Summary Geometry PCM/PTM Related PDB entries

YWR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C22	O7	sing	1.43Å	1.42Å
O7	C18	sing	1.38Å	1.38Å
C19	C18	doub	1.39Å	1.38Å	Aromatic
C19	C20	sing	1.38Å	1.42Å	Aromatic
C18	C17	sing	1.39Å	1.38Å	Aromatic
C20	C15	doub	1.39Å	1.39Å	Aromatic
C17	C16	doub	1.38Å	1.37Å	Aromatic
C15	C16	sing	1.39Å	1.40Å	Aromatic
C15	N2	sing	1.43Å	1.42Å
C10	C9	doub	1.38Å	1.38Å	Aromatic
C10	C11	sing	1.39Å	1.37Å	Aromatic
C9	C8	sing	1.39Å	1.35Å	Aromatic
O8	C11	sing	1.38Å	1.43Å
O8	C23	sing	1.43Å	1.37Å
C7	N2	sing	1.34Å	1.32Å
C7	N1	doub	1.35Å	1.31Å
C11	C12	doub	1.38Å	1.39Å	Aromatic
O9	C1	doub	1.28Å	1.48Å
N2	RU2	sing	1.90Å	2.02Å
C8	N1	sing	1.43Å	1.45Å
C8	C13	doub	1.39Å	1.43Å	Aromatic
O2	C1	sing	1.28Å	1.26Å
O2	RU2	sing	2.40Å	2.08Å
C1	O1	sing	1.28Å	1.26Å
N1	RU1	sing	2.66Å	2.04Å
C12	C13	sing	1.38Å	1.36Å	Aromatic
O1	RU1	sing	1.96Å	2.05Å
RU2	RU1	sing	2.53Å	2.27Å
RU2	O6	sing	2.41Å	2.05Å
RU2	O4	sing	2.12Å	2.04Å
RU1	O5	sing	2.03Å	2.03Å
RU1	O3	sing	2.37Å	2.08Å
O6	C5	sing	1.28Å	1.28Å
O4	C3	sing	1.27Å	1.28Å
O5	C5	sing	1.27Å	1.26Å
C5	O11	doub	1.28Å	1.51Å
O3	C3	sing	1.28Å	1.25Å
C3	O10	doub	1.28Å	1.50Å
C7	H1	sing	0.94Å	1.08Å
C23	H3	sing	0.97Å	1.10Å
C23	H4	sing	0.97Å	1.10Å
C23	H5	sing	0.97Å	1.10Å
C20	H6	sing	0.94Å	1.08Å
C9	H7	sing	0.94Å	1.08Å
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
C22	H12	sing	0.97Å	1.10Å
C22	H13	sing	0.97Å	1.10Å
C22	H14	sing	0.97Å	1.10Å
C12	H15	sing	0.94Å	1.08Å
C19	H16	sing	0.94Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C22	O7	C18	117.1°	121.8°
O7	C22	H12	109.5°	109.5°
O7	C22	H13	109.5°	109.4°
O7	C22	H14	109.5°	109.5°
O7	C18	C19	121.6°	111.8°
O7	C18	C17	119.1°	129.5°
C18	C19	C20	118.3°	120.6°
C19	C18	C17	119.3°	118.8°
C18	C19	H16	120.9°	119.8°
C19	C20	C15	121.7°	121.2°
C19	C20	H6	119.1°	119.4°
C20	C19	H16	120.9°	119.7°
C18	C17	C16	122.6°	120.3°
C18	C17	H11	118.7°	120.5°
C20	C15	C16	118.2°	118.0°
C20	C15	N2	121.6°	117.2°
C15	C20	H6	119.2°	119.4°
C17	C16	C15	119.7°	121.2°
C17	C16	H10	120.2°	119.1°
C16	C17	H11	118.7°	119.2°
C16	C15	N2	120.2°	124.8°
C15	C16	H10	120.2°	119.7°
C15	N2	C7	123.4°	130.5°
C15	N2	RU2	115.9°	117.4°
C9	C10	C11	115.7°	120.3°
C10	C9	C8	119.2°	121.3°
C10	C9	H7	120.4°	119.2°
C9	C10	H8	122.1°	119.2°
C10	C11	O8	112.5°	129.8°
C10	C11	C12	127.0°	118.7°
