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Summary Geometry Related PDB entries

GVY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C3	sing	1.36Å	1.37Å
C2	C3	doub	1.39Å	1.39Å	Aromatic
C2	C1	sing	1.38Å	1.38Å	Aromatic
C3	C4	sing	1.39Å	1.39Å	Aromatic
C1	C6	doub	1.40Å	1.39Å	Aromatic
C4	C5	doub	1.38Å	1.38Å	Aromatic
C6	C5	sing	1.40Å	1.39Å	Aromatic
C6	C7	sing	1.48Å	1.47Å
N1	C7	doub	1.30Å	1.30Å	Aromatic
N1	N2	sing	1.26Å	1.38Å	Aromatic
C7	S1	sing	1.76Å	1.73Å	Aromatic
N2	C8	doub	1.30Å	1.31Å	Aromatic
S1	C8	sing	1.77Å	1.74Å	Aromatic
C8	N3	sing	1.39Å	1.34Å
N3	H1	sing	0.97Å	1.00Å
N3	H2	sing	0.97Å	1.00Å
C4	H3	sing	1.08Å	1.08Å
C5	H4	sing	1.08Å	1.08Å
C1	H5	sing	1.08Å	1.08Å
C2	H6	sing	1.08Å	1.08Å
O1	H7	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C3	C2	120.4°	119.9°
O1	C3	C4	120.1°	119.9°
C3	O1	H7	109.5°	114.0°
C3	C2	C1	120.0°	120.1°
C2	C3	C4	119.5°	120.2°
C3	C2	H6	120.0°	119.9°
C2	C1	C6	121.1°	119.9°
C2	C1	H5	119.5°	120.1°
C1	C2	H6	120.0°	120.0°
C3	C4	C5	120.0°	120.1°
C3	C4	H3	120.0°	120.0°
C1	C6	C5	118.2°	119.8°
C1	C6	C7	121.2°	120.1°
C6	C1	H5	119.4°	120.0°
C4	C5	C6	121.3°	119.9°
C5	C4	H3	120.0°	119.9°
C4	C5	H4	119.4°	120.1°
C5	C6	C7	120.6°	120.1°
C6	C5	H4	119.4°	120.1°
C6	C7	N1	123.8°	126.1°
C6	C7	S1	122.7°	126.0°
C7	N1	N2	113.1°	117.7°
N1	C7	S1	113.5°	107.9°
N1	N2	C8	111.7°	117.7°
C7	S1	C8	86.9°	88.9°
N2	C8	S1	113.6°	107.8°
N2	C8	N3	124.0°	126.1°
S1	C8	N3	122.3°	126.1°
C8	N3	H1	109.5°	120.0°
C8	N3	H2	109.4°	120.0°
H1	N3	H2	109.5°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C3	C2	C4	179.9°	179.5°
O1	C3	C2	C1	179.9°	180.0°
O1	C3	C4	C5	180.0°	180.0°
O1	C3	C4	H3	0.0°	0.3°
O1	C3	C2	H6	0.0°	0.5°
C3	C2	C1	H6	180.0°	179.5°
C3	C2	C1	C6	0.0°	0.3°
C2	C3	C4	C5	0.1°	0.5°
C2	C3	C4	H3	179.9°	179.7°
C3	C2	C1	H5	180.0°	179.8°
C2	C3	O1	H7	180.0°	90.0°
C1	C2	C3	C4	0.0°	0.5°
C2	C1	C6	H5	180.0°	179.9°
C2	C1	C6	C5	0.1°	0.1°
C2	C1	C6	C7	179.6°	180.0°
C3	C4	C5	H3	180.0°	179.7°
C3	C4	C5	C6	0.2°	0.3°
C3	C4	C5	H4	179.8°	179.8°
C4	C3	C2	H6	180.0°	180.0°
C4	C3	O1	H7	0.0°	90.5°
C1	C6	C5	C4	0.2°	0.1°
C1	C6	C5	C7	179.4°	179.9°
C1	C6	C7	N1	18.6°	180.0°
C1	C6	C7	S1	160.6°	0.1°
C1	C6	C5	H4	179.8°	180.0°
C6	C1	C2	H6	179.9°	179.8°
C4	C5	C6	H4	180.0°	179.9°
C4	C5	C6	C7	179.6°	180.0°
C5	C6	C7	N1	162.0°	0.1°
C5	C6	C7	S1	18.8°	180.0°
C6	C5	C4	H3	179.8°	180.0°
C5	C6	C1	H5	179.9°	180.0°
C6	C7	N1	S1	179.3°	179.9°
C6	C7	N1	N2	172.3°	180.0°
C6	C7	S1	C8	178.5°	180.0°
C7	C6	C5	H4	0.3°	0.1°
C7	C6	C1	H5	0.4°	0.1°
C7	N1	N2	C8	11.5°	0.1°
N1	C7	S1	C8	0.7°	0.0°
N2	N1	C7	S1	6.9°	0.1°
N1	N2	C8	S1	10.9°	0.1°
N1	N2	C8	N3	168.9°	179.9°
C7	S1	C8	N2	6.0°	0.0°
C7	S1	C8	N3	173.9°	180.0°
N2	C8	S1	N3	179.9°	180.0°
N2	C8	N3	H1	0.0°	0.1°
N2	C8	N3	H2	120.0°	180.0°
S1	C8	N3	H1	179.9°	179.9°
S1	C8	N3	H2	60.1°	0.0°
C8	N3	H1	H2	120.0°	179.9°
H3	C4	C5	H4	0.2°	0.1°
H5	C1	C2	H6	0.1°	0.3°

221716

PDB entries from 2024-06-26

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