Summary Geometry PCM/PTM Related PDB entries

A1JIA

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	1.24Å
C1	C2	sing	1.47Å	1.49Å
C2	C3	doub	1.37Å	1.35Å	Aromatic
C2	C5	sing	1.46Å	1.44Å	Aromatic
C3	O2	sing	1.34Å	1.37Å	Aromatic
C5	C6	sing	1.47Å	1.45Å
C5	C4	doub	1.37Å	1.34Å	Aromatic
C6	C7	doub	1.33Å	1.50Å
O2	C4	sing	1.33Å	1.37Å	Aromatic
C4	C13	sing	1.51Å	1.48Å
C7	C8	sing	1.50Å	1.52Å
C13	C8	sing	1.53Å	1.54Å
C8	C9	sing	1.51Å	1.51Å
C9	C10	doub	1.33Å	1.39Å	Aromatic
C9	S1	sing	1.76Å	1.85Å	Aromatic
C10	C11	sing	1.39Å	1.45Å	Aromatic
S1	C12	sing	1.76Å	1.85Å	Aromatic
C11	C12	doub	1.34Å	1.44Å	Aromatic
C12	BR1	sing	1.89Å	1.86Å
C6	H1	sing	1.08Å	1.08Å
C7	H2	sing	1.08Å	1.08Å
O1	H3	sing	0.97Å	0.95Å
C3	H4	sing	1.08Å	1.08Å
C8	H5	sing	1.09Å	1.10Å
C10	H7	sing	1.08Å	1.08Å
C11	H9	sing	1.08Å	1.08Å
C13	H12	sing	1.09Å	1.10Å
C13	H13	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O3	C1	O1	121.3°	120.0°
O3	C1	C2	119.8°	120.0°
O1	C1	C2	118.9°	120.0°
C1	O1	H3	109.5°	117.0°
C1	C2	C3	125.4°	127.4°
C1	C2	C5	129.9°	127.4°
C3	C2	C5	104.7°	105.2°
C2	C3	O2	111.4°	108.9°
C2	C3	H4	124.3°	125.6°
C2	C5	C6	130.4°	132.1°
C2	C5	C4	107.7°	106.4°
C3	O2	C4	106.3°	111.1°
O2	C3	H4	124.3°	125.6°
C6	C5	C4	121.8°	121.6°
C5	C6	C7	117.6°	116.9°
C5	C6	H1	121.2°	121.5°
C5	C4	O2	109.9°	108.5°
C5	C4	C13	126.4°	120.9°
C6	C7	C8	117.1°	122.4°
C7	C6	H1	121.2°	121.6°
C6	C7	H2	121.5°	118.8°
O2	C4	C13	123.8°	130.6°
C4	C13	C8	110.1°	108.9°
C4	C13	H12	109.3°	109.6°
C4	C13	H13	109.3°	109.6°
C7	C8	C13	116.3°	112.7°
C7	C8	C9	100.5°	108.8°
C8	C7	H2	121.4°	118.8°
C7	C8	H5	108.5°	108.9°
C13	C8	C9	114.0°	108.8°
C13	C8	H5	108.3°	108.8°
C8	C13	H12	109.3°	109.6°
C8	C13	H13	109.3°	109.6°
C8	C9	C10	125.3°	125.2°
C8	C9	S1	123.7°	125.2°
C9	C8	H5	108.7°	108.8°
C10	C9	S1	110.9°	109.6°
C9	C10	C11	113.8°	114.9°
C9	C10	H7	123.1°	122.5°
C9	S1	C12	90.7°	91.0°
C10	C11	C12	114.4°	114.9°
C11	C10	H7	123.1°	122.5°
C10	C11	H9	122.8°	122.6°
S1	C12	C11	108.2°	109.6°
S1	C12	BR1	123.6°	125.2°
C11	C12	BR1	128.2°	125.2°
C12	C11	H9	122.8°	122.6°
H12	C13	H13	109.4°	109.7°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O3	C1	O1	C2	178.3°	180.0°
O3	C1	C2	C3	40.5°	179.9°
O3	C1	C2	C5	139.5°	0.3°
O3	C1	O1	H3	0.0°	0.0°
O1	C1	C2	C3	137.8°	0.1°
O1	C1	C2	C5	42.1°	179.7°
C1	C2	C3	C5	179.9°	179.7°
C1	C2	C3	O2	179.5°	179.7°
C1	C2	C5	C6	1.1°	0.2°
