Summary Geometry PCM/PTM Related PDB entries

A1ERK

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
S1	C2	sing	1.83Å	1.87Å
C2	C3	sing	1.54Å	1.55Å
C3	C4	sing	1.54Å	1.61Å
C4	C5	sing	1.55Å	1.58Å
S1	C5	sing	1.83Å	1.75Å
C3	N6	sing	1.46Å	1.56Å
N6	C7	sing	1.46Å	1.52Å
S1	O8	doub	1.42Å	1.52Å
S1	O9	doub	1.42Å	1.56Å
C7	C10	sing	1.51Å	1.50Å
C10	C11	doub	1.33Å	1.30Å	Aromatic
C11	C12	sing	1.39Å	1.44Å	Aromatic
C12	C13	doub	1.34Å	1.32Å	Aromatic
C13	S14	sing	1.76Å	1.77Å	Aromatic
C10	S14	sing	1.76Å	1.75Å	Aromatic
C13	O15	sing	1.36Å	1.43Å
O15	C16	sing	1.36Å	1.46Å
C16	C17	doub	1.39Å	1.41Å	Aromatic
C17	C18	sing	1.38Å	1.38Å	Aromatic
C18	C19	doub	1.38Å	1.38Å	Aromatic
C19	C20	sing	1.38Å	1.39Å	Aromatic
C20	C21	doub	1.38Å	1.39Å	Aromatic
C16	C21	sing	1.39Å	1.39Å	Aromatic
N6	C22	sing	1.35Å	1.47Å
C22	C23	sing	1.51Å	1.51Å
C22	O24	doub	1.21Å	1.26Å
C11	H10	sing	1.08Å	1.08Å
C12	H11	sing	1.08Å	1.08Å
C17	H12	sing	1.08Å	1.08Å
C18	H13	sing	1.08Å	1.08Å
C19	H14	sing	1.08Å	1.08Å
C2	H2	sing	1.09Å	1.10Å
C2	H1	sing	1.09Å	1.10Å
C20	H15	sing	1.08Å	1.08Å
C21	H16	sing	1.08Å	1.08Å
C23	H18	sing	1.09Å	1.10Å
C23	H19	sing	1.09Å	1.10Å
C3	H3	sing	1.09Å	1.10Å
C4	H5	sing	1.09Å	1.10Å
C4	H4	sing	1.09Å	1.10Å
C5	H7	sing	1.09Å	1.10Å
C5	H6	sing	1.09Å	1.10Å
C7	H9	sing	1.09Å	1.10Å
C7	H8	sing	1.09Å	1.10Å
C23	CL1	sing	1.80Å	1.79Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
S1	C2	C3	98.9°	105.1°
C2	S1	C5	96.8°	97.0°
C2	S1	O8	111.3°	109.4°
C2	S1	O9	111.6°	109.4°
S1	C2	H2	112.0°	110.3°
S1	C2	H1	112.1°	110.4°
C2	C3	C4	112.3°	108.7°
C2	C3	N6	114.6°	109.7°
C3	C2	H2	112.0°	110.3°
C3	C2	H1	112.0°	110.3°
C2	C3	H3	107.6°	109.6°
C3	C4	C5	108.3°	106.6°
C4	C3	N6	107.6°	109.6°
C4	C3	H3	106.9°	109.7°
C3	C4	H5	109.8°	110.1°
C3	C4	H4	109.8°	110.0°
C4	C5	S1	105.2°	102.5°
C5	C4	H5	109.7°	110.0°
C5	C4	H4	109.7°	110.0°
C4	C5	H7	110.6°	110.8°
C4	C5	H6	110.5°	110.8°
C5	S1	O8	111.7°	109.3°
C5	S1	O9	111.3°	109.3°
S1	C5	H7	110.5°	110.8°
S1	C5	H6	110.5°	110.9°
C3	N6	C7	115.2°	120.0°
C3	N6	C22	115.9°	120.0°
N6	C3	H3	107.4°	109.6°
N6	C7	C10	109.2°	109.5°
C7	N6	C22	128.8°	120.0°
N6	C7	H9	109.5°	109.5°
N6	C7	H8	109.5°	109.5°
O8	S1	O9	113.1°	120.0°
C7	C10	C11	118.0°	125.2°
C7	C10	S14	130.3°	125.1°
C10	C7	H9	109.6°	109.5°
C10	C7	H8	109.5°	109.4°
C10	C11	C12	114.1°	115.0°
C11	C10	S14	111.8°	109.6°
C10	C11	H10	122.9°	122.4°
C11	C12	C13	113.2°	114.7°
C12	C11	H10	123.0°	122.5°
C11	C12	H11	123.4°	122.6°
C12	C13	S14	110.7°	109.6°
C12	C13	O15	122.8°	125.2°
C13	C12	H11	123.4°	122.7°
C13	S14	C10	90.2°	91.0°
S14	C13	O15	126.5°	125.2°
C13	O15	C16	112.2°	118.0°
O15	C16	C17	124.1°	120.1°
O15	C16	C21	116.5°	120.1°
