Summary Geometry PCM/PTM Related PDB entries

A1J46

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
RU1	RU2	sing	2.88Å	2.30Å
RU1	O1	sing	2.13Å	2.04Å
RU2	O2	sing	2.03Å	2.05Å
RU1	O3	sing	2.01Å	2.06Å
RU2	O4	sing	2.21Å	2.06Å
RU2	N2	sing	2.24Å	2.04Å
RU1	N1	sing	2.18Å	2.04Å
N2	C7	sing	1.34Å	1.33Å
N1	C7	doub	1.34Å	1.30Å
O3	C3	doub	1.25Å	1.25Å
O4	C3	sing	1.25Å	1.26Å
O1	C1	sing	1.25Å	1.25Å
O2	C1	doub	1.25Å	1.26Å
C9	C10	sing	1.40Å	1.37Å	Aromatic
N2	C15	sing	1.43Å	1.40Å
C1	C2	sing	1.50Å	1.49Å
C20	C15	sing	1.40Å	1.39Å	Aromatic
N1	C8	sing	1.43Å	1.45Å
C9	C8	doub	1.41Å	1.35Å	Aromatic
C8	C13	sing	1.40Å	1.43Å	Aromatic
C15	C16	doub	1.39Å	1.40Å	Aromatic
C16	C17	sing	1.38Å	1.37Å	Aromatic
C10	C11	doub	1.37Å	1.38Å	Aromatic
C9	C14	sing	1.51Å	1.42Å
C13	C12	doub	1.38Å	1.36Å	Aromatic
C11	C12	sing	1.37Å	1.40Å	Aromatic
C3	C4	sing	1.50Å	1.49Å
C17	C18	doub	1.37Å	1.38Å	Aromatic
C20	C19	doub	1.39Å	1.41Å	Aromatic
C18	C19	sing	1.38Å	1.38Å	Aromatic
C20	C21	sing	1.51Å	1.44Å
C7	H2	sing	0.94Å	1.08Å
C2	H5	sing	0.97Å	1.10Å
C2	H6	sing	0.97Å	1.10Å
C2	H7	sing	0.97Å	1.10Å
C10	H8	sing	0.94Å	1.08Å
C13	H9	sing	0.94Å	1.08Å
C16	H10	sing	0.94Å	1.08Å
C17	H11	sing	0.94Å	1.08Å
C11	H12	sing	0.94Å	1.08Å
C12	H13	sing	0.94Å	1.08Å
C4	H14	sing	0.97Å	1.10Å
C4	H15	sing	0.97Å	1.10Å
C4	H16	sing	0.97Å	1.10Å
C18	H17	sing	0.94Å	1.08Å
C19	H18	sing	0.94Å	1.08Å
C14	H19	sing	0.97Å	1.10Å
C14	H20	sing	0.97Å	1.10Å
C14	H21	sing	0.97Å	1.10Å
C21	H22	sing	0.97Å	1.10Å
C21	H23	sing	0.97Å	1.10Å
C21	H24	sing	0.97Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
RU2	RU1	O1	92.1°	80.2°
RU1	RU2	O2	85.2°	75.2°
RU2	RU1	O3	88.4°	75.8°
RU1	RU2	O4	89.0°	76.5°
RU1	RU2	N2	87.9°	76.4°
RU2	RU1	N1	92.3°	86.7°
O1	RU1	O3	86.3°	117.2°
O1	RU1	N1	93.0°	119.5°
RU1	O1	C1	116.6°	109.6°
O2	RU2	O4	86.1°	109.8°
O2	RU2	N2	93.7°	110.8°
RU2	O2	C1	123.0°	105.6°
O3	RU1	N1	179.0°	115.9°
RU1	O3	C3	120.0°	104.8°
O4	RU2	N2	176.9°	122.5°
RU2	O4	C3	119.3°	112.3°
RU2	N2	C7	119.8°	116.0°
RU2	N2	C15	130.2°	100.3°
RU1	N1	C7	116.2°	115.0°
RU1	N1	C8	124.9°	112.6°
N2	C7	N1	123.1°	123.3°
C7	N2	C15	107.7°	128.5°
N2	C7	H2	118.5°	118.3°
C7	N1	C8	117.3°	127.5°
N1	C7	H2	118.5°	118.4°
O3	C3	O4	123.3°	123.1°
