Summary Geometry PCM/PTM Related PDB entries

A1JR3

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O3	C1	doub	1.22Å	1.25Å
O1	C1	sing	1.35Å	1.26Å
C1	C2	sing	1.47Å	1.49Å
C2	C3	doub	1.37Å	1.35Å	Aromatic
C2	C5	sing	1.46Å	1.43Å	Aromatic
C3	O2	sing	1.34Å	1.37Å	Aromatic
C5	C6	sing	1.51Å	1.51Å
C5	C4	doub	1.34Å	1.35Å	Aromatic
C6	C7	sing	1.53Å	1.55Å
O2	C4	sing	1.34Å	1.38Å	Aromatic
C4	C13	sing	1.51Å	1.48Å
C7	C8	sing	1.53Å	1.52Å
C13	C8	sing	1.53Å	1.54Å
C8	C9	sing	1.51Å	1.51Å
C9	S1	sing	1.76Å	1.85Å	Aromatic
C9	C10	doub	1.33Å	1.38Å	Aromatic
S1	C12	sing	1.76Å	1.85Å	Aromatic
C10	C11	sing	1.38Å	1.47Å	Aromatic
C12	C11	doub	1.34Å	1.34Å	Aromatic
C11	BR1	sing	1.89Å	1.86Å
C3	H1	sing	1.08Å	1.08Å
C6	H2	sing	1.09Å	1.10Å
C6	H3	sing	1.09Å	1.10Å
O1	H4	sing	0.97Å	0.95Å
C7	H5	sing	1.09Å	1.10Å
C7	H6	sing	1.09Å	1.10Å
C8	H7	sing	1.09Å	1.10Å
C10	H8	sing	1.08Å	1.08Å
C12	H9	sing	1.08Å	1.08Å
C13	H10	sing	1.09Å	1.10Å
C13	H11	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O3	C1	O1	121.4°	120.0°
O3	C1	C2	119.4°	120.0°
O1	C1	C2	119.2°	120.0°
C1	O1	H4	109.5°	117.0°
C1	C2	C3	128.2°	127.4°
C1	C2	C5	127.1°	127.3°
C3	C2	C5	104.7°	105.3°
C2	C3	O2	111.5°	108.5°
C2	C3	H1	124.3°	125.7°
C2	C5	C6	128.9°	128.6°
C2	C5	C4	108.2°	106.5°
C3	O2	C4	106.4°	110.9°
O2	C3	H1	124.3°	125.8°
C6	C5	C4	122.8°	124.9°
C5	C6	C7	106.5°	108.4°
C5	C6	H2	110.2°	109.6°
C5	C6	H3	110.2°	109.7°
C5	C4	O2	109.2°	108.8°
C5	C4	C13	126.6°	123.6°
C6	C7	C8	110.0°	109.4°
C7	C6	H2	110.2°	109.7°
C7	C6	H3	110.2°	109.7°
C6	C7	H5	109.3°	109.5°
C6	C7	H6	109.4°	109.5°
O2	C4	C13	124.2°	127.6°
C4	C13	C8	105.6°	108.5°
C4	C13	H10	110.4°	109.6°
C4	C13	H11	110.4°	109.7°
C7	C8	C13	105.7°	109.6°
C7	C8	C9	109.1°	109.5°
C8	C7	H5	109.3°	109.5°
C8	C7	H6	109.3°	109.5°
C7	C8	H7	108.0°	109.5°
C13	C8	C9	117.5°	109.5°
C13	C8	H7	107.9°	109.4°
C8	C13	H10	110.4°	109.7°
C8	C13	H11	110.4°	109.6°
C8	C9	S1	120.3°	125.2°
C8	C9	C10	129.8°	125.2°
C9	C8	H7	108.2°	109.4°
S1	C9	C10	109.8°	109.6°
C9	S1	C12	89.8°	91.0°
C9	C10	C11	109.9°	114.9°
C9	C10	H8	125.0°	122.6°
S1	C12	C11	108.3°	109.6°
S1	C12	H9	125.8°	125.2°
C10	C11	C12	116.9°	114.9°
C10	C11	BR1	122.8°	122.6°
C11	C10	H8	125.1°	122.5°
C12	C11	BR1	120.3°	122.5°
C11	C12	H9	125.8°	125.2°
H2	C6	H3	109.5°	109.7°
H5	C7	H6	109.5°	109.5°
H10	C13	H11	109.5°	109.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O3	C1	O1	C2	179.9°	179.7°
O3	C1	C2	C3	55.5°	179.8°
O3	C1	C2	C5	124.2°	0.6°
O3	C1	O1	H4	0.0°	0.3°
O1	C1	C2	C3	124.6°	0.1°
O1	C1	C2	C5	55.7°	179.7°
C1	C2	C3	C5	179.8°	179.7°
C1	C2	C3	O2	179.9°	180.0°
C1	C2	C5	C6	0.7°	0.0°
C1	C2	C5	C4	179.9°	180.0°
C1	C2	C3	H1	0.1°	0.0°
C2	C1	O1	H4	179.9°	180.0°
C2	C3	O2	H1	180.0°	180.0°
