Summary Geometry PCM/PTM Related PDB entries

ZJO

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C14	C10	doub	1.37Å	1.37Å	Aromatic
C14	C18	sing	1.37Å	1.37Å	Aromatic
C10	C7	sing	1.38Å	1.38Å	Aromatic
C18	C2	doub	1.38Å	1.39Å	Aromatic
C7	C3	doub	1.39Å	1.39Å	Aromatic
C2	C3	sing	1.39Å	1.39Å	Aromatic
C3	N3	sing	1.43Å	1.43Å
C27	C30	doub	1.37Å	1.38Å	Aromatic
C27	C23	sing	1.38Å	1.40Å	Aromatic
C30	C28	sing	1.37Å	1.37Å	Aromatic
C23	C9	doub	1.39Å	1.38Å	Aromatic
N3	RU1	sing	2.24Å	2.05Å
N3	C16	doub	1.34Å	1.32Å
RU1	N2	sing	2.37Å	2.07Å
RU1	RU2	sing	2.69Å	2.30Å
C28	C21	doub	1.38Å	1.38Å	Aromatic
C9	C21	sing	1.39Å	1.39Å	Aromatic
C9	N2	sing	1.43Å	1.44Å
C16	N4	sing	1.34Å	1.32Å
N2	C13	sing	1.34Å	1.32Å
N4	RU2	sing	2.37Å	2.06Å
N4	C1	sing	1.43Å	1.43Å
RU2	N1	sing	2.37Å	2.05Å
RU2	O5	sing	2.19Å	2.39Å
C13	N1	doub	1.34Å	1.31Å
C1	C4	doub	1.39Å	1.38Å	Aromatic
C1	C11	sing	1.39Å	1.38Å	Aromatic
N1	C5	sing	1.43Å	1.42Å
C4	C12	sing	1.38Å	1.39Å	Aromatic
C11	C17	doub	1.38Å	1.38Å	Aromatic
C5	C15	doub	1.39Å	1.39Å	Aromatic
C5	C20	sing	1.39Å	1.37Å	Aromatic
C12	C6	doub	1.37Å	1.36Å	Aromatic
C17	C6	sing	1.37Å	1.36Å	Aromatic
C15	C25	sing	1.38Å	1.39Å	Aromatic
C20	C26	doub	1.38Å	1.40Å	Aromatic
C25	C29	doub	1.37Å	1.36Å	Aromatic
C26	C29	sing	1.37Å	1.37Å	Aromatic
C2	H1	sing	0.94Å	1.08Å
C4	H2	sing	0.93Å	1.08Å
C6	H3	sing	0.94Å	1.08Å
C7	H4	sing	0.94Å	1.08Å
C10	H5	sing	0.94Å	1.08Å
C11	H6	sing	0.94Å	1.08Å
C12	H7	sing	0.94Å	1.08Å
C13	H8	sing	0.94Å	1.08Å
C14	H10	sing	0.94Å	1.08Å
C15	H11	sing	0.94Å	1.08Å
C16	H12	sing	0.94Å	1.08Å
C17	H14	sing	0.94Å	1.08Å
C18	H15	sing	0.94Å	1.08Å
C20	H16	sing	0.94Å	1.08Å
C21	H17	sing	0.94Å	1.08Å
C23	H18	sing	0.94Å	1.08Å
C25	H19	sing	0.94Å	1.08Å
C26	H20	sing	0.94Å	1.08Å
C27	H21	sing	0.94Å	1.08Å
C28	H22	sing	0.94Å	1.08Å
C29	H23	sing	0.95Å	1.08Å
C30	H24	sing	0.94Å	1.08Å
O5	H25	sing	0.86Å	0.95Å
H9	O5	sing	0.86Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C10	C14	C18	124.5°	119.6°
C14	C10	C7	118.8°	120.5°
C14	C10	H5	120.6°	119.9°
C10	C14	H10	117.7°	120.2°
