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Summary Geometry Related PDB entries

NK5

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C6	C5	doub	1.38Å	1.38Å	Aromatic
C6	C1	sing	1.38Å	1.38Å	Aromatic
C5	C4	sing	1.39Å	1.39Å	Aromatic
N13	N14	doub	1.29Å	1.47Å	Aromatic
N13	N12	sing	1.40Å	1.47Å	Aromatic
N14	C15	sing	1.34Å	1.35Å	Aromatic
C1	C2	doub	1.38Å	1.38Å	Aromatic
C4	N12	sing	1.40Å	1.43Å
C4	C3	doub	1.39Å	1.39Å	Aromatic
N12	C16	sing	1.35Å	1.38Å	Aromatic
C15	C16	doub	1.37Å	1.39Å	Aromatic
C15	C17	sing	1.48Å	1.49Å
C2	C3	sing	1.38Å	1.38Å	Aromatic
N18	O19	sing	1.42Å	1.39Å
N18	C17	sing	1.35Å	1.34Å
C17	O20	doub	1.22Å	1.23Å
C2	H1	sing	1.08Å	1.08Å
C3	H2	sing	1.08Å	1.08Å
C1	H3	sing	1.08Å	1.08Å
C6	H4	sing	1.08Å	1.08Å
C16	H5	sing	1.08Å	1.08Å
C5	H6	sing	1.08Å	1.08Å
N18	H7	sing	0.97Å	1.00Å
O19	H8	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C5	C6	C1	120.4°	120.1°
C6	C5	C4	119.6°	120.0°
C5	C6	H4	119.8°	120.0°
C6	C5	H6	120.2°	120.0°
C6	C1	C2	119.9°	120.1°
C6	C1	H3	120.1°	120.0°
C1	C6	H4	119.8°	120.0°
C5	C4	N12	119.7°	120.0°
C5	C4	C3	120.1°	119.9°
C4	C5	H6	120.2°	120.0°
N14	N13	N12	105.0°	108.4°
N13	N14	C15	106.8°	109.5°
N13	N12	C4	114.9°	126.6°
N13	N12	C16	107.7°	106.7°
N14	C15	C16	112.1°	108.5°
N14	C15	C17	121.8°	125.7°
C1	C2	C3	120.4°	120.1°
C1	C2	H1	119.8°	120.0°
C2	C1	H3	120.0°	119.9°
N12	C4	C3	120.2°	120.1°
C4	N12	C16	128.8°	126.7°
C4	C3	C2	119.6°	119.9°
C4	C3	H2	120.2°	120.0°
N12	C16	C15	108.5°	106.8°
N12	C16	H5	125.8°	126.6°
C16	C15	C17	126.1°	125.8°
C15	C16	H5	125.8°	126.6°
C15	C17	N18	114.7°	120.0°
C15	C17	O20	121.2°	120.0°
C3	C2	H1	119.8°	119.9°
C2	C3	H2	120.2°	120.1°
O19	N18	C17	120.6°	120.0°
O19	N18	H7	119.7°	120.0°
N18	O19	H8	109.5°	114.0°
N18	C17	O20	124.1°	120.0°
C17	N18	H7	119.7°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C5	C6	C1	H4	180.0°	180.0°
C6	C5	C4	H6	180.0°	180.0°
C5	C6	C1	C2	0.4°	0.3°
C6	C5	C4	N12	177.1°	180.0°
C6	C5	C4	C3	0.7°	0.3°
C5	C6	C1	H3	179.6°	179.9°
C1	C6	C5	C4	0.1°	0.0°
C6	C1	C2	H3	180.0°	179.8°
C6	C1	C2	C3	0.3°	0.3°
C6	C1	C2	H1	179.6°	179.7°
C1	C6	C5	H6	179.9°	180.0°
C5	C4	N12	N13	20.3°	179.7°
C5	C4	N12	C3	177.8°	179.7°
C5	C4	N12	C16	163.6°	0.3°
C5	C4	C3	C2	0.8°	0.3°
C5	C4	C3	H2	179.2°	179.7°
C4	C5	C6	H4	179.9°	180.0°
N14	N13	N12	C4	151.3°	179.9°
N14	N13	N12	C16	0.6°	0.0°
N13	N14	C15	C16	0.4°	0.4°
N13	N14	C15	C17	178.2°	179.9°
N12	N13	N14	C15	0.1°	0.3°
N13	N12	C4	C16	143.3°	179.9°
N13	N12	C4	C3	161.9°	0.1°
N13	N12	C16	C15	0.8°	0.2°
N13	N12	C16	H5	179.2°	180.0°
N14	C15	C16	N12	0.8°	0.4°
N14	C15	C16	C17	178.5°	179.5°
N14	C15	C17	N18	49.0°	0.1°
N14	C15	C17	O20	130.9°	179.9°
N14	C15	C16	H5	179.2°	179.9°
C1	C2	C3	C4	0.3°	0.0°
C1	C2	C3	H1	180.0°	180.0°
C1	C2	C3	H2	179.8°	180.0°
C2	C1	C6	H4	179.6°	179.7°
C4	N12	C16	C15	146.1°	179.7°
N12	C4	C3	C2	177.0°	180.0°
N12	C4	C3	H2	3.0°	0.0°
C4	N12	C16	H5	33.9°	0.0°
N12	C4	C5	H6	2.9°	0.0°
C3	C4	N12	C16	18.6°	180.0°
C4	C3	C2	H2	180.0°	180.0°
C4	C3	C2	H1	179.8°	180.0°
C3	C4	C5	H6	179.3°	179.7°
N12	C16	C15	H5	180.0°	179.7°
N12	C16	C15	C17	177.7°	179.9°
C16	C15	C17	N18	132.7°	179.5°
C16	C15	C17	O20	47.5°	0.5°
C15	C17	N18	O19	153.9°	180.0°
C15	C17	N18	O20	179.8°	179.9°
C17	C15	C16	H5	2.3°	0.4°
C15	C17	N18	H7	26.0°	0.1°
C3	C2	C1	H3	179.7°	179.9°
O19	N18	C17	H7	180.0°	180.0°
O19	N18	C17	O20	25.9°	0.0°
C17	N18	O19	H8	11.4°	180.0°
O20	C17	N18	H7	154.1°	180.0°
H1	C2	C3	H2	0.2°	0.0°
H1	C2	C1	H3	0.3°	0.1°
H3	C1	C6	H4	0.4°	0.1°
H4	C6	C5	H6	0.1°	0.0°
H7	N18	O19	H8	168.6°	0.0°

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PDB entries from 2026-02-04

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