Summary Geometry PCM/PTM Related PDB entries

ZJK

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O5	RU2	sing	2.07Å	2.37Å
C29	C25	doub	1.37Å	1.37Å	Aromatic
C29	C26	sing	1.37Å	1.36Å	Aromatic
C25	C15	sing	1.38Å	1.40Å	Aromatic
O1	C8	doub	1.24Å	1.25Å
O1	RU2	sing	2.02Å	2.07Å
C26	C20	doub	1.38Å	1.39Å	Aromatic
C8	O2	sing	1.24Å	1.26Å
C15	C5	doub	1.40Å	1.39Å	Aromatic
C20	C5	sing	1.39Å	1.37Å	Aromatic
RU2	N1	sing	1.63Å	2.04Å
RU2	RU1	sing	2.47Å	2.33Å
RU2	N4	sing	1.63Å	2.04Å
C5	N1	sing	1.43Å	1.43Å
C12	C4	doub	1.38Å	1.38Å	Aromatic
C12	C6	sing	1.37Å	1.37Å	Aromatic
C4	C1	sing	1.39Å	1.39Å	Aromatic
O2	RU1	sing	2.03Å	2.09Å
N1	C13	doub	1.35Å	1.32Å
C6	C17	doub	1.37Å	1.36Å	Aromatic
C1	N4	sing	1.44Å	1.43Å
C1	C11	doub	1.40Å	1.38Å	Aromatic
RU1	N2	sing	1.63Å	2.04Å
RU1	N3	sing	1.64Å	2.05Å
C13	N2	sing	1.35Å	1.31Å
N4	C16	sing	1.36Å	1.34Å
C17	C11	sing	1.38Å	1.38Å	Aromatic
N2	C9	sing	1.44Å	1.42Å
C23	C9	doub	1.40Å	1.38Å	Aromatic
C23	C27	sing	1.38Å	1.40Å	Aromatic
C16	N3	doub	1.36Å	1.31Å
C9	C21	sing	1.39Å	1.38Å	Aromatic
N3	C3	sing	1.44Å	1.44Å
C27	C30	doub	1.37Å	1.38Å	Aromatic
C7	C3	doub	1.39Å	1.38Å	Aromatic
C7	C10	sing	1.38Å	1.38Å	Aromatic
C3	C2	sing	1.40Å	1.40Å	Aromatic
C21	C28	doub	1.38Å	1.37Å	Aromatic
C30	C28	sing	1.37Å	1.36Å	Aromatic
C10	C14	doub	1.37Å	1.37Å	Aromatic
C2	C18	doub	1.38Å	1.39Å	Aromatic
C14	C18	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
C8	H5	sing	0.96Å	1.08Å
C10	H7	sing	0.94Å	1.08Å
C11	H8	sing	0.94Å	1.08Å
C12	H9	sing	0.94Å	1.08Å
C13	H10	sing	0.94Å	1.08Å
C14	H12	sing	0.94Å	1.08Å
C15	H13	sing	0.94Å	1.08Å
C16	H14	sing	0.94Å	1.08Å
C17	H16	sing	0.94Å	1.08Å
C18	H17	sing	0.94Å	1.08Å
C20	H18	sing	0.93Å	1.08Å
C21	H19	sing	0.93Å	1.08Å
C23	H20	sing	0.94Å	1.08Å
C25	H21	sing	0.94Å	1.08Å
C26	H22	sing	0.94Å	1.08Å
C27	H23	sing	0.94Å	1.08Å
C28	H24	sing	0.94Å	1.08Å
C29	H25	sing	0.94Å	1.08Å
C30	H26	sing	0.94Å	1.08Å
O5	H27	sing	0.86Å	0.95Å
H6	O5	sing	0.86Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O5	RU2	O1	77.7°	73.9°
O5	RU2	N1	100.6°	104.0°
O5	RU2	RU1	165.7°	125.8°
O5	RU2	N4	100.3°	127.6°
RU2	O5	H27	109.5°	118.1°
RU2	O5	H6	109.5°	118.2°
C25	C29	C26	117.5°	119.4°
C29	C25	C15	120.6°	120.6°
C29	C25	H21	119.7°	119.9°
C25	C29	H25	121.2°	120.3°
C29	C26	C20	122.3°	120.6°
C29	C26	H22	118.8°	119.8°