C16	C17	C18	120.6°	120.0°
C17	C16	C21	119.3°	119.8°
C16	C17	H12	119.7°	120.0°
C17	C18	C19	119.3°	120.1°
C18	C17	H12	119.7°	120.0°
C17	C18	H13	120.3°	120.0°
C18	C19	C20	120.7°	120.1°
C19	C18	H13	120.3°	119.9°
C18	C19	H14	119.7°	120.0°
C19	C20	C21	120.0°	120.1°
C20	C19	H14	119.7°	120.0°
C19	C20	H15	120.0°	119.9°
C20	C21	C16	120.1°	120.0°
C21	C20	H15	120.0°	120.0°
C20	C21	H16	120.0°	120.0°
C16	C21	H16	120.0°	120.0°
N6	C22	C23	122.5°	120.0°
N6	C22	O24	120.8°	120.0°
C23	C22	O24	116.7°	120.0°
C22	C23	H18	109.8°	109.5°
C22	C23	H19	109.8°	109.5°
C22	C23	CL1	108.1°	109.5°
H2	C2	H1	109.5°	110.3°
H18	C23	H19	109.5°	109.4°
H18	C23	CL1	109.8°	109.5°
H19	C23	CL1	109.8°	109.5°
H5	C4	H4	109.5°	110.1°
H7	C5	H6	109.4°	110.7°
H9	C7	H8	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
S1	C2	C3	H2	118.2°	118.9°
S1	C2	C3	H1	118.3°	119.0°
S1	C2	C3	C4	33.8°	27.9°
C2	S1	C5	C4	35.4°	23.2°
C2	S1	C5	O8	116.2°	113.4°
C2	S1	C5	O9	116.4°	113.4°
S1	C2	C3	N6	156.9°	147.7°
C2	S1	O8	O9	126.6°	127.5°
S1	C2	H2	H1	125.0°	122.3°
S1	C2	C3	H3	83.6°	91.9°
C2	S1	C5	H7	83.9°	141.5°
C2	S1	C5	H6	154.7°	95.1°
C2	C3	C4	N6	127.0°	119.8°
C2	C3	C4	H3	117.8°	119.8°
C2	C3	C4	C5	12.0°	47.2°
C3	C2	S1	C5	40.7°	2.1°
C2	C3	N6	H3	119.5°	120.4°
C2	C3	N6	C7	120.0°	120.0°
C3	C2	S1	O8	75.7°	111.3°
C3	C2	S1	O9	156.8°	115.5°
C2	C3	N6	C22	59.2°	60.0°
C3	C2	H2	H1	124.9°	122.1°
C2	C3	C4	H5	107.8°	72.1°
C2	C3	C4	H4	131.7°	166.4°
C3	C4	C5	H5	119.8°	119.3°
C3	C4	C5	H4	119.8°	119.2°
C3	C4	C5	S1	18.4°	42.5°
C4	C3	N6	H3	114.8°	120.4°
C4	C3	N6	C7	114.4°	120.8°
C4	C3	N6	C22	66.4°	59.3°
C4	C3	C2	H2	84.4°	146.8°
C4	C3	C2	H1	152.1°	91.1°
C3	C4	H5	H4	120.6°	121.4°
C3	C4	C5	H7	100.9°	160.7°
C3	C4	C5	H6	137.7°	76.0°
C4	C5	S1	H7	119.4°	118.3°
C4	C5	S1	H6	119.3°	118.3°
C5	C4	C3	N6	139.0°	167.0°
C4	C5	S1	O8	80.8°	136.6°
C4	C5	S1	O9	151.8°	90.2°
C5	C4	C3	H3	105.9°	72.6°
C5	C4	H5	H4	120.5°	121.4°
C4	C5	H7	H6	122.0°	123.3°
C5	S1	O8	O9	126.5°	127.4°
C5	S1	C2	H2	77.5°	121.0°
C5	S1	C2	H1	159.0°	116.8°
S1	C5	C4	H5	138.2°	76.9°
S1	C5	C4	H4	101.4°	161.7°
S1	C5	H7	H6	122.0°	123.5°
C3	N6	C7	C22	179.1°	180.0°
C3	N6	C7	C10	98.5°	90.0°
C3	N6	C22	C23	179.4°	180.0°
C3	N6	C22	O24	1.5°	0.0°
N6	C3	C2	H2	38.7°	93.3°
N6	C3	C2	H1	84.8°	28.7°
N6	C3	C4	H5	19.2°	47.7°
N6	C3	C4	H4	101.2°	73.7°
C3	N6	C7	H9	141.5°	30.0°
C3	N6	C7	H8	21.5°	150.0°
N6	C7	C10	H9	120.0°	120.0°
N6	C7	C10	H8	120.0°	120.0°
N6	C7	C10	C11	56.2°	90.0°
N6	C7	C10	S14	123.6°	89.7°
C7	N6	C22	C23	1.5°	0.0°
C7	N6	C22	O24	177.6°	180.0°
C7	N6	C3	H3	0.4°	0.4°
N6	C7	H9	H8	120.1°	120.0°
O8	S1	C2	H2	166.0°	7.6°
O8	S1	C2	H1	42.5°	129.8°
O8	S1	C5	H7	159.9°	105.1°
