Summary Geometry PCM/PTM Related PDB entries

A1C4L

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C4	C5	sing	1.54Å	1.52Å
C4	S2	sing	1.83Å	1.66Å
C5	C6	sing	1.54Å	1.55Å
C12	C11	doub	1.38Å	1.39Å	Aromatic
C12	C13	sing	1.38Å	1.39Å	Aromatic
C11	C10	sing	1.38Å	1.40Å	Aromatic
O1	S2	doub	1.42Å	1.44Å
S2	O3	doub	1.42Å	1.44Å
S2	C7	sing	1.83Å	1.67Å
C13	C14	doub	1.38Å	1.39Å	Aromatic
C6	C7	sing	1.55Å	1.54Å
C6	N8	sing	1.47Å	1.49Å
C10	C9	sing	1.51Å	1.52Å
C10	C15	doub	1.38Å	1.40Å	Aromatic
C14	C15	sing	1.38Å	1.40Å	Aromatic
C20	C21	doub	1.38Å	1.39Å	Aromatic
C20	C19	sing	1.38Å	1.39Å	Aromatic
N8	C9	sing	1.46Å	1.48Å
N8	C16	sing	1.35Å	1.35Å
C21	C22	sing	1.39Å	1.40Å	Aromatic
C18	C16	sing	1.51Å	1.52Å
C18	C19	sing	1.51Å	1.52Å
C16	O17	doub	1.21Å	1.21Å
C29	C28	doub	1.35Å	1.38Å	Aromatic
C29	N25	sing	1.37Å	1.34Å	Aromatic
C19	C24	doub	1.38Å	1.39Å	Aromatic
C28	C27	sing	1.41Å	1.39Å	Aromatic
C22	N25	sing	1.40Å	1.36Å
C22	C23	doub	1.39Å	1.41Å	Aromatic
N25	C26	sing	1.37Å	1.33Å	Aromatic
C24	C23	sing	1.38Å	1.40Å	Aromatic
C27	C26	doub	1.35Å	1.38Å	Aromatic
C4	H1	sing	1.09Å	1.10Å
C4	H2	sing	1.09Å	1.10Å
C5	H3	sing	1.09Å	1.10Å
C5	H4	sing	1.09Å	1.10Å
C6	H5	sing	1.09Å	1.10Å
C7	H6	sing	1.09Å	1.10Å
C7	H7	sing	1.09Å	1.10Å
C11	H8	sing	1.08Å	1.08Å
C12	H9	sing	1.08Å	1.08Å
C15	H10	sing	1.08Å	1.08Å
C18	H11	sing	1.09Å	1.10Å
C18	H12	sing	1.09Å	1.10Å
C21	H13	sing	1.08Å	1.08Å
C23	H14	sing	1.08Å	1.08Å
C24	H15	sing	1.08Å	1.08Å
C27	H16	sing	1.08Å	1.08Å
C9	H17	sing	1.09Å	1.10Å
C9	H18	sing	1.09Å	1.10Å
C13	H19	sing	1.08Å	1.08Å
C14	H20	sing	1.08Å	1.08Å
C20	H21	sing	1.08Å	1.08Å
C26	H22	sing	1.08Å	1.08Å
C28	H23	sing	1.08Å	1.08Å
C29	H24	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C5	C4	S2	101.9°	105.1°
C4	C5	C6	107.7°	108.7°
C5	C4	H1	111.3°	110.3°
C5	C4	H2	111.3°	110.3°
C4	C5	H3	109.9°	109.7°
C4	C5	H4	109.9°	109.6°
C4	S2	O1	111.9°	109.3°
C4	S2	O3	109.3°	109.3°
C4	S2	C7	101.0°	97.0°
S2	C4	H1	111.3°	110.3°
S2	C4	H2	111.3°	110.3°
C5	C6	C7	107.3°	106.7°
C5	C6	N8	111.3°	110.0°
C6	C5	H3	109.9°	109.7°
C6	C5	H4	109.9°	109.6°
C5	C6	H5	108.8°	110.1°
C11	C12	C13	121.0°	120.0°
C12	C11	C10	120.2°	120.0°
C12	C11	H8	119.9°	120.0°
C11	C12	H9	119.5°	120.0°
C12	C13	C14	119.1°	120.0°
C13	C12	H9	119.5°	120.0°
C12	C13	H19	120.5°	120.0°
C11	C10	C9	124.2°	120.0°
C11	C10	C15	118.4°	120.0°
C10	C11	H8	119.9°	120.0°
O1	S2	O3	111.4°	119.9°
O1	S2	C7	110.7°	109.3°
O3	S2	C7	112.1°	109.5°
S2	C7	C6	106.3°	102.6°
S2	C7	H6	110.2°	110.8°
S2	C7	H7	110.3°	110.9°