C11	C10	H8	122.1°	120.5°
C9	C8	N1	122.1°	116.7°
C9	C8	C13	123.0°	117.8°
C8	C9	H7	120.4°	119.4°
C11	O8	C23	117.0°	121.8°
O8	C11	C12	118.6°	111.4°
O8	C23	H3	109.5°	109.5°
O8	C23	H4	109.5°	109.5°
O8	C23	H5	109.5°	109.5°
N2	C7	N1	121.7°	122.1°
C7	N2	RU2	119.8°	110.7°
N2	C7	H1	119.1°	118.8°
C7	N1	C8	114.2°	128.4°
C7	N1	RU1	117.3°	125.3°
N1	C7	H1	119.2°	119.0°
C11	C12	C13	115.4°	120.6°
C11	C12	H15	122.3°	119.7°
O9	C1	O2	120.1°	119.7°
O9	C1	O1	113.0°	119.9°
N2	RU2	O2	90.3°	106.7°
N2	RU2	RU1	89.6°	114.4°
N2	RU2	O6	92.7°	87.7°
N2	RU2	O4	178.7°	128.0°
N1	C8	C13	114.9°	125.5°
C8	N1	RU1	126.2°	106.3°
C8	C13	C12	118.4°	121.2°
C8	C13	H9	120.8°	119.8°
C1	O2	RU2	119.0°	125.4°
O2	C1	O1	126.7°	120.4°
O2	RU2	RU1	86.9°	64.8°
O2	RU2	O6	175.3°	115.6°
O2	RU2	O4	90.9°	123.1°
C1	O1	RU1	114.9°	95.2°
N1	RU1	O1	89.7°	109.6°
N1	RU1	RU2	91.0°	65.7°
N1	RU1	O5	91.1°	121.6°
N1	RU1	O3	178.7°	119.9°
C12	C13	H9	120.8°	119.1°
C13	C12	H15	122.3°	119.6°
O1	RU1	RU2	92.4°	108.8°
O1	RU1	O5	178.2°	125.7°
O1	RU1	O3	89.0°	80.7°
RU1	RU2	O6	89.5°	52.6°
RU1	RU2	O4	90.0°	100.6°
RU2	RU1	O5	89.3°	107.6°
RU2	RU1	O3	88.8°	55.4°
O6	RU2	O4	86.0°	84.3°
RU2	O6	C5	117.6°	123.0°
RU2	O4	C3	118.4°	95.1°
O5	RU1	O3	90.2°	88.5°
RU1	O5	C5	119.4°	92.9°
RU1	O3	C3	118.4°	121.1°
O6	C5	O5	122.8°	118.8°
O6	C5	O11	116.2°	120.7°
O4	C3	O3	124.1°	118.3°
O4	C3	O10	111.4°	120.9°
O5	C5	O11	121.0°	120.5°
O3	C3	O10	124.4°	120.9°
H3	C23	H4	109.5°	109.4°
H3	C23	H5	109.4°	109.5°
H4	C23	H5	109.5°	109.4°
H12	C22	H13	109.5°	109.4°
H12	C22	H14	109.4°	109.5°
H13	C22	H14	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C22	O7	C18	C19	6.8°	178.8°
C22	O7	C18	C17	176.1°	1.4°
O7	C22	H12	H13	120.0°	119.8°
O7	C22	H12	H14	120.0°	120.2°
O7	C22	H13	H14	120.0°	120.0°
O7	C18	C19	C17	177.1°	179.8°
O7	C18	C19	C20	177.7°	179.8°
O7	C18	C17	C16	178.4°	180.0°
O7	C18	C17	H11	1.6°	0.1°
C18	O7	C22	H12	180.0°	60.4°
C18	O7	C22	H13	60.0°	179.7°
C18	O7	C22	H14	60.0°	59.7°
O7	C18	C19	H16	2.3°	0.2°
C18	C19	C20	H16	180.0°	179.6°
C18	C19	C20	C15	4.0°	0.7°
C19	C18	C17	C16	4.4°	0.2°
C18	C19	C20	H6	176.0°	180.0°
C19	C18	C17	H11	175.5°	179.8°
C20	C19	C18	C17	5.2°	0.4°
C19	C20	C15	H6	180.0°	179.3°
C19	C20	C15	C16	1.7°	0.8°
C19	C20	C15	N2	179.9°	179.8°
C18	C17	C16	H11	180.0°	179.9°
C18	C17	C16	C15	2.1°	0.4°