O3	C3	C4	119.7°	118.9°
O4	C3	C4	117.0°	118.0°
O1	C1	O2	123.0°	123.0°
O1	C1	C2	117.1°	118.8°
O2	C1	C2	119.9°	118.2°
C10	C9	C8	120.5°	118.0°
C9	C10	C11	119.8°	121.9°
C10	C9	C14	120.3°	119.9°
C9	C10	H8	120.1°	119.0°
N2	C15	C20	118.3°	117.5°
N2	C15	C16	121.6°	123.3°
C1	C2	H5	109.5°	109.8°
C1	C2	H6	109.5°	109.7°
C1	C2	H7	109.4°	109.6°
C20	C15	C16	120.1°	119.1°
C15	C20	C19	119.5°	118.2°
C15	C20	C21	119.2°	121.4°
N1	C8	C9	120.6°	118.0°
N1	C8	C13	118.5°	122.9°
C9	C8	C13	121.0°	119.0°
C8	C9	C14	119.3°	122.0°
C8	C13	C12	118.3°	121.1°
C8	C13	H9	120.9°	119.7°
C15	C16	C17	119.4°	121.0°
C15	C16	H10	120.3°	119.7°
C16	C17	C18	121.5°	120.0°
C17	C16	H10	120.3°	119.2°
C16	C17	H11	119.3°	119.8°
C10	C11	C12	120.6°	119.7°
C11	C10	H8	120.1°	119.1°
C10	C11	H12	119.7°	120.1°
C9	C14	H19	109.5°	109.9°
C9	C14	H20	109.5°	110.0°
C9	C14	H21	109.4°	109.6°
C13	C12	C11	119.9°	120.2°
C12	C13	H9	120.8°	119.2°
C13	C12	H13	120.1°	119.8°
C12	C11	H12	119.7°	120.2°
C11	C12	H13	120.0°	120.1°
C3	C4	H14	109.5°	109.8°
C3	C4	H15	109.4°	109.6°
C3	C4	H16	109.5°	109.6°
C17	C18	C19	120.2°	119.8°
C18	C17	H11	119.3°	120.2°
C17	C18	H17	119.9°	120.2°
C20	C19	C18	119.2°	121.8°
C19	C20	C21	121.3°	120.3°
C20	C19	H18	120.4°	119.1°
C19	C18	H17	119.9°	120.1°
C18	C19	H18	120.4°	119.2°
C20	C21	H22	109.5°	110.0°
C20	C21	H23	109.4°	109.9°
C20	C21	H24	109.5°	109.5°
H5	C2	H6	109.5°	109.3°
H5	C2	H7	109.5°	109.2°
H6	C2	H7	109.5°	109.2°
H14	C4	H15	109.5°	109.3°
H14	C4	H16	109.5°	109.3°
H15	C4	H16	109.5°	109.3°
H19	C14	H20	109.5°	108.9°
H19	C14	H21	109.5°	109.4°
H20	C14	H21	109.5°	109.1°
H22	C21	H23	109.5°	108.7°
H22	C21	H24	109.5°	109.1°
H23	C21	H24	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
RU2	RU1	O1	O3	88.2°	68.4°
RU2	RU1	O1	N1	92.4°	80.6°
RU1	RU2	O2	O4	89.3°	69.4°
RU1	RU2	O2	N2	87.6°	68.9°
RU2	RU1	O3	N1	134.3°	79.2°
RU1	RU2	O4	N2	0.7°	63.9°
RU1	RU2	N2	C7	4.0°	43.5°
RU2	RU1	N1	C7	5.4°	5.8°
RU2	RU1	O3	C3	0.2°	59.9°
RU1	RU2	O4	C3	0.5°	11.1°
RU2	RU1	O1	C1	0.9°	1.0°
RU1	RU2	O2	C1	0.5°	53.8°
RU1	RU2	N2	C15	164.7°	174.0°
RU2	RU1	N1	C8	170.7°	151.6°
O1	RU1	RU2	O2	0.2°	25.3°
O1	RU1	O3	N1	42.0°	150.0°
O1	RU1	RU2	O4	86.3°	89.7°
O1	RU1	RU2	N2	93.7°	141.5°