C13	C14	C15	120.1°	120.0°
C14	C13	H19	120.4°	120.0°
C13	C14	H20	119.9°	120.0°
C7	C6	N8	111.0°	110.0°
C7	C6	H5	108.8°	110.0°
C6	C7	H6	110.3°	110.8°
C6	C7	H7	110.3°	110.8°
C6	N8	C9	116.1°	120.0°
C6	N8	C16	123.2°	120.0°
N8	C6	H5	109.5°	110.0°
C9	C10	C15	117.3°	120.1°
C10	C9	N8	114.4°	109.5°
C10	C9	H17	108.2°	109.5°
C10	C9	H18	108.2°	109.5°
C10	C15	C14	121.1°	120.0°
C10	C15	H10	119.5°	119.9°
C14	C15	H10	119.5°	120.1°
C15	C14	H20	119.9°	120.0°
C21	C20	C19	120.5°	120.0°
C20	C21	C22	124.0°	119.9°
C20	C21	H13	118.0°	120.0°
C21	C20	H21	119.7°	120.0°
C20	C19	C18	120.1°	119.9°
C20	C19	C24	117.7°	120.2°
C19	C20	H21	119.8°	120.0°
C9	N8	C16	120.7°	120.0°
N8	C9	H17	108.2°	109.5°
N8	C9	H18	108.2°	109.5°
N8	C16	C18	122.6°	120.0°
N8	C16	O17	121.5°	120.0°
C21	C22	N25	122.0°	120.0°
C21	C22	C23	113.9°	119.9°
C22	C21	H13	118.0°	120.1°
C16	C18	C19	113.0°	109.4°
C18	C16	O17	115.9°	120.0°
C16	C18	H11	108.6°	109.5°
C16	C18	H12	108.6°	109.5°
C18	C19	C24	122.1°	120.0°
C19	C18	H11	108.6°	109.5°
C19	C18	H12	108.6°	109.5°
C28	C29	N25	106.3°	108.2°
C29	C28	C27	107.5°	107.5°
C29	C28	H23	126.2°	126.3°
C28	C29	H24	126.9°	125.9°
C29	N25	C22	122.9°	125.7°
C29	N25	C26	112.6°	108.7°
N25	C29	H24	126.9°	125.9°
C19	C24	C23	121.0°	120.1°
C19	C24	H15	119.5°	120.0°
C28	C27	C26	107.8°	107.5°
C28	C27	H16	126.1°	126.3°
C27	C28	H23	126.3°	126.2°
N25	C22	C23	124.1°	120.1°
C22	N25	C26	124.5°	125.6°
C22	C23	C24	122.8°	119.9°
C22	C23	H14	118.6°	120.1°
N25	C26	C27	105.9°	108.1°
N25	C26	H22	127.1°	125.9°
C24	C23	H14	118.6°	120.0°
C23	C24	H15	119.5°	120.0°
C26	C27	H16	126.1°	126.2°
C27	C26	H22	127.1°	125.9°
H1	C4	H2	109.5°	110.3°
H3	C5	H4	109.5°	109.5°
H6	C7	H7	109.5°	110.7°
H11	C18	H12	109.4°	109.5°
H17	C9	H18	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C5	C4	S2	H1	118.7°	118.9°
C5	C4	S2	H2	118.8°	118.9°
C4	C5	C6	H3	119.7°	119.9°
C4	C5	C6	H4	119.7°	119.8°
C5	C4	S2	O1	153.5°	115.5°
C5	C4	S2	O3	82.5°	111.4°
C5	C4	S2	C7	35.7°	2.1°
C4	C5	C6	C7	27.9°	47.2°
C4	C5	C6	N8	149.5°	166.5°
C5	C4	H1	H2	123.5°	122.1°
C4	C5	H3	H4	120.8°	120.4°
C4	C5	C6	H5	89.7°	72.1°
S2	C4	C5	C6	40.0°	27.9°
C4	S2	O1	O3	122.8°	127.3°
C4	S2	O1	C7	111.8°	105.1°
C4	S2	O3	C7	111.1°	105.1°
C4	S2	C7	C6	20.0°	23.2°
S2	C4	H1	H2	123.5°	122.2°
S2	C4	C5	H3	159.8°	147.8°
S2	C4	C5	H4	79.7°	91.9°
C4	S2	C7	H6	139.5°	141.5°
C4	S2	C7	H7	99.5°	95.1°
C5	C6	C7	S2	3.0°	42.4°
C5	C6	C7	N8	121.8°	119.3°
C5	C6	C7	H5	117.6°	119.3°
C5	C6	N8	H5	120.4°	121.4°
