	178.2°	179.7°
C4	C3	C2	C1	0.9°	0.6°
C3	C4	C5	H1	180.0°	179.6°
C3	C4	C5	C6	3.3°	0.4°
C3	C4	C5	O	174.6°	179.7°
C4	C3	C2	H12	179.1°	180.0°
C2	C1	C	C6	176.2°	180.0°
C2	C1	C	N	144.4°	0.0°
C2	C1	C6	C5	0.6°	0.0°
C2	C1	C6	H2	179.4°	180.0°
C1	C2	C3	H11	179.1°	180.0°
C4	C5	C6	C1	2.2°	0.0°
C4	C5	C6	O	177.6°	179.9°
C4	C5	O	C7	179.8°	0.1°
C4	C5	C6	H2	177.8°	179.9°
C5	C4	C3	H11	178.2°	180.0°
C	C1	C6	C5	176.8°	180.0°
C	C1	C6	H2	3.2°	0.1°
C1	C	N1	H3	179.7°	180.0°
C1	C	N	H9	0.0°	180.0°
C1	C	N	H10	180.0°	0.0°
C	C1	C2	H12	1.7°	0.2°
C6	C1	C	N	31.8°	180.0°
C1	C6	C5	H2	180.0°	180.0°
C1	C6	C5	O	175.4°	180.0°
C6	C1	C2	H12	177.9°	179.7°
N	C	N1	H3	0.0°	0.1°
C	N	H9	H10	180.0°	180.0°
C6	C5	O	C7	2.0°	180.0°
C6	C5	C4	H1	176.7°	180.0°
C5	O	C7	C8	178.6°	180.0°
O	C5	C4	H1	5.4°	0.1°
O	C5	C6	H2	4.5°	0.0°
C5	O	C7	H4	59.0°	60.0°
C5	O	C7	H5	61.7°	60.0°
O	C7	C8	H4	119.6°	119.9°
O	C7	C8	H5	119.7°	120.0°
O	C7	H4	H5	121.1°	120.0°
O	C7	C8	H6	180.0°	180.0°
O	C7	C8	H7	60.0°	60.0°
O	C7	C8	H8	60.0°	60.0°
C8	C7	H4	H5	121.1°	120.0°
C7	C8	H6	H7	120.0°	119.9°
C7	C8	H6	H8	120.0°	120.0°
C7	C8	H7	H8	120.0°	120.0°
H1	C4	C3	H11	1.8°	0.3°
H4	C7	C8	H6	60.3°	60.0°
H4	C7	C8	H7	179.6°	59.9°
H4	C7	C8	H8	59.6°	179.9°
H5	C7	C8	H6	60.4°	60.0°
H5	C7	C8	H7	59.7°	180.0°
H5	C7	C8	H8	179.7°	60.0°
H6	C8	H7	H8	119.9°	120.1°
H11	C3	C2	H12	0.9°	0.6°

223166

PDB entries from 2024-07-31

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