O1	RU1	N1	C7	97.6°	82.6°
O1	RU1	O3	C3	92.0°	11.0°
RU1	O1	C1	O2	1.5°	50.1°
RU1	O1	C1	C2	178.9°	129.2°
O1	RU1	N1	C8	97.0°	74.8°
O2	RU2	RU1	O3	86.1°	146.8°
O2	RU2	O4	N2	86.0°	132.5°
O2	RU2	RU1	N1	93.2°	95.4°
O2	RU2	N2	C7	89.1°	24.6°
O2	RU2	O4	C3	84.8°	79.7°
RU2	O2	C1	O1	1.4°	86.4°
O2	RU2	N2	C15	110.2°	117.8°
RU2	O2	C1	C2	179.0°	92.8°
O3	RU1	RU2	O4	0.1°	31.8°
O3	RU1	RU2	N2	179.9°	97.0°
O3	RU1	N1	C7	139.6°	66.7°
RU1	O3	C3	O4	0.7°	81.4°
O3	RU1	O1	C1	87.4°	69.3°
O3	RU1	N1	C8	55.0°	135.9°
RU1	O3	C3	C4	179.5°	97.9°
O4	RU2	RU1	N1	179.4°	149.6°
O4	RU2	N2	C7	3.3°	107.5°
RU2	O4	C3	O3	0.8°	37.2°
O4	RU2	O2	C1	88.8°	15.6°
O4	RU2	N2	C15	164.0°	110.1°
RU2	O4	C3	C4	179.4°	142.1°
N2	RU2	RU1	N1	0.6°	20.8°
RU2	N2	C7	C15	164.7°	129.9°
RU2	N2	C7	N1	9.7°	58.6°
N2	RU2	O4	C3	1.2°	52.8°
N2	RU2	O2	C1	88.1°	122.7°
RU2	N2	C15	C20	152.3°	66.1°
RU2	N2	C15	C16	30.7°	109.4°
RU2	N2	C7	H2	170.3°	122.8°
RU1	N1	C7	N2	10.1°	28.8°
RU1	N1	C7	C8	166.5°	153.5°
N1	RU1	O3	C3	134.1°	139.1°
N1	RU1	O1	C1	93.3°	79.6°
RU1	N1	C8	C9	45.1°	49.7°
RU1	N1	C8	C13	134.3°	126.4°
RU1	N1	C7	H2	170.0°	152.6°
N2	C7	N1	H2	180.0°	178.6°
C7	N2	C15	C20	45.2°	158.4°
N2	C7	N1	C8	176.6°	177.7°
C7	N2	C15	C16	131.8°	26.1°
N1	C7	N2	C15	174.4°	171.5°
C7	N1	C8	C9	149.7°	156.4°
C7	N1	C8	C13	30.9°	27.6°
O3	C3	O4	C4	179.8°	179.3°
O3	C3	C4	H14	0.0°	3.7°
O3	C3	C4	H15	120.0°	123.8°
O3	C3	C4	H16	120.0°	116.3°
O4	C3	C4	H14	179.7°	175.6°
O4	C3	C4	H15	59.8°	55.6°
O4	C3	C4	H16	60.2°	64.3°
O1	C1	O2	C2	179.6°	179.3°
O1	C1	C2	H5	179.6°	2.7°
O1	C1	C2	H6	59.6°	122.8°
O1	C1	C2	H7	60.4°	117.2°
O2	C1	C2	H5	0.0°	178.0°
O2	C1	C2	H6	120.0°	57.9°
O2	C1	C2	H7	120.0°	62.1°
C10	C9	C8	N1	179.5°	179.3°
C10	C9	C8	C14	179.9°	177.0°
C10	C9	C8	C13	0.1°	3.1°
C9	C10	C11	H8	180.0°	179.6°
C9	C10	C11	C12	0.5°	0.5°
C9	C10	C11	H12	179.5°	179.4°
C10	C9	C14	H19	90.1°	135.9°
C10	C9	C14	H20	149.9°	16.0°
C10	C9	C14	H21	29.9°	103.9°
N2	C15	C20	C16	177.0°	175.7°
N2	C15	C16	C17	178.6°	178.5°
N2	C15	C20	C19	178.9°	179.1°
N2	C15	C20	C21	2.0°	3.9°
C15	N2	C7	H2	5.7°	7.1°
N2	C15	C16	H10	1.4°	2.9°
C1	C2	H5	H6	120.0°	120.3°
C1	C2	H5	H7	120.0°	120.2°
C1	C2	H6	H7	120.0°	120.2°
C20	C15	C16	C17	1.7°	3.1°