C5	C6	N8	C9	60.7°	96.3°
C5	C6	N8	C16	120.8°	83.8°
C6	C5	C4	H1	158.8°	146.8°
C6	C5	C4	H2	78.7°	91.0°
C6	C5	H3	H4	120.8°	120.4°
C5	C6	C7	H6	116.5°	160.7°
C5	C6	C7	H7	122.5°	76.0°
C11	C12	C13	H9	180.0°	180.0°
C12	C11	C10	H8	180.0°	179.8°
C11	C12	C13	C14	0.3°	0.0°
C12	C11	C10	C9	179.2°	179.8°
C12	C11	C10	C15	0.9°	0.2°
C11	C12	C13	H19	179.7°	180.0°
C13	C12	C11	C10	0.1°	0.0°
C12	C13	C14	H19	180.0°	180.0°
C12	C13	C14	C15	0.1°	0.4°
C13	C12	C11	H8	179.9°	179.8°
C12	C13	C14	H20	179.9°	179.9°
C11	C10	C9	C15	178.3°	180.0°
C11	C10	C15	C14	1.3°	0.5°
C11	C10	C9	N8	29.3°	86.2°
C10	C11	C12	H9	179.8°	180.0°
C11	C10	C15	H10	178.7°	180.0°
C11	C10	C9	H17	150.0°	33.8°
C11	C10	C9	H18	91.4°	153.7°
O1	S2	O3	C7	124.7°	127.5°
O1	S2	C7	C6	138.7°	90.2°
O1	S2	C4	H1	87.7°	125.6°
O1	S2	C4	H2	34.8°	3.4°
O1	S2	C7	H6	101.9°	28.2°
O1	S2	C7	H7	19.2°	151.5°
O3	S2	C7	C6	96.3°	136.6°
O3	S2	C4	H1	36.2°	7.5°
O3	S2	C4	H2	158.7°	129.7°
O3	S2	C7	H6	23.2°	105.1°
O3	S2	C7	H7	144.2°	18.3°
S2	C7	C6	H6	119.5°	118.3°
S2	C7	C6	H7	119.5°	118.4°
S2	C7	C6	N8	124.8°	161.7°
C7	S2	C4	H1	154.5°	121.0°
C7	S2	C4	H2	83.0°	116.8°
S2	C7	C6	H5	114.6°	76.9°
S2	C7	H6	H7	121.5°	123.5°
C13	C14	C15	C10	0.9°	0.6°
C13	C14	C15	H20	180.0°	179.6°
C14	C13	C12	H9	179.7°	180.0°
C13	C14	C15	H10	179.1°	179.9°
C7	C6	N8	H5	120.2°	121.3°
C7	C6	N8	C9	58.8°	21.0°
C7	C6	N8	C16	119.8°	159.0°
C7	C6	C5	H3	147.6°	167.1°
C7	C6	C5	H4	91.9°	72.6°
C6	C7	H6	H7	121.5°	123.3°
C6	N8	C9	C10	117.3°	92.1°
C6	N8	C9	C16	178.6°	180.0°
C6	N8	C16	C18	1.6°	6.6°
C6	N8	C16	O17	176.9°	173.4°
N8	C6	C5	H3	90.8°	73.6°
N8	C6	C5	H4	29.8°	46.6°
N8	C6	C7	H6	5.4°	80.0°
N8	C6	C7	H7	115.7°	43.3°
C6	N8	C9	H17	122.0°	147.9°
C6	N8	C9	H18	3.5°	27.9°
C9	C10	C15	C14	179.7°	179.5°
C10	C9	N8	H17	120.7°	120.0°
C10	C9	N8	H18	120.7°	120.0°
C10	C9	N8	C16	64.2°	87.9°
C9	C10	C11	H8	0.8°	0.0°
C9	C10	C15	H10	0.3°	0.0°
C10	C9	H17	H18	117.8°	120.0°
C10	C15	C14	H10	180.0°	179.5°
C15	C10	C9	N8	152.5°	93.8°
C15	C10	C11	H8	179.1°	180.0°
C15	C10	C9	H17	31.8°	146.2°
C15	C10	C9	H18	86.8°	26.3°
C10	C15	C14	H20	179.1°	179.8°
C15	C14	C13	H19	180.0°	179.7°
C21	C20	C19	H21	180.0°	180.0°
C20	C21	C22	H13	180.0°	179.8°
C21	C20	C19	C18	178.5°	180.0°
C21	C20	C19	C24	1.7°	0.3°
C20	C21	C22	N25	179.9°	179.8°
C20	C21	C22	C23	0.0°	0.2°
C19	C20	C21	C22	0.6°	0.0°
C20	C19	C18	C16	83.4°	90.3°
C20	C19	C18	C24	176.7°	179.7°
C20	C19	C24	C23	2.2°	0.2°
C20	C19	C18	H11	156.1°	149.7°
C20	C19	C18	H12	37.2°	29.7°
C19	C20	C21	H13	179.4°	179.8°
