Summary Geometry PCM/PTM Related PDB entries

YMQ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C4	C3	sing	1.50Å	1.49Å
O3	C3	sing	1.25Å	1.24Å
O3	RU1	sing	2.08Å	2.05Å
C3	O4	doub	1.25Å	1.26Å
C23	O7	sing	1.43Å	1.37Å
O1	RU1	sing	2.20Å	2.05Å
O1	C1	sing	1.26Å	1.27Å
RU1	N1	sing	1.74Å	2.04Å
RU1	RU2	sing	2.31Å	2.28Å
O7	C11	sing	1.38Å	1.43Å
C10	C11	doub	1.38Å	1.37Å	Aromatic
C10	C9	sing	1.38Å	1.37Å	Aromatic
O4	RU2	sing	2.01Å	2.05Å
C11	C12	sing	1.39Å	1.40Å	Aromatic
C9	C8	doub	1.39Å	1.35Å	Aromatic
C2	C1	sing	1.50Å	1.49Å
C1	O2	doub	1.25Å	1.27Å
C8	C13	sing	1.39Å	1.43Å	Aromatic
C8	N1	sing	1.43Å	1.45Å
C12	C13	doub	1.38Å	1.37Å	Aromatic
N1	C7	doub	1.35Å	1.30Å
O2	RU2	sing	2.00Å	2.05Å
RU2	N2	sing	1.61Å	2.04Å
C7	N2	sing	1.35Å	1.32Å
N2	C15	sing	1.43Å	1.40Å
C15	C16	doub	1.39Å	1.39Å	Aromatic
C15	C20	sing	1.39Å	1.40Å	Aromatic
C16	C17	sing	1.38Å	1.36Å	Aromatic
C20	C19	doub	1.38Å	1.41Å	Aromatic
C17	C18	doub	1.39Å	1.38Å	Aromatic
C19	C18	sing	1.38Å	1.38Å	Aromatic
C18	O8	sing	1.38Å	1.37Å
O8	C22	sing	1.43Å	1.42Å
C12	H1	sing	0.94Å	1.08Å
C22	H2	sing	0.97Å	1.10Å
C22	H3	sing	0.97Å	1.10Å
C22	H4	sing	0.97Å	1.10Å
C13	H5	sing	0.94Å	1.08Å
C23	H6	sing	0.97Å	1.10Å
C23	H7	sing	0.97Å	1.10Å
C23	H8	sing	0.97Å	1.10Å
C16	H9	sing	0.94Å	1.08Å
C17	H10	sing	0.94Å	1.08Å
C7	H12	sing	0.94Å	1.08Å
C2	H15	sing	0.97Å	1.10Å
C2	H16	sing	0.97Å	1.10Å
C2	H17	sing	0.97Å	1.10Å
C20	H18	sing	0.94Å	1.08Å
C9	H19	sing	0.94Å	1.08Å
C10	H20	sing	0.94Å	1.08Å
C4	H21	sing	0.97Å	1.10Å
C4	H22	sing	0.97Å	1.10Å
C4	H23	sing	0.97Å	1.10Å
C19	H24	sing	0.94Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C4	C3	O3	120.0°	118.1°
C4	C3	O4	116.0°	117.4°
C3	C4	H21	109.5°	109.8°
C3	C4	H22	109.5°	109.6°
C3	C4	H23	109.4°	109.6°
C3	O3	RU1	120.0°	109.2°
O3	C3	O4	124.0°	124.5°
O3	RU1	O1	88.1°	91.3°
O3	RU1	N1	177.8°	175.8°
O3	RU1	RU2	88.2°	88.2°
C3	O4	RU2	118.0°	115.0°
C23	O7	C11	126.9°	121.8°
O7	C23	H6	109.5°	109.5°
O7	C23	H7	109.5°	109.4°
O7	C23	H8	109.5°	109.5°
RU1	O1	C1	118.8°	118.3°
O1	RU1	N1	90.6°	90.0°
O1	RU1	RU2	89.5°	83.3°
O1	C1	C2	115.8°	117.7°
O1	C1	O2	123.2°	125.4°
N1	RU1	RU2	90.0°	87.9°
RU1	N1	C8	127.6°	111.9°
RU1	N1	C7	119.4°	117.0°
RU1	RU2	O4	89.8°	88.5°