C18	C17	C16	H10	177.9°	180.0°
C17	C18	C19	H16	174.8°	180.0°
C20	C15	C16	C17	0.7°	0.7°
C20	C15	C16	N2	178.2°	178.9°
C20	C15	N2	C7	69.3°	176.9°
C20	C15	N2	RU2	99.8°	18.0°
C20	C15	C16	H10	179.3°	179.7°
C15	C20	C19	H16	176.0°	179.7°
C17	C16	C15	H10	180.0°	179.6°
C17	C16	C15	N2	178.9°	179.6°
C16	C15	N2	C7	112.6°	4.2°
C16	C15	N2	RU2	78.3°	161.0°
C16	C15	C20	H6	178.3°	179.8°
C15	C16	C17	H11	177.9°	179.6°
C15	N2	C7	RU2	168.7°	165.9°
C15	N2	C7	N1	176.3°	178.6°
C15	N2	RU2	O2	84.7°	113.3°
C15	N2	RU2	RU1	171.7°	177.3°
C15	N2	RU2	O6	98.9°	130.6°
C15	N2	RU2	O4	113.8°	49.7°
C15	N2	C7	H1	3.6°	1.4°
N2	C15	C20	H6	0.2°	0.8°
N2	C15	C16	H10	1.1°	0.8°
C9	C10	C11	H8	180.0°	179.5°
C10	C9	C8	H7	180.0°	179.2°
C9	C10	C11	O8	177.7°	179.9°
C9	C10	C11	C12	13.7°	0.4°
C10	C9	C8	N1	178.3°	179.8°
C10	C9	C8	C13	1.7°	0.7°
C11	C10	C9	C8	7.8°	0.7°
C10	C11	O8	C12	165.4°	179.6°
C10	C11	O8	C23	164.1°	1.7°
C10	C11	C12	C13	12.0°	0.2°
C11	C10	C9	H7	172.2°	179.8°
C10	C11	C12	H15	168.0°	179.8°
C9	C8	N1	C7	45.1°	174.5°
C9	C8	N1	C13	179.9°	179.5°
C9	C8	N1	RU1	117.2°	7.5°
C9	C8	C13	C12	0.1°	0.5°
C8	C9	C10	H8	172.2°	179.8°
C9	C8	C13	H9	179.9°	179.8°
O8	C11	C12	C13	175.1°	179.9°
C11	O8	C23	H3	180.0°	59.4°
C11	O8	C23	H4	60.0°	179.3°
C11	O8	C23	H5	60.0°	60.8°
O8	C11	C10	H8	2.3°	0.4°
O8	C11	C12	H15	4.9°	0.1°
C23	O8	C11	C12	1.3°	177.9°
O8	C23	H3	H4	120.0°	120.0°
O8	C23	H3	H5	120.0°	120.1°
O8	C23	H4	H5	120.0°	120.0°
N2	C7	N1	H1	180.0°	179.9°
N2	C7	N1	C8	173.4°	176.7°
C7	N2	RU2	O2	84.8°	54.7°
N2	C7	N1	RU1	9.4°	5.6°
C7	N2	RU2	RU1	2.1°	14.7°
C7	N2	RU2	O6	91.6°	61.4°
C7	N2	RU2	O4	76.6°	142.3°
N1	C7	N2	RU2	7.6°	12.7°
C7	N1	C8	RU1	162.3°	178.0°
C7	N1	C8	C13	135.0°	6.0°
C7	N1	RU1	O1	86.2°	105.7°
C7	N1	RU1	RU2	6.2°	3.3°
C7	N1	RU1	O5	95.4°	93.2°
C7	N1	RU1	O3	73.1°	15.4°
C11	C12	C13	C8	4.4°	0.2°
C11	C12	C13	H15	180.0°	179.9°
C12	C11	C10	H8	166.2°	180.0°
C11	C12	C13	H9	175.6°	180.0°
O9	C1	O2	O1	174.6°	179.9°
O9	C1	O2	RU2	179.3°	127.4°
O9	C1	O1	RU1	176.8°	124.9°
N2	RU2	O2	C1	85.3°	97.7°
N2	RU2	O2	RU1	89.6°	109.7°
N2	RU2	O2	O6	130.1°	95.6°
N2	RU2	O2	O4	179.6°	164.1°
N2	RU2	RU1	N1	1.8°	8.1°
N2	RU2	RU1	O1	87.9°	111.7°
N2	RU2	RU1	O6	92.7°	66.2°
N2	RU2	RU1	O4	178.7°	140.6°
N2	RU2	O6	O4	179.7°	128.5°
N2	RU2	RU1	O5	92.9°	109.2°
N2	RU2	RU1	O3	176.9°	175.5°