C14	C18	C2	117.3°	120.4°
C18	C14	H10	117.8°	120.2°
C14	C18	H15	121.3°	119.9°
C10	C7	C3	117.5°	120.6°
C10	C7	H4	121.3°	119.5°
C7	C10	H5	120.6°	119.6°
C18	C2	C3	118.3°	120.7°
C18	C2	H1	120.9°	119.8°
C2	C18	H15	121.3°	119.6°
C7	C3	C2	123.5°	118.1°
C7	C3	N3	119.2°	125.2°
C3	C7	H4	121.2°	119.9°
C2	C3	N3	117.3°	116.7°
C3	C2	H1	120.8°	119.5°
C3	N3	RU1	127.5°	112.6°
C3	N3	C16	115.5°	129.5°
C30	C27	C23	116.8°	120.5°
C27	C30	C28	123.5°	119.6°
C30	C27	H21	121.6°	119.9°
C27	C30	H24	118.3°	120.2°
C27	C23	C9	119.7°	120.6°
C27	C23	H18	120.1°	119.8°
C23	C27	H21	121.6°	119.6°
C30	C28	C21	120.2°	120.5°
C30	C28	H22	119.9°	119.9°
C28	C30	H24	118.3°	120.2°
C23	C9	C21	122.6°	118.3°
C23	C9	N2	118.4°	116.4°
C9	C23	H18	120.1°	119.6°
RU1	N3	C16	116.8°	117.9°
N3	RU1	N2	94.6°	153.4°
N3	RU1	RU2	91.4°	86.1°
N3	C16	N4	121.3°	122.4°
N3	C16	H12	119.3°	118.6°
N2	RU1	RU2	88.9°	78.7°
RU1	N2	C9	119.4°	111.9°
RU1	N2	C13	119.8°	118.2°
RU1	RU2	N4	88.6°	78.8°
RU1	RU2	N1	90.6°	81.4°
RU1	RU2	O5	165.4°	49.9°
C28	C21	C9	117.2°	120.5°
C28	C21	H17	121.4°	119.6°
C21	C28	H22	119.9°	119.6°
C21	C9	N2	119.0°	125.3°
C9	C21	H17	121.4°	119.9°
C9	N2	C13	119.6°	129.8°
C16	N4	RU2	119.6°	115.6°
C16	N4	C1	115.5°	128.1°
N4	C16	H12	119.4°	119.0°
N2	C13	N1	121.0°	121.7°
N2	C13	H8	119.5°	119.1°
RU2	N4	C1	119.9°	109.8°
N4	RU2	N1	96.4°	134.3°
N4	RU2	O5	103.5°	63.4°
N4	C1	C4	117.4°	116.4°
N4	C1	C11	120.5°	125.6°
N1	RU2	O5	96.0°	72.3°
RU2	N1	C13	119.5°	108.5°
RU2	N1	C5	122.7°	111.9°
RU2	O5	H25	109.5°	113.4°
RU2	O5	H9	109.5°	114.7°
C13	N1	C5	116.8°	128.8°
N1	C13	H8	119.5°	119.2°
C4	C1	C11	122.1°	117.9°
C1	C4	C12	119.1°	120.9°
C1	C4	H2	120.5°	119.4°
C1	C11	C17	118.7°	120.7°
C1	C11	H6	120.7°	119.9°
N1	C5	C15	120.6°	124.7°
N1	C5	C20	116.2°	117.1°
C4	C12	C6	117.5°	120.5°
C12	C4	H2	120.4°	119.7°
C4	C12	H7	121.3°	119.7°
C11	C17	C6	118.5°	120.5°
C17	C11	H6	120.7°	119.4°
C11	C17	H14	120.7°	119.7°
C15	C5	C20	123.0°	118.1°
C5	C15	C25	116.1°	120.6°
C5	C15	H11	122.0°	119.9°
C5	C20	C26	118.2°	120.7°