O8	S1	C5	H6	38.6°	18.3°
O9	S1	C2	H2	38.6°	125.6°
O9	S1	C2	H1	84.9°	3.4°
O9	S1	C5	H7	32.4°	28.1°
O9	S1	C5	H6	88.9°	151.5°
C7	C10	C11	S14	179.8°	179.7°
C7	C10	C11	C12	179.8°	179.7°
C7	C10	S14	C13	179.9°	179.7°
C10	C7	N6	C22	82.4°	90.0°
C7	C10	C11	H10	0.2°	0.3°
C10	C7	H9	H8	120.1°	120.0°
C10	C11	C12	H10	180.0°	180.0°
C10	C11	C12	C13	0.6°	0.0°
C11	C10	S14	C13	0.0°	0.0°
C10	C11	C12	H11	179.5°	180.0°
C11	C10	C7	H9	63.8°	150.0°
C11	C10	C7	H8	176.1°	30.0°
C11	C12	C13	H11	180.0°	180.0°
C11	C12	C13	S14	0.5°	0.0°
C12	C11	C10	S14	0.3°	0.0°
C11	C12	C13	O15	179.3°	180.0°
C12	C13	S14	O15	178.7°	180.0°
C12	C13	S14	C10	0.3°	0.0°
C12	C13	O15	C16	30.9°	175.5°
C13	C12	C11	H10	179.4°	180.0°
S14	C13	O15	C16	147.7°	4.5°
S14	C13	C12	H11	179.5°	180.0°
C10	S14	C13	O15	179.0°	180.0°
S14	C10	C11	H10	179.7°	180.0°
S14	C10	C7	H9	116.4°	30.3°
S14	C10	C7	H8	3.7°	150.3°
C13	O15	C16	C17	50.9°	77.1°
C13	O15	C16	C21	126.2°	103.2°
O15	C13	C12	H11	0.7°	0.1°
O15	C16	C17	C21	177.0°	179.7°
O15	C16	C17	C18	179.1°	179.7°
O15	C16	C21	C20	179.2°	179.8°
O15	C16	C17	H12	0.9°	0.3°
O15	C16	C21	H16	0.8°	0.3°
C16	C17	C18	H12	180.0°	179.9°
C16	C17	C18	C19	0.9°	0.0°
C17	C16	C21	C20	1.9°	0.1°
C16	C17	C18	H13	179.1°	180.0°
C17	C16	C21	H16	178.1°	180.0°
C17	C18	C19	H13	180.0°	179.9°
C17	C18	C19	C20	0.4°	0.0°
C18	C17	C16	C21	2.0°	0.0°
C17	C18	C19	H14	179.6°	179.9°
C18	C19	C20	H14	180.0°	180.0°
C18	C19	C20	C21	0.5°	0.1°
C19	C18	C17	H12	179.1°	179.9°
C18	C19	C20	H15	179.5°	180.0°
C19	C20	C21	H15	180.0°	180.0°
C19	C20	C21	C16	0.7°	0.1°
C20	C19	C18	H13	179.6°	180.0°
C19	C20	C21	H16	179.3°	180.0°
C20	C21	C16	H16	180.0°	179.9°
C21	C20	C19	H14	179.5°	180.0°
C21	C16	C17	H12	177.9°	180.0°
C16	C21	C20	H15	179.3°	179.9°
N6	C22	C23	O24	179.1°	180.0°
N6	C22	C23	H18	136.7°	60.0°
N6	C22	C23	H19	16.3°	60.0°
C22	N6	C3	H3	178.8°	179.6°
C22	N6	C7	H9	37.5°	150.0°
C22	N6	C7	H8	157.6°	30.0°
N6	C22	C23	CL1	103.5°	180.0°
C22	C23	H18	H19	120.6°	120.1°
C22	C23	H18	CL1	118.7°	120.0°
C22	C23	H19	CL1	118.7°	120.0°
O24	C22	C23	H18	42.4°	120.0°
O24	C22	C23	H19	162.8°	120.0°
O24	C22	C23	CL1	77.4°	0.0°
H10	C11	C12	H11	0.6°	0.0°
H12	C17	C18	H13	0.9°	0.0°
H13	C18	C19	H14	0.4°	0.0°
H14	C19	C20	H15	0.5°	0.0°
H2	C2	C3	H3	158.1°	27.0°
H1	C2	C3	H3	34.6°	149.1°
H15	C20	C21	H16	0.7°	0.0°
H18	C23	H19	CL1	120.7°	120.0°
H3	C3	C4	H5	134.4°	168.1°
H3	C3	C4	H4	13.9°	46.6°
H5	C4	C5	H7	18.9°	41.4°
H5	C4	C5	H6	102.5°	164.7°
H4	C4	C5	H7	139.3°	80.0°
H4	C4	C5	H6	17.9°	43.2°

Release date:	2026-06-10
Definition date:	2025-06-06
Last modified:	2026-06-05
Release status:	REL
Processing site:	PDBC
Derived from:	9V6W