C3	C2	C5	C6	179.5°	179.7°
C3	C2	C5	C4	0.4°	0.3°
C2	C3	O2	C4	0.2°	0.2°
C5	C2	C3	O2	0.3°	0.3°
C2	C5	C6	C4	179.0°	179.9°
C2	C5	C6	C7	167.8°	163.8°
C2	C5	C4	O2	0.3°	0.2°
C2	C5	C4	C13	179.4°	179.9°
C5	C2	C3	H1	179.6°	179.7°
C2	C5	C6	H2	48.3°	44.1°
C2	C5	C6	H3	72.7°	76.4°
C3	O2	C4	C5	0.1°	0.0°
C3	O2	C4	C13	179.6°	179.9°
C5	C6	C7	H2	119.5°	119.7°
C5	C6	C7	H3	119.5°	119.7°
C6	C5	C4	O2	179.5°	179.8°
C6	C5	C4	C13	0.2°	0.1°
C5	C6	C7	C8	50.1°	49.3°
C5	C6	H2	H3	121.3°	120.5°
C5	C6	C7	H5	70.0°	70.7°
C5	C6	C7	H6	170.2°	169.2°
C4	C5	C6	C7	13.2°	16.2°
C5	C4	O2	C13	179.7°	179.8°
C5	C4	C13	C8	22.4°	17.0°
C4	C5	C6	H2	132.7°	135.9°
C4	C5	C6	H3	106.4°	103.5°
C5	C4	C13	H10	141.8°	136.7°
C5	C4	C13	H11	97.0°	102.7°
C6	C7	C8	H5	120.1°	120.0°
C6	C7	C8	H6	120.1°	119.9°
C6	C7	C8	C13	75.8°	69.8°
C6	C7	C8	C9	157.0°	170.1°
C7	C6	H2	H3	121.4°	120.6°
C6	C7	H5	H6	119.8°	120.0°
C6	C7	C8	H7	39.5°	50.2°
O2	C4	C13	C8	157.2°	163.2°
C4	O2	C3	H1	179.8°	179.8°
O2	C4	C13	H10	37.8°	43.5°
O2	C4	C13	H11	83.4°	77.1°
C4	C13	C8	C7	56.5°	50.2°
C4	C13	C8	H10	119.4°	119.7°
C4	C13	C8	H11	119.4°	119.7°
C4	C13	C8	C9	178.5°	170.3°
C4	C13	C8	H7	58.9°	69.8°
C4	C13	H10	H11	121.8°	120.5°
C7	C8	C13	C9	122.0°	120.1°
C7	C8	C13	H7	115.4°	120.0°
C7	C8	C9	H7	117.4°	120.0°
C7	C8	C9	S1	1.8°	60.0°
C7	C8	C9	C10	178.2°	120.3°
C8	C7	C6	H2	169.6°	168.9°
C8	C7	C6	H3	69.4°	70.5°
C8	C7	H5	H6	119.8°	120.1°
C7	C8	C13	H10	175.9°	169.9°
C7	C8	C13	H11	62.9°	69.5°
C13	C8	C9	H7	122.4°	119.9°
C13	C8	C9	S1	122.0°	60.1°
C13	C8	C9	C10	61.6°	119.6°
C13	C8	C7	H5	44.3°	50.1°
C13	C8	C7	H6	164.2°	170.2°
C8	C13	H10	H11	121.8°	120.5°
C8	C9	S1	C10	177.1°	179.8°
C8	C9	S1	C12	164.7°	179.9°
C8	C9	C10	C11	154.7°	180.0°
C9	C8	C7	H5	83.0°	69.9°
C9	C8	C7	H6	36.9°	50.2°
C8	C9	C10	H8	25.3°	0.0°
C9	C8	C13	H10	62.1°	70.0°
C9	C8	C13	H11	59.1°	50.6°
S1	C9	C10	C11	22.0°	0.2°
C9	S1	C12	C11	1.5°	0.4°
S1	C9	C8	H7	115.6°	180.0°
S1	C9	C10	H8	157.9°	179.7°
C9	S1	C12	H9	178.5°	179.9°
C10	C9	S1	C12	12.4°	0.3°
C9	C10	C11	H8	180.0°	180.0°
C9	C10	C11	C12	25.3°	0.0°
C9	C10	C11	BR1	154.7°	180.0°
C10	C9	C8	H7	60.8°	0.3°
S1	C12	C11	C10	15.0°	0.3°
S1	C12	C11	H9	180.0°	179.8°
S1	C12	C11	BR1	165.0°	179.7°
C10	C11	C12	BR1	180.0°	180.0°
C10	C11	C12	H9	165.0°	180.0°
C12	C11	C10	H8	154.7°	180.0°
BR1	C11	C10	H8	25.4°	0.0°
BR1	C11	C12	H9	15.0°	0.0°
H2	C6	C7	H5	49.5°	49.0°
H2	C6	C7	H6	70.3°	71.1°
H3	C6	C7	H5	170.5°	169.6°
H3	C6	C7	H6	50.6°	49.5°
H5	C7	C8	H7	159.5°	170.1°
H6	C7	C8	H7	80.6°	69.8°
H7	C8	C13	H10	60.5°	49.9°
H7	C8	C13	H11	178.3°	170.5°

Release date:	2026-08-12
Definition date:	2025-10-14
Last modified:	2026-08-07
Release status:	REL
Processing site:	PDBE
Derived from:	9RN5