C5	C20	H16	120.9°	119.5°
C12	C6	C17	124.0°	119.6°
C12	C6	H3	118.0°	120.2°
C6	C12	H7	121.3°	119.9°
C17	C6	H3	118.0°	120.2°
C6	C17	H14	120.7°	119.9°
C15	C25	C29	122.4°	120.5°
C25	C15	H11	122.0°	119.5°
C15	C25	H19	118.8°	119.6°
C20	C26	C29	120.3°	120.5°
C26	C20	H16	120.9°	119.7°
C20	C26	H20	119.9°	119.6°
C25	C29	C26	119.8°	119.6°
C29	C25	H19	118.8°	120.0°
C25	C29	H23	120.1°	120.1°
C29	C26	H20	119.9°	119.9°
C26	C29	H23	120.1°	120.2°
H25	O5	H9	109.5°	106.3°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C10	C14	C18	H10	180.0°	180.0°
C14	C10	C7	H5	180.0°	179.6°
C10	C14	C18	C2	2.5°	0.0°
C14	C10	C7	C3	0.0°	1.0°
C14	C10	C7	H4	180.0°	179.6°
C10	C14	C18	H15	177.5°	180.0°
C18	C14	C10	C7	0.5°	0.3°
C14	C18	C2	H15	180.0°	179.9°
C14	C18	C2	C3	3.9°	0.4°
C14	C18	C2	H1	176.1°	179.8°
C18	C14	C10	H5	179.5°	179.9°
C10	C7	C3	H4	180.0°	178.6°
C10	C7	C3	C2	1.7°	1.3°
C10	C7	C3	N3	179.7°	179.8°
C7	C10	C14	H10	179.4°	179.7°
C18	C2	C3	C7	3.7°	1.0°
C18	C2	C3	H1	180.0°	179.8°
C18	C2	C3	N3	177.7°	179.6°
C2	C18	C14	H10	177.5°	180.0°
C7	C3	C2	N3	178.7°	178.6°
C7	C3	N3	RU1	130.3°	168.4°
C7	C3	N3	C16	54.4°	8.5°
C7	C3	C2	H1	176.3°	179.1°
C3	C7	C10	H5	180.0°	179.4°
C2	C3	N3	RU1	48.4°	13.1°
C2	C3	N3	C16	126.8°	170.0°
C2	C3	C7	H4	178.3°	179.9°
C3	C2	C18	H15	176.1°	179.6°
C3	N3	RU1	C16	175.2°	177.3°
C3	N3	RU1	N2	95.7°	93.4°
C3	N3	RU1	RU2	175.3°	148.3°
C3	N3	C16	N4	166.8°	174.8°
N3	C3	C2	H1	2.3°	0.6°
N3	C3	C7	H4	0.3°	1.6°
C3	N3	C16	H12	13.2°	6.1°
C30	C27	C23	H21	180.0°	179.7°
C27	C30	C28	H24	180.0°	180.0°
C30	C27	C23	C9	1.7°	1.0°
C27	C30	C28	C21	0.9°	0.0°
C30	C27	C23	H18	178.2°	179.5°
C27	C30	C28	H22	179.1°	180.0°
C23	C27	C30	C28	0.2°	0.3°
C27	C23	C9	H18	180.0°	178.6°
C27	C23	C9	C21	3.2°	1.4°
C27	C23	C9	N2	178.0°	179.7°
C23	C27	C30	H24	179.7°	179.8°
C30	C28	C21	H22	180.0°	180.0°
C30	C28	C21	C9	0.5°	0.5°
C30	C28	C21	H17	179.5°	180.0°
C28	C30	C27	H21	179.7°	180.0°
C23	C9	N2	RU1	68.3°	10.2°
C23	C9	C21	C28	2.6°	1.1°
C23	C9	C21	N2	178.8°	178.2°
C23	C9	N2	C13	123.9°	172.6°