RU1	RU2	O2	89.2°	94.0°
RU1	RU2	N2	89.6°	93.1°
O7	C11	C10	116.4°	111.6°
O7	C11	C12	126.0°	129.6°
C11	C10	C9	122.9°	120.7°
C10	C11	C12	117.2°	118.8°
C11	C10	H20	118.6°	119.7°
C10	C9	C8	120.4°	121.1°
C10	C9	H19	119.8°	119.3°
C9	C10	H20	118.6°	119.6°
O4	RU2	O2	89.1°	92.2°
O4	RU2	N2	175.3°	176.9°
C11	C12	C13	121.0°	120.3°
C11	C12	H1	119.5°	120.5°
C9	C8	C13	118.9°	117.9°
C9	C8	N1	120.1°	117.7°
C8	C9	H19	119.8°	119.6°
C2	C1	O2	121.0°	116.8°
C1	C2	H15	109.5°	109.8°
C1	C2	H16	109.5°	109.6°
C1	C2	H17	109.5°	109.6°
C1	O2	RU2	119.0°	116.4°
C13	C8	N1	120.8°	124.4°
C8	C13	C12	119.5°	121.2°
C8	C13	H5	120.3°	119.6°
C8	N1	C7	112.6°	130.5°
C13	C12	H1	119.5°	119.2°
C12	C13	H5	120.3°	119.1°
N1	C7	N2	120.5°	121.9°
N1	C7	H12	119.8°	119.0°
O2	RU2	N2	95.6°	90.3°
RU2	N2	C7	119.5°	117.4°
RU2	N2	C15	126.0°	110.5°
C7	N2	C15	114.1°	130.2°
N2	C7	H12	119.7°	119.1°
N2	C15	C16	118.5°	124.3°
N2	C15	C20	119.4°	117.8°
C16	C15	C20	122.0°	117.8°
C15	C16	C17	118.8°	121.2°
C15	C16	H9	120.6°	119.7°
C15	C20	C19	117.7°	121.2°
C15	C20	H18	121.1°	119.6°
C16	C17	C18	120.6°	120.3°
C17	C16	H9	120.6°	119.0°
C16	C17	H10	119.7°	119.2°
C20	C19	C18	119.3°	120.6°
C19	C20	H18	121.1°	119.2°
C20	C19	H24	120.4°	119.6°
C17	C18	C19	121.4°	118.8°
C17	C18	O8	125.1°	129.6°
C18	C17	H10	119.7°	120.5°
C19	C18	O8	113.5°	111.6°
C18	C19	H24	120.4°	119.8°
C18	O8	C22	126.3°	121.8°
O8	C22	H2	109.5°	109.5°
O8	C22	H3	109.5°	109.3°
O8	C22	H4	109.5°	109.5°
H2	C22	H3	109.4°	109.4°
H2	C22	H4	109.4°	109.6°
H3	C22	H4	109.5°	109.5°
H6	C23	H7	109.5°	109.5°
H6	C23	H8	109.4°	109.6°
H7	C23	H8	109.5°	109.4°
H15	C2	H16	109.4°	109.3°
H15	C2	H17	109.5°	109.2°
H16	C2	H17	109.5°	109.3°
H21	C4	H22	109.4°	109.3°
H21	C4	H23	109.5°	109.3°
H22	C4	H23	109.5°	109.2°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C4	C3	O3	O4	179.6°	179.5°
C4	C3	O3	RU1	175.8°	132.7°
C4	C3	O4	RU2	176.9°	140.8°
C3	C4	H21	H22	120.0°	120.3°
C3	C4	H21	H23	120.0°	120.3°
C3	C4	H22	H23	120.0°	120.1°
C3	O3	RU1	O1	87.0°	55.7°
C3	O3	RU1	N1	33.1°	51.7°
C3	O3	RU1	RU2	2.5°	27.6°
O3	C3	O4	RU2	2.7°	38.7°
O3	C3	C4	H21	0.0°	1.1°
O3	C3	C4	H22	120.0°	121.2°
O3	C3	C4	H23	120.0°	118.9°
RU1	O3	C3	O4	3.7°	46.8°