C26	C29	H25	121.3°	120.3°
C25	C15	C5	122.0°	121.0°
C25	C15	H13	119.0°	119.1°
C15	C25	H21	119.7°	119.6°
C8	O1	RU2	117.0°	110.7°
O1	C8	O2	126.5°	126.3°
O1	C8	H5	116.7°	116.8°
O1	RU2	N1	177.6°	170.9°
O1	RU2	RU1	90.0°	83.7°
O1	RU2	N4	90.5°	77.2°
C26	C20	C5	121.2°	121.2°
C26	C20	H18	119.4°	119.4°
C20	C26	H22	118.8°	119.6°
C8	O2	RU1	118.5°	111.7°
O2	C8	H5	116.7°	116.9°
C15	C5	C20	116.3°	117.2°
C15	C5	N1	120.2°	123.8°
C5	C15	H13	119.0°	119.9°
C20	C5	N1	123.5°	118.9°
C5	C20	H18	119.4°	119.4°
N1	RU2	RU1	91.5°	90.8°
N1	RU2	N4	91.5°	110.3°
RU2	N1	C5	124.8°	122.6°
RU2	N1	C13	116.0°	115.9°
RU1	RU2	N4	86.9°	92.5°
RU2	RU1	O2	87.3°	87.3°
RU2	RU1	N2	88.3°	87.1°
RU2	RU1	N3	92.6°	84.8°
RU2	N4	C1	118.8°	124.5°
RU2	N4	C16	121.3°	109.3°
C5	N1	C13	117.8°	120.5°
C4	C12	C6	124.7°	120.6°
C12	C4	C1	121.0°	121.1°
C12	C4	H2	119.5°	119.5°
C4	C12	H9	117.6°	119.5°
C12	C6	C17	114.3°	119.4°
C12	C6	H3	122.8°	120.3°
C6	C12	H9	117.7°	119.9°
C4	C1	N4	124.6°	117.7°
C4	C1	C11	113.4°	117.3°
C1	C4	H2	119.5°	119.5°
O2	RU1	N2	170.7°	159.6°
O2	RU1	N3	95.4°	89.6°
N1	C13	N2	124.3°	126.2°
N1	C13	H10	117.9°	116.6°
C6	C17	C11	121.5°	120.5°
C17	C6	H3	122.8°	120.3°
C6	C17	H16	119.2°	119.9°
N4	C1	C11	121.9°	125.0°
C1	N4	C16	118.8°	123.6°
C1	C11	C17	124.9°	121.1°
C1	C11	H8	117.5°	120.1°
N2	RU1	N3	92.9°	109.4°
RU1	N2	C13	119.5°	119.7°
RU1	N2	C9	121.1°	117.2°
RU1	N3	C16	115.9°	116.1°
RU1	N3	C3	126.0°	117.6°
C13	N2	C9	119.3°	122.2°
N2	C13	H10	117.8°	117.0°
N4	C16	N3	122.1°	124.1°
N4	C16	H14	119.0°	117.9°
C17	C11	H8	117.6°	118.8°
C11	C17	H16	119.2°	119.6°
N2	C9	C23	125.5°	125.4°
N2	C9	C21	117.0°	117.5°
C9	C23	C27	119.8°	121.1°
C23	C9	C21	117.5°	117.1°
C9	C23	H20	120.1°	120.1°
C23	C27	C30	122.8°	120.5°
C27	C23	H20	120.1°	118.8°
C23	C27	H23	118.6°	119.6°
C16	N3	C3	115.6°	123.4°
N3	C16	H14	119.0°	117.9°
C9	C21	C28	121.3°	121.3°
C9	C21	H19	119.3°	119.3°
N3	C3	C7	118.1°	118.1°
N3	C3	C2	125.3°	124.8°
C27	C30	C28	115.7°	119.4°
C30	C27	H23	118.6°	119.9°
C27	C30	H26	122.2°	120.3°
C3	C7	C10	122.3°	121.2°
C7	C3	C2	116.5°	117.1°
C3	C7	H4	118.9°	119.5°
C7	C10	C14	121.7°	120.6°
C10	C7	H4	118.8°	119.3°
C7	C10	H7	119.1°	119.6°
C3	C2	C18	119.7°	121.1°
C3	C2	H1	120.1°	120.0°
C21	C28	C30	122.8°	120.5°
C28	C21	H19	119.4°	119.4°
C21	C28	H24	118.6°	119.6°
C30	C28	H24	118.6°	119.9°