C23	C9	C21	H17	177.5°	179.3°
C9	C23	C27	H21	178.3°	179.3°
N3	RU1	N2	RU2	91.3°	56.4°
N3	RU1	N2	C9	73.5°	85.9°
RU1	N3	C16	N4	17.4°	2.0°
N3	RU1	N2	C13	94.2°	91.6°
N3	RU1	RU2	N4	1.3°	28.3°
N3	RU1	RU2	N1	97.7°	166.9°
N3	RU1	RU2	O5	145.0°	92.9°
RU1	N3	C16	H12	162.6°	177.1°
C16	N3	RU1	N2	79.5°	83.9°
C16	N3	RU1	RU2	9.5°	29.0°
N3	C16	N4	H12	180.0°	179.1°
N3	C16	N4	RU2	16.4°	34.0°
N3	C16	N4	C1	171.5°	177.4°
RU1	N2	C9	C21	112.8°	168.0°
RU1	N2	C9	C13	167.8°	177.2°
N2	RU1	RU2	N4	93.3°	173.6°
N2	RU1	RU2	N1	3.1°	35.1°
N2	RU1	RU2	O5	120.4°	109.1°
RU1	N2	C13	N1	0.1°	0.3°
RU1	N2	C13	H8	179.9°	178.9°
RU2	RU1	N2	C9	164.9°	142.3°
RU1	RU2	N4	C16	6.8°	42.3°
RU2	RU1	N2	C13	2.9°	35.2°
RU1	RU2	N4	N1	90.5°	66.1°
RU1	RU2	N4	O5	171.7°	50.6°
RU1	RU2	N4	C1	160.9°	163.5°
RU1	RU2	N1	O5	167.0°	50.5°
RU1	RU2	N1	C13	4.6°	54.1°
RU1	RU2	N1	C5	163.7°	158.0°
RU1	RU2	O5	H25	180.0°	169.3°
RU1	RU2	O5	H9	60.0°	68.2°
C28	C21	C9	H17	180.0°	179.5°
C28	C21	C9	N2	178.7°	179.3°
C21	C28	C30	H24	179.1°	180.0°
C21	C9	N2	C13	54.9°	9.1°
C21	C9	C23	H18	176.7°	179.9°
C9	C21	C28	H22	179.5°	179.5°
C9	N2	C13	N1	167.6°	176.7°
C9	N2	C13	H8	12.4°	4.1°
N2	C9	C21	H17	1.3°	1.1°
N2	C9	C23	H18	2.0°	1.7°
C16	N4	RU2	C1	154.0°	154.2°
C16	N4	RU2	N1	83.6°	108.4°
C16	N4	RU2	O5	178.6°	92.9°
C16	N4	C1	C4	143.5°	172.3°
C16	N4	C1	C11	36.8°	10.0°
N2	C13	N1	RU2	3.5°	42.2°
N2	C13	N1	H8	180.0°	179.2°
N2	C13	N1	C5	165.4°	177.0°
N4	RU2	N1	O5	104.3°	14.5°
N4	RU2	N1	C13	84.1°	119.1°
RU2	N4	C1	C4	61.4°	37.6°
RU2	N4	C1	C11	118.3°	140.1°
N4	RU2	N1	C5	107.6°	93.0°
RU2	N4	C16	H12	163.6°	146.9°
N4	RU2	O5	H25	34.8°	71.5°
N4	RU2	O5	H9	85.3°	166.1°
C1	N4	RU2	N1	70.4°	97.4°
C1	N4	RU2	O5	27.4°	112.9°
N4	C1	C4	C11	179.7°	177.9°
N4	C1	C4	C12	178.7°	179.7°
N4	C1	C11	C17	176.7°	179.2°
N4	C1	C4	H2	1.3°	1.8°
N4	C1	C11	H6	3.4°	1.6°
C1	N4	C16	H12	8.5°	1.7°
RU2	N1	C13	C5	168.9°	140.8°
RU2	N1	C5	C15	117.7°	124.1°
RU2	N1	C5	C20	57.4°	59.3°
RU2	N1	C13	H8	176.5°	138.7°
N1	RU2	O5	H25	63.3°	96.9°
N1	RU2	O5	H9	176.6°	25.5°
O5	RU2	N1	C13	171.6°	104.6°