O3	RU1	O1	N1	178.2°	176.0°
O3	RU1	O1	RU2	88.2°	88.1°
O3	RU1	O1	C1	93.2°	93.7°
O3	RU1	N1	RU2	35.6°	24.1°
O3	RU1	RU2	O4	0.8°	8.6°
O3	RU1	N1	C8	142.2°	166.5°
O3	RU1	N1	C7	44.5°	21.9°
O3	RU1	RU2	O2	89.9°	100.7°
O3	RU1	RU2	N2	174.5°	168.8°
C3	O4	RU2	RU1	0.5°	8.9°
C3	O4	RU2	O2	88.7°	85.1°
C3	O4	RU2	N2	84.1°	131.7°
O4	C3	C4	H21	179.6°	178.4°
O4	C3	C4	H22	60.4°	58.3°
O4	C3	C4	H23	59.6°	61.5°
C23	O7	C11	C10	135.4°	178.8°
C23	O7	C11	C12	51.8°	1.4°
O7	C23	H6	H7	120.0°	119.9°
O7	C23	H6	H8	120.0°	120.1°
O7	C23	H7	H8	120.0°	120.0°
O1	RU1	N1	RU2	89.5°	83.3°
O1	RU1	RU2	O4	87.3°	82.9°
RU1	O1	C1	C2	175.3°	174.2°
RU1	O1	C1	O2	7.1°	5.8°
O1	RU1	N1	C8	88.3°	86.0°
O1	RU1	N1	C7	98.5°	85.6°
O1	RU1	RU2	O2	1.8°	9.2°
O1	RU1	RU2	N2	97.4°	99.7°
C1	O1	RU1	N1	85.0°	82.3°
C1	O1	RU1	RU2	5.0°	5.6°
O1	C1	C2	O2	177.6°	180.0°
O1	C1	O2	RU2	5.1°	16.3°
O1	C1	C2	H15	0.0°	1.4°
O1	C1	C2	H16	120.0°	121.5°
O1	C1	C2	H17	120.0°	118.6°
N1	RU1	RU2	O4	177.9°	173.1°
RU1	N1	C8	C9	72.7°	18.5°
RU1	N1	C8	C13	112.6°	159.4°
RU1	N1	C8	C7	173.6°	170.2°
N1	RU1	RU2	O2	88.8°	81.0°
N1	RU1	RU2	N2	6.8°	9.4°
RU1	N1	C7	N2	5.7°	8.6°
RU1	N1	C7	H12	174.2°	171.8°
RU1	RU2	O4	O2	89.2°	94.0°
RU1	RU2	O4	N2	83.6°	122.8°
RU1	RU2	O2	C1	0.8°	16.4°
RU2	RU1	N1	C8	177.8°	169.4°
RU2	RU1	N1	C7	9.0°	2.2°
RU1	RU2	O2	N2	89.6°	93.2°
RU1	RU2	N2	C7	7.1°	16.1°
RU1	RU2	N2	C15	179.7°	177.8°
O7	C11	C10	C12	173.4°	179.8°
O7	C11	C10	C9	178.7°	179.7°
O7	C11	C12	C13	177.2°	180.0°
O7	C11	C12	H1	2.8°	0.1°
C11	O7	C23	H6	180.0°	59.7°
C11	O7	C23	H7	60.0°	179.6°
C11	O7	C23	H8	60.0°	60.5°
O7	C11	C10	H20	1.3°	0.2°
C11	C10	C9	H20	180.0°	179.5°
C11	C10	C9	C8	1.9°	1.3°
C10	C11	C12	C13	4.5°	0.2°
C10	C11	C12	H1	175.5°	179.9°
C11	C10	C9	H19	178.1°	179.6°
C9	C10	C11	C12	5.3°	0.5°
C10	C9	C8	H19	180.0°	178.3°
C10	C9	C8	C13	2.3°	1.7°
C10	C9	C8	N1	177.1°	179.7°
O4	RU2	O2	C1	90.6°	72.3°
O4	RU2	O2	N2	179.4°	178.2°
O4	RU2	N2	C7	90.7°	138.8°
O4	RU2	N2	C15	96.8°	55.1°
C11	C12	C13	C8	0.6°	0.7°
C11	C12	C13	H1	180.0°	179.9°
C11	C12	C13	H5	179.5°	180.0°
C12	C11	C10	H20	174.7°	179.9°
C9	C8	C13	N1	174.7°	177.9°
C9	C8	C13	C12	2.9°	1.4°
C9	C8	N1	C7	113.6°	171.3°
C9	C8	C13	H5	177.0°	179.3°
C8	C9	C10	H20	178.1°	179.3°