C28	C30	H26	122.1°	120.3°
C10	C14	C18	116.2°	119.4°
C14	C10	H7	119.1°	119.9°
C10	C14	H12	121.9°	120.3°
C2	C18	C14	123.4°	120.6°
C18	C2	H1	120.1°	118.9°
C2	C18	H17	118.3°	119.6°
C18	C14	H12	121.9°	120.3°
C14	C18	H17	118.3°	119.8°
H27	O5	H6	109.5°	108.6°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O5	RU2	O1	C8	170.7°	94.5°
O5	RU2	O1	N1	44.1°	77.5°
O5	RU2	O1	RU1	172.7°	130.1°
O5	RU2	O1	N4	100.4°	135.9°
O5	RU2	N1	RU1	172.3°	127.3°
O5	RU2	N1	N4	100.7°	139.8°
O5	RU2	RU1	N4	120.8°	141.7°
O5	RU2	N1	C5	0.4°	36.5°
O5	RU2	RU1	O2	26.3°	50.6°
O5	RU2	N1	C13	166.7°	132.1°
O5	RU2	N4	C1	5.5°	40.5°
O5	RU2	RU1	N2	145.5°	109.8°
O5	RU2	RU1	N3	121.6°	140.5°
O5	RU2	N4	C16	162.1°	157.6°
RU2	O5	H27	H6	120.0°	138.2°
C25	C29	C26	H25	180.0°	179.9°
C29	C25	C15	H21	180.0°	179.5°
C25	C29	C26	C20	2.5°	0.3°
C29	C25	C15	C5	0.0°	2.2°
C29	C25	C15	H13	180.0°	179.1°
C25	C29	C26	H22	177.5°	180.0°
C26	C29	C25	C15	1.2°	0.5°
C29	C26	C20	H22	180.0°	179.7°
C29	C26	C20	C5	2.6°	1.8°
C29	C26	C20	H18	177.4°	179.8°
C26	C29	C25	H21	178.8°	179.9°
C25	C15	C5	H13	180.0°	176.8°
C25	C15	C5	C20	0.1°	3.5°
C25	C15	C5	N1	179.9°	178.7°
C15	C25	C29	H25	178.8°	179.5°
O1	C8	O2	H5	180.0°	180.0°
C8	O1	RU2	N1	126.7°	17.0°
C8	O1	RU2	RU1	1.9°	35.7°
C8	O1	RU2	N4	88.8°	129.7°
O1	C8	O2	RU1	8.9°	40.0°
RU2	O1	C8	O2	4.1°	57.8°
O1	RU2	N1	RU1	128.6°	52.2°
O1	RU2	N1	N4	144.5°	145.1°
O1	RU2	RU1	N4	90.5°	76.8°
O1	RU2	N1	C5	43.3°	111.6°
O1	RU2	RU1	O2	4.0°	14.3°
O1	RU2	N1	C13	123.0°	56.9°
O1	RU2	N4	C1	83.0°	98.2°
O1	RU2	RU1	N2	175.8°	174.7°
O1	RU2	RU1	N3	91.3°	75.6°
O1	RU2	N4	C16	84.5°	100.0°
RU2	O1	C8	H5	175.9°	122.2°
O1	RU2	O5	H27	180.0°	46.7°
O1	RU2	O5	H6	60.0°	179.2°
C26	C20	C5	C15	1.3°	3.3°
C26	C20	C5	H18	180.0°	178.0°
C26	C20	C5	N1	178.7°	178.7°
C20	C26	C29	H25	177.5°	179.8°
C8	O2	RU1	RU2	7.7°	4.0°
C8	O2	RU1	N2	69.6°	70.2°
C8	O2	RU1	N3	84.6°	88.8°
C15	C5	C20	N1	180.0°	175.4°
C15	C5	N1	RU2	127.6°	143.6°
C15	C5	N1	C13	38.5°	24.4°
C15	C5	C20	H18	178.7°	178.7°
C5	C15	C25	H21	180.0°	178.2°
C20	C5	N1	RU2	52.5°	41.3°
C20	C5	N1	C13	141.5°	150.7°
C20	C5	C15	H13	179.9°	179.6°
C5	C20	C26	H22	177.4°	178.5°
N1	RU2	RU1	N4	91.4°	110.4°
RU2	N1	C5	C13	166.0°	168.0°
N1	RU2	RU1	O2	174.1°	158.5°
N1	RU2	N4	C1	95.6°	87.1°
N1	RU2	RU1	N2	2.3°	1.8°
N1	RU2	RU1	N3	90.6°	111.6°