O5	RU2	N1	C5	3.3°	107.5°
RU2	O5	H25	H9	120.1°	127.0°
C13	N1	C5	C15	50.9°	15.7°
C13	N1	C5	C20	134.0°	160.9°
C1	C4	C12	H2	180.0°	178.4°
C4	C1	C11	C17	3.0°	1.6°
C1	C4	C12	C6	2.0°	1.3°
C4	C1	C11	H6	177.0°	179.3°
C1	C4	C12	H7	177.9°	179.1°
C11	C1	C4	C12	1.0°	1.8°
C1	C11	C17	H6	180.0°	179.2°
C1	C11	C17	C6	1.9°	0.7°
C11	C1	C4	H2	179.0°	179.7°
C1	C11	C17	H14	178.1°	179.3°
N1	C5	C15	C20	174.8°	176.6°
N1	C5	C15	C25	179.7°	179.3°
N1	C5	C20	C26	180.0°	179.2°
C5	N1	C13	H8	14.6°	2.1°
N1	C5	C15	H11	0.3°	3.3°
N1	C5	C20	H16	0.0°	1.7°
C4	C12	C6	H7	180.0°	179.6°
C4	C12	C6	C17	3.2°	0.3°
C4	C12	C6	H3	176.7°	179.6°
C11	C17	C6	C12	1.2°	0.1°
C11	C17	C6	H14	180.0°	180.0°
C11	C17	C6	H3	178.7°	179.9°
C5	C15	C25	H11	180.0°	177.5°
C15	C5	C20	C26	5.0°	2.4°
C5	C15	C25	C29	2.6°	1.8°
C15	C5	C20	H16	175.0°	178.6°
C5	C15	C25	H19	177.4°	178.6°
C20	C5	C15	C25	5.5°	2.7°
C5	C20	C26	H16	180.0°	179.0°
C5	C20	C26	C29	1.4°	1.1°
C20	C5	C15	H11	174.4°	179.8°
C5	C20	C26	H20	178.5°	179.1°
C12	C6	C17	H3	180.0°	180.0°
C6	C12	C4	H2	177.9°	179.7°
C12	C6	C17	H14	178.8°	179.9°
C6	C17	C11	H6	178.1°	179.9°
C17	C6	C12	H7	176.7°	179.9°
C15	C25	C29	H19	180.0°	179.6°
C15	C25	C29	C26	0.7°	0.4°
C15	C25	C29	H23	179.3°	179.5°
C20	C26	C29	C25	1.3°	0.1°
C20	C26	C29	H20	180.0°	179.8°
C20	C26	C29	H23	178.7°	179.8°
C25	C29	C26	H23	180.0°	179.9°
C29	C25	C15	H11	177.4°	179.2°
C25	C29	C26	H20	178.7°	179.9°
C29	C26	C20	H16	178.6°	179.8°
C26	C29	C25	H19	179.3°	179.9°
H1	C2	C18	H15	3.9°	0.2°
H2	C4	C12	H7	2.1°	0.7°
H3	C6	C12	H7	3.3°	0.0°
H3	C6	C17	H14	1.3°	0.1°
H4	C7	C10	H5	0.0°	0.8°
H5	C10	C14	H10	0.6°	0.1°
H6	C11	C17	H14	1.9°	0.1°
H10	C14	C18	H15	2.5°	0.0°
H11	C15	C25	H19	2.6°	1.1°
H16	C20	C26	H20	1.5°	0.0°
H17	C21	C28	H22	0.5°	0.0°
H18	C23	C27	H21	1.7°	0.7°
H19	C25	C29	H23	0.7°	0.1°
H20	C26	C29	H23	1.3°	0.0°
H21	C27	C30	H24	0.3°	0.0°
H22	C28	C30	H24	0.9°	0.0°

Release date:	2023-09-13
Definition date:	2023-06-27
Last modified:	2026-07-31
Release status:	REL
Processing site:	PDBE
Derived from:	8PH8