C15	C20	C19	C21	179.0°	177.0°
C15	C20	C19	C18	1.1°	2.3°
C20	C15	C16	H10	178.3°	178.4°
C15	C20	C19	H18	178.9°	178.3°
C15	C20	C21	H22	89.5°	163.8°
C15	C20	C21	H23	150.5°	44.1°
C15	C20	C21	H24	30.5°	76.3°
N1	C8	C9	C13	179.4°	176.2°
N1	C8	C9	C14	0.6°	3.7°
N1	C8	C13	C12	179.7°	178.8°
C8	N1	C7	H2	3.5°	0.9°
N1	C8	C13	H9	0.3°	2.6°
C8	C9	C10	C11	0.3°	2.0°
C9	C8	C13	C12	0.3°	2.8°
C8	C9	C10	H8	179.7°	178.4°
C9	C8	C13	H9	179.7°	178.6°
C8	C9	C14	H19	90.1°	41.1°
C8	C9	C14	H20	29.9°	160.9°
C8	C9	C14	H21	149.9°	79.1°
C13	C8	C9	C14	180.0°	179.8°
C8	C13	C12	H9	180.0°	178.6°
C8	C13	C12	C11	0.0°	1.3°
C8	C13	C12	H13	180.0°	178.9°
C15	C16	C17	H10	180.0°	178.6°
C15	C16	C17	C18	0.7°	1.4°
C16	C15	C20	C19	1.9°	3.4°
C16	C15	C20	C21	179.1°	179.6°
C15	C16	C17	H11	179.2°	178.8°
C16	C17	C18	H11	180.0°	179.9°
C16	C17	C18	C19	0.1°	0.1°
C16	C17	C18	H17	180.0°	179.9°
C11	C10	C9	C14	179.6°	179.1°
C10	C11	C12	C13	0.3°	0.1°
C10	C11	C12	H12	180.0°	179.9°
C10	C11	C12	H13	179.6°	179.9°
C14	C9	C10	H8	0.5°	1.2°
C9	C14	H19	H20	120.0°	120.6°
C9	C14	H19	H21	120.0°	120.3°
C9	C14	H20	H21	120.0°	120.2°
C13	C12	C11	H13	180.0°	179.8°
C13	C12	C11	H12	179.7°	179.8°
C12	C11	C10	H8	179.5°	179.9°
C11	C12	C13	H9	180.0°	179.9°
C3	C4	H14	H15	120.0°	120.2°
C3	C4	H14	H16	120.0°	120.2°
C3	C4	H15	H16	120.0°	120.1°
C17	C18	C19	C20	0.1°	0.6°
C17	C18	C19	H17	180.0°	179.9°
C18	C17	C16	H10	179.3°	179.9°
C17	C18	C19	H18	179.9°	180.0°
C20	C19	C18	H18	180.0°	179.4°
C20	C19	C18	H17	179.8°	179.4°
C19	C20	C21	H22	89.5°	13.1°
C19	C20	C21	H23	30.5°	132.8°
C19	C20	C21	H24	150.5°	106.8°
C18	C19	C20	C21	179.9°	179.3°
C19	C18	C17	H11	180.0°	180.0°
C21	C20	C19	H18	0.1°	1.3°
C20	C21	H22	H23	120.0°	120.4°
C20	C21	H22	H24	120.0°	120.2°
C20	C21	H23	H24	120.0°	120.4°
H5	C2	H6	H7	120.0°	119.4°
H8	C10	C11	H12	0.5°	0.2°
H9	C13	C12	H13	0.0°	0.3°
H10	C16	C17	H11	0.7°	0.2°
H11	C17	C18	H17	0.0°	0.1°
H12	C11	C12	H13	0.4°	0.0°
H14	C4	H15	H16	120.0°	119.5°
H17	C18	C19	H18	0.2°	0.0°
H19	C14	H20	H21	120.0°	119.3°
H22	C21	H23	H24	120.0°	119.2°

Release date:	2026-09-02
Definition date:	2026-04-14
Last modified:	2026-09-01
Release status:	REL
Processing site:	PDBE
Derived from:	29MY