C2	C1	O2	RU2	177.5°	163.7°
C1	C2	H15	H16	120.0°	120.3°
C1	C2	H15	H17	120.0°	120.2°
C1	C2	H16	H17	120.0°	120.1°
C1	O2	RU2	N2	88.8°	109.6°
O2	C1	C2	H15	177.6°	178.6°
O2	C1	C2	H16	57.6°	58.5°
O2	C1	C2	H17	62.3°	61.4°
C8	C13	C12	H5	180.0°	179.3°
C13	C8	N1	C7	61.1°	10.8°
C8	C13	C12	H1	179.4°	179.4°
C13	C8	C9	H19	177.7°	180.0°
N1	C8	C13	C12	177.7°	179.3°
C8	N1	C7	N2	180.0°	178.3°
N1	C8	C13	H5	2.3°	1.4°
C8	N1	C7	H12	0.0°	2.1°
N1	C8	C9	H19	2.9°	1.9°
N1	C7	N2	RU2	2.1°	19.1°
N1	C7	N2	H12	180.0°	179.6°
N1	C7	N2	C15	175.5°	178.0°
O2	RU2	N2	C7	82.0°	78.0°
O2	RU2	N2	C15	90.5°	88.2°
RU2	N2	C7	C15	173.4°	162.9°
RU2	N2	C15	C16	56.6°	156.0°
RU2	N2	C15	C20	123.7°	25.6°
RU2	N2	C7	H12	177.9°	161.3°
C7	N2	C15	C16	130.5°	7.7°
C7	N2	C15	C20	49.2°	170.6°
N2	C15	C16	C20	179.7°	178.4°
N2	C15	C16	C17	178.4°	179.8°
N2	C15	C20	C19	178.8°	179.6°
N2	C15	C16	H9	1.6°	1.6°
C15	N2	C7	H12	4.5°	1.6°
N2	C15	C20	H18	1.2°	0.7°
C15	C16	C17	H9	180.0°	178.6°
C16	C15	C20	C19	0.9°	1.1°
C15	C16	C17	C18	2.7°	1.0°
C15	C16	C17	H10	177.3°	179.3°
C16	C15	C20	H18	179.1°	179.2°
C20	C15	C16	C17	1.9°	1.4°
C15	C20	C19	H18	180.0°	179.7°
C15	C20	C19	C18	3.0°	0.5°
C20	C15	C16	H9	178.1°	180.0°
C15	C20	C19	H24	177.0°	179.6°
C16	C17	C18	H10	180.0°	179.6°
C16	C17	C18	C19	0.7°	0.4°
C16	C17	C18	O8	179.8°	179.8°
C20	C19	C18	C17	2.2°	0.2°
C20	C19	C18	H24	180.0°	179.9°
C20	C19	C18	O8	177.4°	180.0°
C17	C18	C19	O8	179.6°	179.8°
C17	C18	O8	C22	23.8°	0.5°
C18	C17	C16	H9	177.3°	179.7°
C17	C18	C19	H24	177.7°	179.9°
C19	C18	O8	C22	156.7°	179.3°
C19	C18	C17	H10	179.3°	180.0°
C18	C19	C20	H18	177.1°	179.8°
C18	O8	C22	H2	180.0°	60.4°
C18	O8	C22	H3	60.0°	179.8°
C18	O8	C22	H4	60.0°	59.8°
O8	C18	C17	H10	0.2°	0.2°
O8	C18	C19	H24	2.7°	0.1°
O8	C22	H2	H3	120.0°	119.8°
O8	C22	H2	H4	120.0°	120.2°
O8	C22	H3	H4	120.0°	120.0°
H1	C12	C13	H5	0.5°	0.1°
H2	C22	H3	H4	120.0°	120.1°
H6	C23	H7	H8	120.0°	120.1°
H9	C16	C17	H10	2.7°	0.7°
H15	C2	H16	H17	120.0°	119.5°
H18	C20	C19	H24	3.0°	0.1°
H19	C9	C10	H20	1.9°	1.0°
H21	C4	H22	H23	120.0°	119.5°

Release date:	2023-07-19
Definition date:	2023-06-19
Last modified:	2026-09-16
Release status:	REL
Processing site:	PDBE
Derived from:	8PFV