N2	RU2	O6	C5	96.6°	169.3°
N2	RU2	O4	C3	78.3°	175.0°
RU2	N2	C7	H1	172.4°	167.4°
N1	C8	C13	C12	180.0°	180.0°
C8	N1	RU1	O1	75.6°	72.4°
C8	N1	RU1	RU2	167.9°	174.8°
C8	N1	RU1	O5	102.8°	88.7°
C8	N1	RU1	O3	88.7°	162.8°
C8	N1	C7	H1	6.6°	3.2°
N1	C8	C9	H7	1.8°	0.6°
N1	C8	C13	H9	0.0°	0.3°
C13	C8	N1	RU1	62.7°	172.0°
C8	C13	C12	H9	180.0°	179.7°
C13	C8	C9	H7	178.3°	179.8°
C8	C13	C12	H15	175.7°	179.8°
O2	C1	O1	RU1	1.9°	55.2°
C1	O2	RU2	RU1	4.3°	12.0°
C1	O2	RU2	O6	44.8°	2.1°
C1	O2	RU2	O4	94.3°	98.3°
RU2	O2	C1	O1	4.8°	52.7°
O2	RU2	RU1	N1	92.1°	89.6°
O2	RU2	RU1	O1	2.4°	14.0°
O2	RU2	RU1	O6	176.9°	164.0°
O2	RU2	RU1	O4	90.9°	121.7°
O2	RU2	O6	O4	49.6°	124.1°
O2	RU2	RU1	O5	176.8°	153.1°
O2	RU2	RU1	O3	86.6°	77.7°
O2	RU2	O6	C5	33.5°	83.3°
O2	RU2	O4	C3	83.2°	24.5°
C1	O1	RU1	N1	92.3°	31.4°
C1	O1	RU1	RU2	1.4°	38.7°
C1	O1	RU1	O5	151.8°	168.4°
C1	O1	RU1	O3	87.4°	87.1°
N1	RU1	O1	RU2	91.0°	70.1°
N1	RU1	O1	O5	115.8°	160.1°
N1	RU1	O1	O3	179.7°	118.6°
N1	RU1	RU2	O5	91.1°	117.4°
N1	RU1	RU2	O3	178.7°	167.3°
N1	RU1	RU2	O6	90.9°	74.4°
N1	RU1	RU2	O4	176.9°	148.7°
N1	RU1	O5	O3	179.7°	124.7°
N1	RU1	O5	C5	97.8°	33.7°
N1	RU1	O3	C3	85.9°	83.9°
RU1	N1	C7	H1	170.6°	174.5°
O1	RU1	RU2	O5	179.2°	139.1°
O1	RU1	RU2	O3	89.0°	63.7°
O1	RU1	RU2	O6	179.3°	178.0°
O1	RU1	RU2	O4	93.3°	107.7°
O1	RU1	O5	O3	64.4°	77.4°
O1	RU1	O5	C5	146.4°	168.3°
O1	RU1	O3	C3	99.0°	168.8°
RU1	RU2	O6	O4	90.0°	108.0°
RU2	RU1	O5	O3	88.7°	52.8°
RU1	RU2	O6	C5	6.9°	67.2°
RU1	RU2	O4	C3	3.8°	42.2°
RU2	RU1	O5	C5	6.8°	38.2°
RU2	RU1	O3	C3	6.7°	70.5°
O6	RU2	RU1	O5	0.2°	43.0°
O6	RU2	RU1	O3	90.4°	118.3°
O6	RU2	O4	C3	93.2°	92.5°
RU2	O6	C5	O5	14.4°	64.3°
RU2	O6	C5	O11	162.3°	115.7°
O4	RU2	RU1	O5	85.8°	31.4°
O4	RU2	RU1	O3	4.3°	44.0°
O4	RU2	O6	C5	83.1°	40.8°
RU2	O4	C3	O3	0.6°	2.5°
RU2	O4	C3	O10	175.7°	177.4°
RU1	O5	C5	O6	14.4°	6.7°
RU1	O5	C5	O11	162.1°	173.3°
O5	RU1	O3	C3	82.6°	42.2°
RU1	O3	C3	O4	5.7°	61.8°
O3	RU1	O5	C5	82.0°	91.0°
RU1	O3	C3	O10	170.2°	118.2°
O6	C5	O5	O11	176.5°	180.0°
O4	C3	O3	O10	175.9°	179.9°
H3	C23	H4	H5	120.0°	120.0°
H6	C20	C19	H16	4.0°	0.4°
H7	C9	C10	H8	7.8°	0.6°
H9	C13	C12	H15	4.4°	0.1°
H10	C16	C17	H11	2.1°	0.0°
H12	C22	H13	H14	120.0°	120.0°

Release date:	2023-07-19
Definition date:	2023-06-22
Last modified:	2026-09-16
Release status:	REL
Processing site:	PDBE
Derived from:	8PFW