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Summary Geometry Related PDB entries

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Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C9	O3	sing	1.45Å	1.41Å
O1	C1	doub	1.22Å	1.23Å
O2	C8	doub	1.22Å	1.22Å
O3	C8	sing	1.35Å	1.38Å
C8	N1	sing	1.35Å	1.39Å
C1	N	sing	1.35Å	1.40Å
C1	O	sing	1.35Å	1.38Å
N	C2	sing	1.40Å	1.44Å
C7	C2	doub	1.39Å	1.40Å	Aromatic
C7	C6	sing	1.39Å	1.41Å	Aromatic
C2	C3	sing	1.39Å	1.40Å	Aromatic
N1	C6	sing	1.40Å	1.42Å
O	C	sing	1.45Å	1.41Å
C6	C5	doub	1.39Å	1.41Å	Aromatic
C3	C4	doub	1.38Å	1.39Å	Aromatic
C5	C4	sing	1.38Å	1.39Å	Aromatic
N1	H1	sing	0.97Å	1.00Å
C4	H2	sing	1.08Å	1.08Å
C5	H3	sing	1.08Å	1.08Å
C7	H4	sing	1.08Å	1.08Å
N	H5	sing	0.97Å	1.00Å
C	H6	sing	1.09Å	1.10Å
C	H7	sing	1.09Å	1.10Å
C	H8	sing	1.09Å	1.10Å
C3	H9	sing	1.08Å	1.08Å
C9	H10	sing	1.09Å	1.10Å
C9	H11	sing	1.09Å	1.10Å
C9	H12	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C9	O3	C8	116.1°	117.0°
O3	C9	H10	109.5°	109.5°
O3	C9	H11	109.5°	109.5°
O3	C9	H12	109.4°	109.5°
O1	C1	N	125.2°	120.0°
O1	C1	O	121.4°	120.0°
O2	C8	O3	120.6°	120.0°
O2	C8	N1	128.9°	120.0°
O3	C8	N1	110.6°	120.1°
C8	N1	C6	123.9°	120.0°
C8	N1	H1	118.1°	120.0°
N	C1	O	113.3°	120.0°
C1	N	C2	130.7°	120.0°
C1	N	H5	114.6°	120.0°
C1	O	C	116.7°	117.0°
N	C2	C7	114.4°	120.1°
N	C2	C3	125.5°	120.0°
C2	N	H5	114.6°	120.0°
C2	C7	C6	119.0°	119.9°
C7	C2	C3	120.1°	119.9°
C2	C7	H4	120.5°	120.1°
C7	C6	N1	122.1°	120.0°
C7	C6	C5	121.0°	119.9°
C6	C7	H4	120.5°	120.0°
C2	C3	C4	120.4°	120.0°
C2	C3	H9	119.8°	119.9°
N1	C6	C5	116.9°	120.1°
C6	N1	H1	118.0°	120.0°
O	C	H6	109.5°	109.4°
O	C	H7	109.5°	109.5°
O	C	H8	109.5°	109.5°
C6	C5	C4	118.9°	120.1°
C6	C5	H3	120.6°	119.9°
C3	C4	C5	120.7°	120.2°
C3	C4	H2	119.7°	119.9°
C4	C3	H9	119.8°	120.0°
C5	C4	H2	119.6°	119.9°
C4	C5	H3	120.6°	120.0°
H6	C	H7	109.5°	109.5°
H6	C	H8	109.5°	109.5°
H7	C	H8	109.5°	109.5°
H10	C9	H11	109.5°	109.4°
H10	C9	H12	109.5°	109.5°
H11	C9	H12	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C9	O3	C8	O2	1.0°	0.0°
C9	O3	C8	N1	179.6°	180.0°
O3	C9	H10	H11	120.0°	120.0°
O3	C9	H10	H12	120.0°	120.0°
O3	C9	H11	H12	120.0°	120.0°
O1	C1	N	O	179.3°	179.9°
O1	C1	N	C2	178.2°	4.7°
O1	C1	O	C	57.4°	0.1°
O1	C1	N	H5	1.8°	175.3°
O2	C8	O3	N1	179.5°	180.0°
O2	C8	N1	C6	1.3°	5.2°
O2	C8	N1	H1	178.7°	174.6°
O3	C8	N1	C6	179.3°	174.9°
O3	C8	N1	H1	0.7°	5.4°
C8	O3	C9	H10	180.0°	60.0°
C8	O3	C9	H11	60.0°	60.0°
C8	O3	C9	H12	60.0°	180.0°
C8	N1	C6	C7	14.0°	146.7°
C8	N1	C6	H1	180.0°	179.8°
C8	N1	C6	C5	165.1°	33.4°
C1	N	C2	H5	180.0°	180.0°
C1	N	C2	C7	165.4°	35.6°
C1	N	C2	C3	14.0°	144.1°
N	C1	O	C	123.2°	180.0°
O	C1	N	C2	1.1°	175.4°
O	C1	N	H5	178.9°	4.6°
C1	O	C	H6	180.0°	60.0°
C1	O	C	H7	60.0°	60.0°
C1	O	C	H8	60.0°	180.0°
N	C2	C7	C3	179.4°	179.7°
N	C2	C7	C6	179.2°	180.0°
N	C2	C3	C4	178.6°	179.8°
N	C2	C7	H4	0.8°	0.3°
N	C2	C3	H9	1.4°	0.3°
C2	C7	C6	H4	180.0°	179.7°
C2	C7	C6	N1	178.5°	180.0°
C2	C7	C6	C5	0.5°	0.0°
C7	C2	C3	C4	0.7°	0.5°
C7	C2	N	H5	14.6°	144.4°
C7	C2	C3	H9	179.3°	180.0°
C6	C7	C2	C3	0.2°	0.3°
C7	C6	N1	C5	179.1°	180.0°
C7	C6	C5	C4	0.8°	0.0°
C7	C6	N1	H1	166.0°	33.1°
C7	C6	C5	H3	179.2°	180.0°
C2	C3	C4	H9	180.0°	179.5°
C2	C3	C4	C5	0.4°	0.5°
C2	C3	C4	H2	179.6°	179.7°
C3	C2	C7	H4	179.7°	180.0°
C3	C2	N	H5	166.0°	35.8°
N1	C6	C5	C4	178.3°	180.0°
N1	C6	C5	H3	1.7°	0.0°
N1	C6	C7	H4	1.5°	0.2°
O	C	H6	H7	120.0°	120.0°
O	C	H6	H8	120.0°	120.0°
O	C	H7	H8	120.0°	120.0°
C6	C5	C4	C3	0.3°	0.3°
C6	C5	C4	H3	180.0°	180.0°
C5	C6	N1	H1	14.9°	146.9°
C6	C5	C4	H2	179.7°	180.0°
C5	C6	C7	H4	179.5°	179.7°
C3	C4	C5	H2	180.0°	179.8°
C3	C4	C5	H3	179.7°	179.8°
C5	C4	C3	H9	179.5°	180.0°
H2	C4	C5	H3	0.3°	0.0°
H2	C4	C3	H9	0.4°	0.2°
H6	C	H7	H8	120.0°	120.0°
H10	C9	H11	H12	120.0°	120.0°

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PDB entries from 2024-07-10

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