RU2	N1	C13	N2	7.7°	7.8°
N1	RU2	N4	C16	96.8°	74.7°
RU2	N1	C13	H10	172.3°	166.0°
N1	RU2	O5	H27	1.7°	142.4°
N1	RU2	O5	H6	121.7°	8.3°
RU1	RU2	N1	C5	171.9°	163.8°
RU2	RU1	O2	N2	61.9°	74.1°
RU2	RU1	O2	N3	92.3°	84.9°
RU1	RU2	N1	C13	5.6°	4.8°
RU1	RU2	N4	C1	173.0°	178.9°
RU2	RU1	N2	N3	92.5°	83.5°
RU2	RU1	N2	C13	0.5°	1.4°
RU1	RU2	N4	C16	5.5°	17.1°
RU2	RU1	N2	C9	178.2°	168.1°
RU2	RU1	N3	C16	7.2°	20.2°
RU2	RU1	N3	C3	168.5°	178.2°
RU1	RU2	O5	H27	148.9°	116.2°
RU1	RU2	O5	H6	91.1°	109.6°
N4	RU2	N1	C5	101.2°	103.3°
RU2	N4	C1	C4	61.7°	37.6°
N4	RU2	RU1	O2	94.5°	91.1°
N4	RU2	N1	C13	92.6°	88.2°
RU2	N4	C1	C16	167.9°	159.3°
RU2	N4	C1	C11	114.0°	142.6°
N4	RU2	RU1	N2	93.7°	108.6°
N4	RU2	RU1	N3	0.8°	1.2°
RU2	N4	C16	N3	13.0°	40.9°
RU2	N4	C16	H14	167.1°	134.3°
N4	RU2	O5	H27	91.8°	12.3°
N4	RU2	O5	H6	28.2°	121.8°
C5	N1	C13	N2	175.0°	161.0°
C5	N1	C13	H10	5.0°	25.2°
N1	C5	C15	H13	0.1°	4.5°
N1	C5	C20	H18	1.3°	3.3°
C4	C12	C6	H9	180.0°	179.8°
C12	C4	C1	H2	180.0°	179.9°
C4	C12	C6	C17	0.9°	0.1°
C12	C4	C1	N4	179.1°	180.0°
C12	C4	C1	C11	3.1°	0.2°
C4	C12	C6	H3	179.1°	179.9°
C6	C12	C4	C1	0.9°	0.3°
C12	C6	C17	H3	180.0°	180.0°
C12	C6	C17	C11	0.2°	0.0°
C6	C12	C4	H2	179.1°	179.8°
C12	C6	C17	H16	179.8°	179.9°
C4	C1	N4	C11	175.7°	179.8°
C4	C1	N4	C16	106.2°	163.1°
C4	C1	C11	C17	3.9°	0.1°
C4	C1	C11	H8	176.1°	180.0°
C1	C4	C12	H9	179.0°	179.9°
O2	RU1	N2	N3	154.3°	157.7°
O2	RU1	N2	C13	61.4°	75.6°
O2	RU1	N2	C9	116.4°	93.9°
O2	RU1	N3	C16	80.4°	107.5°
O2	RU1	N3	C3	81.0°	90.9°
RU1	O2	C8	H5	171.1°	140.0°
N1	C13	N2	RU1	5.3°	5.9°
N1	C13	N2	H10	180.0°	173.7°
N1	C13	N2	C9	176.9°	163.1°
C6	C17	C11	C1	2.3°	0.0°
C6	C17	C11	H16	180.0°	179.9°
C6	C17	C11	H8	177.7°	179.9°
C17	C6	C12	H9	179.2°	179.9°
N4	C1	C11	C17	180.0°	179.9°
C1	N4	C16	N3	179.5°	157.1°
N4	C1	C4	H2	0.9°	0.1°
N4	C1	C11	H8	0.0°	0.2°
C1	N4	C16	H14	0.5°	27.8°
C11	C1	N4	C16	78.1°	16.7°
C1	C11	C17	H8	180.0°	180.0°
C11	C1	C4	H2	176.9°	179.9°
C1	C11	C17	H16	177.7°	180.0°
RU1	N2	C13	C9	177.8°	169.0°
RU1	N2	C9	C23	108.4°	160.1°
N2	RU1	N3	C16	95.6°	64.8°
RU1	N2	C9	C21	73.6°	20.7°
N2	RU1	N3	C3	103.0°	96.7°
RU1	N2	C13	H10	174.7°	167.8°
N3	RU1	N2	C13	93.0°	82.1°
RU1	N3	C16	N4	13.2°	44.8°
N3	RU1	N2	C9	89.3°	108.4°
RU1	N3	C16	C3	163.3°	160.4°
RU1	N3	C3	C7	49.0°	37.0°
RU1	N3	C3	C2	133.2°	143.5°