C1	C2	C5	C4	179.1°	179.7°
C2	C1	O1	H3	178.3°	180.0°
C1	C2	C3	H4	0.5°	0.2°
C2	C3	O2	H4	180.0°	180.0°
C3	C2	C5	C6	178.9°	179.9°
C3	C2	C5	C4	0.9°	0.0°
C2	C3	O2	C4	0.1°	0.0°
C5	C2	C3	O2	0.5°	0.0°
C2	C5	C6	C4	177.8°	179.9°
C2	C5	C6	C7	172.8°	163.4°
C2	C5	C4	O2	0.9°	0.0°
C2	C5	C4	C13	179.1°	179.9°
C2	C5	C6	H1	7.3°	16.6°
C5	C2	C3	H4	179.5°	180.0°
C3	O2	C4	C5	0.6°	0.0°
C3	O2	C4	C13	179.4°	179.9°
C5	C6	C7	H1	180.0°	179.9°
C6	C5	C4	O2	179.1°	179.9°
C6	C5	C4	C13	0.9°	0.2°
C5	C6	C7	C8	7.4°	1.7°
C5	C6	C7	H2	172.7°	178.3°
C4	C5	C6	C7	9.5°	16.7°
C5	C4	O2	C13	180.0°	179.9°
C5	C4	C13	C8	22.6°	30.7°
C4	C5	C6	H1	170.5°	163.2°
C5	C4	C13	H12	97.5°	150.5°
C5	C4	C13	H13	142.7°	89.1°
C6	C7	C8	H2	180.0°	180.0°
C6	C7	C8	C13	31.5°	33.8°
C6	C7	C8	C9	155.1°	87.0°
C6	C7	C8	H5	90.9°	154.5°
O2	C4	C13	C8	157.3°	149.2°
C4	O2	C3	H4	179.9°	180.0°
O2	C4	C13	H12	82.6°	29.3°
O2	C4	C13	H13	37.2°	91.0°
C4	C13	C8	C7	37.3°	45.3°
C4	C13	C8	H12	120.1°	119.9°
C4	C13	C8	H13	120.1°	119.8°
C4	C13	C8	C9	153.7°	75.5°
C4	C13	C8	H5	85.1°	166.2°
C4	C13	H12	H13	119.7°	120.3°
C7	C8	C13	C9	116.3°	120.8°
C7	C8	C13	H5	122.5°	120.8°
C7	C8	C9	H5	113.9°	118.5°
C7	C8	C9	C10	67.0°	120.0°
C7	C8	C9	S1	110.8°	59.7°
C8	C7	C6	H1	172.7°	178.4°
C7	C8	C13	H12	82.8°	165.2°
C7	C8	C13	H13	157.4°	74.5°
C13	C8	C9	H5	121.0°	118.3°
C13	C8	C9	C10	167.8°	116.8°
C13	C8	C9	S1	14.4°	63.5°
C13	C8	C7	H2	148.5°	146.2°
C8	C13	H12	H13	119.7°	120.3°
C8	C9	C10	S1	178.0°	179.7°
C8	C9	C10	C11	172.8°	180.0°
C8	C9	S1	C12	179.1°	179.9°
C9	C8	C7	H2	24.9°	93.0°
C8	C9	C10	H7	7.2°	0.1°
C9	C8	C13	H12	33.5°	44.4°
C9	C8	C13	H13	86.2°	164.7°
C9	C10	C11	H7	180.0°	180.0°
C10	C9	S1	C12	2.8°	0.3°
C9	C10	C11	C12	13.7°	0.0°
C10	C9	C8	H5	46.8°	1.5°
C9	C10	C11	H9	166.3°	180.0°
S1	C9	C10	C11	5.3°	0.3°
C9	S1	C12	C11	9.9°	0.4°
C9	S1	C12	BR1	169.2°	179.9°
S1	C9	C8	H5	135.4°	178.1°
S1	C9	C10	H7	174.7°	179.8°
C10	C11	C12	S1	15.1°	0.3°
C10	C11	C12	H9	180.0°	180.0°
C10	C11	C12	BR1	164.0°	180.0°
S1	C12	C11	BR1	179.1°	179.7°
S1	C12	C11	H9	164.9°	179.7°
C12	C11	C10	H7	166.2°	179.9°
BR1	C12	C11	H9	16.0°	0.0°
H1	C6	C7	H2	7.3°	1.6°
H2	C7	C8	H5	89.1°	25.4°
H5	C8	C13	H12	154.7°	74.0°
H5	C8	C13	H13	35.0°	46.4°
H7	C10	C11	H9	13.7°	0.0°

Release date:	2026-05-20
Definition date:	2025-06-26
Last modified:	2026-05-15
Release status:	REL
Processing site:	PDBE
Derived from:	9RMO