C20	C19	C24	H15	177.7°	179.7°
C9	N8	C16	C18	180.0°	173.4°
C9	N8	C16	O17	1.5°	6.6°
C9	N8	C6	H5	178.9°	142.3°
N8	C9	H17	H18	117.7°	120.0°
N8	C16	C18	O17	178.6°	180.0°
N8	C16	C18	C19	162.1°	176.5°
C16	N8	C6	H5	0.4°	37.7°
N8	C16	C18	H11	77.4°	63.5°
N8	C16	C18	H12	41.5°	56.5°
C16	N8	C9	H17	56.6°	32.1°
C16	N8	C9	H18	175.1°	152.1°
C21	C22	N25	C29	40.4°	0.4°
C21	C22	N25	C23	179.9°	180.0°
C21	C22	N25	C26	140.3°	180.0°
C21	C22	C23	C24	0.6°	0.2°
C21	C22	C23	H14	179.3°	179.7°
C22	C21	C20	H21	179.4°	180.0°
C16	C18	C19	H11	120.5°	120.0°
C16	C18	C19	H12	120.5°	120.0°
C16	C18	C19	C24	100.0°	90.0°
C16	C18	H11	H12	118.3°	120.1°
C19	C18	C16	O17	19.3°	3.5°
C18	C19	C24	C23	179.0°	180.0°
C19	C18	H11	H12	118.4°	120.0°
C18	C19	C24	H15	1.0°	0.0°
C18	C19	C20	H21	1.5°	0.0°
O17	C16	C18	H11	101.2°	116.5°
O17	C16	C18	H12	139.9°	123.5°
C28	C29	N25	H24	180.0°	179.8°
C29	C28	C27	H23	180.0°	179.9°
C28	C29	N25	C22	179.5°	180.0°
C28	C29	N25	C26	0.1°	0.4°
C29	C28	C27	C26	0.1°	0.0°
C29	C28	C27	H16	179.9°	179.7°
N25	C29	C28	C27	0.0°	0.2°
C29	N25	C22	C26	179.4°	179.6°
C29	N25	C22	C23	139.5°	179.6°
C29	N25	C26	C27	0.1°	0.3°
C29	N25	C26	H22	179.9°	179.7°
N25	C29	C28	H23	180.0°	179.9°
C19	C24	C23	C22	1.8°	0.0°
C19	C24	C23	H15	180.0°	179.9°
C24	C19	C18	H11	20.6°	30.0°
C24	C19	C18	H12	139.5°	150.0°
C19	C24	C23	H14	178.2°	180.0°
C24	C19	C20	H21	178.4°	179.7°
C28	C27	C26	N25	0.1°	0.2°
C28	C27	C26	H16	180.0°	179.8°
C28	C27	C26	H22	179.9°	179.9°
C27	C28	C29	H24	180.0°	180.0°
N25	C22	C23	C24	179.3°	179.8°
C22	N25	C26	C27	179.6°	180.0°
N25	C22	C21	H13	0.1°	0.1°
N25	C22	C23	H14	0.7°	0.3°
C22	N25	C26	H22	0.4°	0.0°
C22	N25	C29	H24	0.5°	0.2°
C23	C22	N25	C26	39.8°	0.0°
C22	C23	C24	H14	180.0°	180.0°
C23	C22	C21	H13	180.0°	179.9°
C22	C23	C24	H15	178.2°	179.9°
N25	C26	C27	H22	180.0°	179.9°
N25	C26	C27	H16	179.9°	179.9°
C26	N25	C29	H24	179.9°	179.9°
C26	C27	C28	H23	179.9°	179.9°
H1	C4	C5	H3	81.5°	93.3°
H1	C4	C5	H4	39.1°	27.0°
H2	C4	C5	H3	41.0°	28.9°
H2	C4	C5	H4	161.5°	149.1°
H3	C5	C6	H5	30.0°	47.7°
H4	C5	C6	H5	150.6°	168.0°
H5	C6	C7	H6	126.0°	41.4°
H5	C6	C7	H7	4.9°	164.7°
H8	C11	C12	H9	0.2°	0.2°
H9	C12	C13	H19	0.3°	0.0°
H10	C15	C14	H20	0.9°	0.3°
H13	C21	C20	H21	0.6°	0.2°
H14	C23	C24	H15	1.8°	0.0°
H16	C27	C26	H22	0.1°	0.1°
H16	C27	C28	H23	0.0°	0.2°
H19	C13	C14	H20	0.1°	0.1°
H23	C28	C29	H24	0.0°	0.1°

Release date:	2026-05-13
Definition date:	2026-01-09
Last modified:	2026-05-08
Release status:	REL
Processing site:	RCSB
Derived from:	10AK