RU1	N3	C16	H14	166.8°	130.3°
C13	N2	C9	C23	69.3°	9.2°
C13	N2	C9	C21	108.7°	170.0°
N4	C16	N3	H14	180.0°	175.1°
N4	C16	N3	C3	176.6°	154.8°
C11	C17	C6	H3	179.7°	180.0°
N2	C9	C23	C21	178.0°	179.2°
N2	C9	C23	C27	178.2°	179.7°
N2	C9	C21	C28	178.0°	179.6°
C9	N2	C13	H10	3.1°	23.2°
N2	C9	C21	H19	2.0°	0.7°
N2	C9	C23	H20	1.8°	1.1°
C9	C23	C27	H20	180.0°	179.2°
C9	C23	C27	C30	1.4°	0.5°
C23	C9	C21	C28	0.2°	0.3°
C23	C9	C21	H19	179.8°	180.0°
C9	C23	C27	H23	178.6°	179.8°
C27	C23	C9	C21	0.1°	0.5°
C23	C27	C30	H23	180.0°	179.8°
C23	C27	C30	C28	3.1°	0.1°
C23	C27	C30	H26	176.9°	179.9°
C16	N3	C3	C7	112.4°	162.8°
C16	N3	C3	C2	65.5°	16.6°
C9	C21	C28	H19	180.0°	179.7°
C9	C21	C28	C30	2.1°	0.0°
C21	C9	C23	H20	179.8°	179.7°
C9	C21	C28	H24	177.9°	179.8°
N3	C3	C7	C2	178.0°	179.5°
N3	C3	C7	C10	179.8°	179.8°
N3	C3	C2	C18	179.5°	179.7°
N3	C3	C2	H1	0.5°	0.2°
N3	C3	C7	H4	0.2°	1.1°
C3	N3	C16	H14	3.5°	30.1°
C27	C30	C28	C21	3.5°	0.1°
C27	C30	C28	H26	180.0°	180.0°
C30	C27	C23	H20	178.6°	179.6°
C27	C30	C28	H24	176.6°	179.9°
C3	C7	C10	H4	180.0°	178.7°
C3	C7	C10	C14	1.2°	0.7°
C7	C3	C2	C18	2.7°	0.3°
C7	C3	C2	H1	177.3°	179.6°
C3	C7	C10	H7	178.8°	179.6°
C10	C7	C3	C2	1.8°	0.7°
C7	C10	C14	H7	180.0°	179.7°
C7	C10	C14	C18	3.0°	0.3°
C7	C10	C14	H12	177.0°	179.7°
C3	C2	C18	H1	180.0°	179.9°
C3	C2	C18	C14	0.8°	0.1°
C2	C3	C7	H4	178.2°	179.4°
C3	C2	C18	H17	179.2°	179.9°
C21	C28	C30	H24	180.0°	179.8°
C21	C28	C30	H26	176.5°	179.9°
C30	C28	C21	H19	177.8°	179.7°
C28	C30	C27	H23	176.9°	179.9°
C10	C14	C18	C2	2.1°	0.1°
C10	C14	C18	H12	180.0°	180.0°
C14	C10	C7	H4	178.8°	179.4°
C10	C14	C18	H17	177.9°	179.9°
C2	C18	C14	H17	180.0°	179.8°
C2	C18	C14	H12	177.9°	179.9°
C14	C18	C2	H1	179.2°	180.0°
C18	C14	C10	H7	176.9°	180.0°
H1	C2	C18	H17	0.8°	0.2°
H2	C4	C12	H9	1.0°	0.0°
H3	C6	C12	H9	0.9°	0.1°
H3	C6	C17	H16	0.2°	0.0°
H4	C7	C10	H7	1.2°	0.9°
H7	C10	C14	H12	3.0°	0.0°
H8	C11	C17	H16	2.3°	0.0°
H12	C14	C18	H17	2.0°	0.1°
H13	C15	C25	H21	0.0°	1.4°
H18	C20	C26	H22	2.6°	0.5°
H19	C21	C28	H24	2.1°	0.1°
H20	C23	C27	H23	1.4°	0.6°
H21	C25	C29	H25	1.2°	0.0°
H22	C26	C29	H25	2.5°	0.0°
H23	C27	C30	H26	3.1°	0.1°
H24	C28	C30	H26	3.5°	0.1°

Release date:	2023-09-13
Definition date:	2023-06-27
Last modified:	2026-07-31
Release status:	REL
Processing site:	PDBE
Derived from:	8PH5