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Summary Geometry Related PDB entries

VCZ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O2	C6	doub	1.22Å	1.23Å
O3	C6	sing	1.35Å	1.26Å
C6	C5	sing	1.47Å	1.44Å
C5	C4	doub	1.40Å	1.39Å	Aromatic
C5	C7	sing	1.40Å	1.39Å	Aromatic
C4	C3	sing	1.38Å	1.37Å	Aromatic
C7	C8	doub	1.38Å	1.37Å	Aromatic
C3	C2	doub	1.39Å	1.39Å	Aromatic
C8	C2	sing	1.40Å	1.41Å	Aromatic
C8	N1	sing	1.40Å	1.42Å
C2	O1	sing	1.36Å	1.36Å
N1	C9	sing	1.35Å	1.35Å
O1	C1	sing	1.43Å	1.43Å
C9	O4	doub	1.21Å	1.25Å
C9	C10	sing	1.51Å	1.50Å
C7	H1	sing	1.08Å	1.08Å
C4	H2	sing	1.08Å	1.08Å
C3	H3	sing	1.08Å	1.08Å
C1	H4	sing	1.09Å	1.10Å
C1	H5	sing	1.09Å	1.10Å
C1	H6	sing	1.09Å	1.10Å
O3	H7	sing	0.97Å	0.95Å
N1	H8	sing	0.97Å	1.00Å
C10	H9	sing	1.09Å	1.10Å
C10	H10	sing	1.09Å	1.10Å
C10	H11	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O2	C6	O3	125.9°	120.0°
O2	C6	C5	115.2°	120.0°
O3	C6	C5	118.9°	120.0°
C6	O3	H7	109.5°	117.0°
C6	C5	C4	119.2°	120.1°
C6	C5	C7	120.4°	120.0°
C4	C5	C7	120.3°	119.9°
C5	C4	C3	120.6°	120.0°
C5	C4	H2	119.7°	120.0°
C5	C7	C8	119.7°	119.8°
C5	C7	H1	120.2°	120.1°
C4	C3	C2	119.8°	120.1°
C3	C4	H2	119.7°	119.9°
C4	C3	H3	120.1°	119.9°
C7	C8	C2	120.1°	119.9°
C7	C8	N1	121.7°	120.0°
C8	C7	H1	120.2°	120.1°
C3	C2	C8	119.5°	120.2°
C3	C2	O1	123.7°	119.9°
C2	C3	H3	120.2°	119.9°
C2	C8	N1	118.2°	120.0°
C8	C2	O1	116.7°	119.9°
C8	N1	C9	125.2°	120.0°
C8	N1	H8	117.4°	120.0°
C2	O1	C1	118.2°	117.0°
N1	C9	O4	122.8°	120.0°
N1	C9	C10	115.1°	120.0°
C9	N1	H8	117.4°	120.0°
O1	C1	H4	109.5°	109.5°
O1	C1	H5	109.4°	109.5°
O1	C1	H6	109.5°	109.5°
O4	C9	C10	122.1°	120.0°
C9	C10	H9	109.5°	109.5°
C9	C10	H10	109.5°	109.5°
C9	C10	H11	109.5°	109.4°
H4	C1	H5	109.5°	109.5°
H4	C1	H6	109.5°	109.4°
H5	C1	H6	109.5°	109.5°
H9	C10	H10	109.5°	109.5°
H9	C10	H11	109.5°	109.5°
H10	C10	H11	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O2	C6	O3	C5	178.2°	179.9°
O2	C6	C5	C4	16.7°	179.9°
O2	C6	C5	C7	159.5°	0.1°
O2	C6	O3	H7	0.0°	0.0°
O3	C6	C5	C4	164.9°	0.0°
O3	C6	C5	C7	18.9°	180.0°
C6	C5	C4	C7	176.2°	180.0°
C6	C5	C4	C3	177.8°	180.0°
C6	C5	C7	C8	179.0°	180.0°
C6	C5	C7	H1	1.0°	0.3°
C6	C5	C4	H2	2.2°	0.1°
C5	C6	O3	H7	178.2°	180.0°
C5	C4	C3	H2	180.0°	179.9°
C4	C5	C7	C8	2.8°	0.0°
C5	C4	C3	C2	0.3°	0.0°
C4	C5	C7	H1	177.2°	179.7°
C5	C4	C3	H3	179.7°	179.9°
C7	C5	C4	C3	1.5°	0.0°
C5	C7	C8	H1	180.0°	179.7°
C5	C7	C8	C2	2.2°	0.0°
C5	C7	C8	N1	180.0°	179.7°
C7	C5	C4	H2	178.5°	179.9°
C4	C3	C2	H3	180.0°	179.9°
C4	C3	C2	C8	0.9°	0.1°
C4	C3	C2	O1	178.7°	180.0°
C7	C8	C2	C3	0.4°	0.0°
C7	C8	C2	N1	177.9°	179.7°
C7	C8	C2	O1	177.6°	180.0°
C7	C8	N1	C9	47.0°	34.7°
C7	C8	N1	H8	133.0°	145.3°
C3	C2	C8	O1	178.0°	179.9°
C3	C2	C8	N1	178.3°	179.7°
C3	C2	O1	C1	10.7°	0.1°
C2	C3	C4	H2	179.7°	179.9°
C2	C8	N1	C9	130.8°	145.6°
C8	C2	O1	C1	171.4°	180.0°
C2	C8	C7	H1	177.7°	179.7°
C8	C2	C3	H3	179.1°	180.0°
C2	C8	N1	H8	49.2°	34.5°
N1	C8	C2	O1	0.3°	0.2°
C8	N1	C9	H8	180.0°	179.9°
C8	N1	C9	O4	8.0°	4.4°
C8	N1	C9	C10	172.7°	175.8°
N1	C8	C7	H1	0.0°	0.0°
O1	C2	C3	H3	1.2°	0.1°
C2	O1	C1	H4	180.0°	180.0°
C2	O1	C1	H5	60.0°	60.0°
C2	O1	C1	H6	60.0°	60.1°
N1	C9	O4	C10	179.3°	179.8°
N1	C9	C10	H9	179.3°	90.3°
N1	C9	C10	H10	60.7°	29.8°
N1	C9	C10	H11	59.3°	149.7°
O1	C1	H4	H5	120.0°	120.0°
O1	C1	H4	H6	120.0°	120.0°
O1	C1	H5	H6	120.0°	120.0°
O4	C9	N1	H8	172.0°	175.5°
O4	C9	C10	H9	0.0°	89.9°
O4	C9	C10	H10	120.0°	150.0°
O4	C9	C10	H11	120.0°	30.1°
C10	C9	N1	H8	7.4°	4.3°
C9	C10	H9	H10	120.0°	120.1°
C9	C10	H9	H11	120.0°	120.0°
C9	C10	H10	H11	120.0°	120.0°
H2	C4	C3	H3	0.3°	0.0°
H4	C1	H5	H6	120.0°	120.0°
H9	C10	H10	H11	120.0°	120.0°

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PDB entries from 2024-07-10

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