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Summary Geometry Related PDB entries

VTC

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C6	C5	doub	1.38Å	1.34Å	Aromatic
C6	C7	sing	1.39Å	1.36Å	Aromatic
C5	C4	sing	1.38Å	1.36Å	Aromatic
C7	N1	sing	1.40Å	1.33Å
C7	C8	doub	1.39Å	1.36Å	Aromatic
C4	C3	doub	1.39Å	1.35Å	Aromatic
C8	C3	sing	1.39Å	1.34Å	Aromatic
C3	O1	sing	1.36Å	1.38Å
O1	C2	sing	1.35Å	1.34Å
C2	O	doub	1.21Å	1.26Å
C2	N	sing	1.35Å	1.39Å
C1	N	sing	1.46Å	1.51Å
N	C	sing	1.47Å	1.46Å
N1	H1	sing	0.97Å	1.00Å
N1	H2	sing	0.97Å	1.00Å
C8	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
C5	H7	sing	1.08Å	1.08Å
C6	H8	sing	1.08Å	1.08Å
C4	H9	sing	1.08Å	1.08Å
C	H10	sing	1.09Å	1.10Å
C	H11	sing	1.09Å	1.10Å
C	H12	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C5	C6	C7	118.8°	120.1°
C6	C5	C4	121.7°	120.1°
C6	C5	H7	119.1°	119.9°
C5	C6	H8	120.6°	120.0°
C6	C7	N1	117.9°	120.1°
C6	C7	C8	122.1°	119.9°
C7	C6	H8	120.6°	120.0°
C5	C4	C3	116.1°	120.1°
C4	C5	H7	119.2°	119.9°
C5	C4	H9	122.0°	120.0°
N1	C7	C8	118.8°	120.1°
C7	N1	H1	109.5°	120.0°
C7	N1	H2	109.4°	120.0°
C7	C8	C3	115.4°	119.9°
C7	C8	H3	122.3°	120.1°
C4	C3	C8	125.5°	120.0°
C4	C3	O1	112.8°	120.0°
C3	C4	H9	121.9°	119.9°
C8	C3	O1	120.0°	120.0°
C3	C8	H3	122.3°	120.0°
C3	O1	C2	115.6°	116.9°
O1	C2	O	122.2°	120.0°
O1	C2	N	117.3°	120.0°
O	C2	N	120.5°	120.0°
C2	N	C1	122.1°	120.0°
C2	N	C	110.7°	120.0°
C1	N	C	111.7°	120.0°
N	C1	H4	109.5°	109.5°
N	C1	H5	109.5°	109.5°
N	C1	H6	109.5°	109.5°
N	C	H10	109.5°	109.4°
N	C	H11	109.4°	109.5°
N	C	H12	109.5°	109.5°
H1	N1	H2	109.5°	120.0°
H4	C1	H5	109.5°	109.4°
H4	C1	H6	109.5°	109.5°
H5	C1	H6	109.5°	109.4°
H10	C	H11	109.5°	109.5°
H10	C	H12	109.5°	109.5°
H11	C	H12	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C5	C6	C7	H8	180.0°	179.9°
C6	C5	C4	H7	180.0°	179.7°
C5	C6	C7	N1	165.1°	180.0°
C5	C6	C7	C8	2.6°	0.2°
C6	C5	C4	C3	0.3°	0.4°
C6	C5	C4	H9	179.7°	179.7°
C7	C6	C5	C4	0.3°	0.1°
C6	C7	N1	C8	168.1°	179.8°
C6	C7	C8	C3	5.8°	0.2°
C6	C7	N1	H1	180.0°	179.7°
C6	C7	N1	H2	60.0°	0.5°
C6	C7	C8	H3	174.2°	179.8°
C7	C6	C5	H7	179.7°	179.7°
C5	C4	C3	H9	180.0°	179.9°
C5	C4	C3	C8	4.1°	0.3°
C5	C4	C3	O1	161.0°	179.7°
C4	C5	C6	H8	179.7°	180.0°
N1	C7	C8	C3	161.8°	180.0°
C7	N1	H1	H2	120.0°	179.8°
N1	C7	C8	H3	18.2°	0.0°
N1	C7	C6	H8	14.9°	0.0°
C7	C8	C3	C4	6.7°	0.0°
C7	C8	C3	H3	180.0°	180.0°
C7	C8	C3	O1	157.5°	180.0°
C8	C7	N1	H1	11.9°	0.1°
C8	C7	N1	H2	131.9°	179.8°
C8	C7	C6	H8	177.4°	179.7°
C4	C3	C8	O1	164.2°	180.0°
C4	C3	O1	C2	81.2°	102.9°
C4	C3	C8	H3	173.3°	180.0°
C3	C4	C5	H7	179.7°	180.0°
C8	C3	O1	C2	84.8°	77.1°
C8	C3	C4	H9	175.9°	179.7°
C3	O1	C2	O	4.3°	4.9°
C3	O1	C2	N	178.4°	175.1°
O1	C3	C8	H3	22.6°	0.0°
O1	C3	C4	H9	19.0°	0.2°
O1	C2	O	N	177.2°	180.0°
O1	C2	N	C1	18.0°	180.0°
O1	C2	N	C	152.6°	0.0°
O	C2	N	C1	164.7°	0.0°
O	C2	N	C	30.1°	180.0°
C2	N	C1	C	134.2°	180.0°
C2	N	C1	H4	180.0°	0.0°
C2	N	C1	H5	60.0°	120.0°
C2	N	C1	H6	60.0°	120.0°
C2	N	C	H10	180.0°	90.0°
C2	N	C	H11	60.0°	30.0°
C2	N	C	H12	60.0°	150.0°
N	C1	H4	H5	120.0°	120.0°
N	C1	H4	H6	120.0°	120.1°
N	C1	H5	H6	120.0°	120.0°
C1	N	C	H10	40.5°	90.0°
C1	N	C	H11	160.5°	150.0°
C1	N	C	H12	79.5°	30.0°
C	N	C1	H4	45.8°	180.0°
C	N	C1	H5	74.2°	60.0°
C	N	C1	H6	165.8°	60.0°
N	C	H10	H11	120.0°	120.0°
N	C	H10	H12	120.0°	120.0°
N	C	H11	H12	120.0°	120.0°
H4	C1	H5	H6	120.0°	119.9°
H7	C5	C6	H8	0.3°	0.3°
H7	C5	C4	H9	0.3°	0.0°
H10	C	H11	H12	120.0°	120.0°

250359

PDB entries from 2026-03-11

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