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Summary Geometry Related PDB entries

6HD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C	N	sing	1.47Å	1.45Å
N	C1	sing	1.38Å	1.33Å
C1	N1	sing	1.37Å	1.32Å	Aromatic
C1	N3	doub	1.31Å	1.35Å	Aromatic
N1	C2	sing	1.38Å	1.40Å	Aromatic
N3	C8	sing	1.36Å	1.38Å	Aromatic
C2	C8	doub	1.41Å	1.39Å	Aromatic
C2	C3	sing	1.39Å	1.39Å	Aromatic
C8	C7	sing	1.39Å	1.39Å	Aromatic
C3	C4	doub	1.37Å	1.39Å	Aromatic
C7	C5	doub	1.39Å	1.39Å	Aromatic
C4	C5	sing	1.40Å	1.40Å	Aromatic
C5	C6	sing	1.48Å	1.50Å
C6	O	doub	1.22Å	1.24Å
C6	N2	sing	1.35Å	1.33Å
N2	H1	sing	0.97Å	1.00Å
N2	H2	sing	0.97Å	1.00Å
C4	H3	sing	1.08Å	1.08Å
C3	H4	sing	1.08Å	1.08Å
C7	H5	sing	1.08Å	1.08Å
N1	H6	sing	0.97Å	1.00Å
N	H8	sing	0.97Å	1.00Å
C	H9	sing	1.09Å	1.10Å
C	H10	sing	1.09Å	1.10Å
C	H11	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C	N	C1	123.8°	120.0°
C	N	H8	105.8°	120.0°
N	C	H9	109.5°	109.4°
N	C	H10	109.5°	109.5°
N	C	H11	109.5°	109.5°
N	C1	N1	124.5°	125.1°
N	C1	N3	121.8°	125.0°
C1	N	H8	105.8°	120.0°
N1	C1	N3	113.7°	109.9°
C1	N1	C2	104.2°	107.4°
C1	N1	H6	127.9°	126.3°
C1	N3	C8	106.8°	109.5°
N1	C2	C8	109.7°	106.1°
N1	C2	C3	130.4°	133.7°
C2	N1	H6	127.9°	126.3°
N3	C8	C2	105.5°	107.1°
N3	C8	C7	132.9°	133.4°
C8	C2	C3	119.8°	120.2°
C2	C8	C7	121.5°	119.5°
C2	C3	C4	118.9°	120.2°
C2	C3	H4	120.6°	119.9°
C8	C7	C5	118.5°	119.6°
C8	C7	H5	120.7°	120.3°
C3	C4	C5	121.1°	120.4°
C3	C4	H3	119.4°	119.8°
C4	C3	H4	120.5°	119.9°
C7	C5	C4	120.1°	120.1°
C7	C5	C6	118.1°	119.9°
C5	C7	H5	120.7°	120.2°
C4	C5	C6	121.7°	120.0°
C5	C4	H3	119.4°	119.8°
C5	C6	O	119.3°	120.0°
C5	C6	N2	118.0°	120.0°
O	C6	N2	122.7°	120.0°
C6	N2	H1	120.0°	120.0°
C6	N2	H2	120.0°	120.0°
H1	N2	H2	120.0°	120.1°
H9	C	H10	109.5°	109.4°
H9	C	H11	109.4°	109.5°
H10	C	H11	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C	N	C1	H8	121.9°	179.9°
C	N	C1	N1	0.7°	0.1°
C	N	C1	N3	179.9°	180.0°
N	C	H9	H10	120.0°	120.0°
N	C	H9	H11	120.0°	120.0°
N	C	H10	H11	120.0°	120.0°
N	C1	N1	N3	179.3°	180.0°
N	C1	N1	C2	179.2°	180.0°
N	C1	N3	C8	179.0°	179.9°
N	C1	N1	H6	0.8°	0.0°
C1	N	C	H9	180.0°	60.0°
C1	N	C	H10	60.0°	59.9°
C1	N	C	H11	60.0°	180.0°
C1	N1	C2	H6	180.0°	180.0°
N1	C1	N3	C8	0.3°	0.0°
C1	N1	C2	C8	0.3°	0.0°
C1	N1	C2	C3	178.1°	179.7°
N1	C1	N	H8	122.6°	180.0°
N3	C1	N1	C2	0.0°	0.0°
C1	N3	C8	C2	0.5°	0.0°
C1	N3	C8	C7	176.9°	180.0°
N3	C1	N1	H6	179.9°	180.0°
N3	C1	N	H8	58.1°	0.0°
N1	C2	C8	N3	0.5°	0.1°
N1	C2	C8	C3	178.1°	179.8°
N1	C2	C8	C7	177.3°	180.0°
N1	C2	C3	C4	176.6°	180.0°
N1	C2	C3	H4	3.4°	0.1°
N3	C8	C2	C7	177.7°	179.9°
N3	C8	C2	C3	178.6°	179.7°
N3	C8	C7	C5	176.4°	180.0°
N3	C8	C7	H5	3.5°	0.1°
C8	C2	C3	C4	1.1°	0.3°
C2	C8	C7	C5	0.6°	0.0°
C8	C2	C3	H4	178.9°	179.7°
C2	C8	C7	H5	179.4°	180.0°
C8	C2	N1	H6	179.8°	180.0°
C3	C2	C8	C7	0.8°	0.2°
C2	C3	C4	H4	180.0°	180.0°
C2	C3	C4	C5	0.1°	0.0°
C2	C3	C4	H3	179.9°	180.0°
C3	C2	N1	H6	1.9°	0.3°
C8	C7	C5	H5	180.0°	180.0°
C8	C7	C5	C4	1.7°	0.3°
C8	C7	C5	C6	175.3°	180.0°
C3	C4	C5	C7	1.5°	0.2°
C3	C4	C5	H3	180.0°	180.0°
C3	C4	C5	C6	175.4°	180.0°
C7	C5	C4	C6	176.9°	179.8°
C7	C5	C6	O	6.2°	0.3°
C7	C5	C6	N2	172.3°	179.5°
C7	C5	C4	H3	178.5°	179.7°
C4	C5	C6	O	176.8°	180.0°
C4	C5	C6	N2	4.7°	0.3°
C5	C4	C3	H4	179.9°	180.0°
C4	C5	C7	H5	178.3°	179.7°
C5	C6	O	N2	178.4°	179.7°
C5	C6	N2	H1	178.4°	179.7°
C5	C6	N2	H2	1.6°	0.3°
C6	C5	C4	H3	4.6°	0.0°
C6	C5	C7	H5	4.7°	0.0°
O	C6	N2	H1	0.0°	0.0°
O	C6	N2	H2	180.0°	180.0°
C6	N2	H1	H2	180.0°	180.0°
H3	C4	C3	H4	0.1°	0.0°
H8	N	C	H9	58.1°	120.1°
H8	N	C	H10	61.9°	120.0°
H8	N	C	H11	178.0°	0.0°
H9	C	H10	H11	120.0°	120.0°

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PDB entries from 2024-10-09

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