Summary Geometry PCM/PTM Related PDB entries

A1EBR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	O2	sing	1.35Å	1.33Å
C1	O1	doub	1.21Å	1.21Å
C1	C3	sing	1.48Å	1.47Å
C10	C11	sing	1.51Å	1.49Å
C10	N1	sing	1.47Å	1.47Å
C11	C14	doub	1.32Å	1.37Å	Aromatic
C11	S2	sing	1.75Å	1.74Å	Aromatic
C12	S2	sing	1.76Å	1.74Å	Aromatic
C12	C13	doub	1.40Å	1.40Å	Aromatic
C12	C18	sing	1.40Å	1.39Å	Aromatic
C13	C15	sing	1.41Å	1.39Å	Aromatic
C13	C14	sing	1.45Å	1.47Å	Aromatic
C15	C16	doub	1.36Å	1.39Å	Aromatic
C16	C17	sing	1.39Å	1.39Å	Aromatic
C17	C18	doub	1.38Å	1.39Å	Aromatic
C2	O2	sing	1.45Å	1.44Å
C3	C4	doub	1.34Å	1.33Å
C4	C5	sing	1.48Å	1.34Å
C5	O3	doub	1.22Å	1.22Å
C5	N1	sing	1.35Å	1.33Å
C6	C9	sing	1.54Å	1.54Å
C6	N1	sing	1.47Å	1.47Å
C6	C7	sing	1.54Å	1.54Å
C7	C8	sing	1.55Å	1.52Å
C8	S1	sing	1.83Å	1.77Å
C9	S1	sing	1.83Å	1.79Å
O4	S1	doub	1.42Å	1.44Å
O5	S1	doub	1.42Å	1.44Å
C4	H12	sing	1.08Å	1.08Å
C6	H13	sing	1.09Å	1.10Å
C7	H14	sing	1.09Å	1.10Å
C7	H15	sing	1.09Å	1.10Å
C8	H16	sing	1.09Å	1.10Å
C8	H17	sing	1.09Å	1.10Å
C10	H2	sing	1.09Å	1.10Å
C10	H1	sing	1.09Å	1.10Å
C15	H4	sing	1.08Å	1.08Å
C17	H6	sing	1.08Å	1.08Å
C14	H3	sing	1.08Å	1.08Å
C16	H5	sing	1.08Å	1.08Å
C18	H7	sing	1.08Å	1.08Å
C2	H9	sing	1.09Å	1.10Å
C2	H8	sing	1.09Å	1.10Å
C2	H10	sing	1.09Å	1.10Å
C3	H11	sing	1.08Å	1.08Å
C9	H19	sing	1.09Å	1.10Å
C9	H18	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O2	C1	O1	122.6°	120.0°
O2	C1	C3	111.6°	120.0°
C1	O2	C2	115.6°	117.0°
O1	C1	C3	125.8°	120.0°
C1	C3	C4	123.8°	120.0°
C1	C3	H11	118.1°	120.0°
C11	C10	N1	118.5°	109.4°
C10	C11	C14	133.9°	124.3°
C10	C11	S2	117.6°	124.3°
C11	C10	H2	107.2°	109.5°
C11	C10	H1	107.2°	109.5°
C10	N1	C5	123.2°	120.0°
C10	N1	C6	120.7°	120.0°
N1	C10	H2	107.1°	109.5°
N1	C10	H1	107.2°	109.5°
C14	C11	S2	108.5°	111.4°
C11	C14	C13	115.1°	114.9°
C11	C14	H3	122.5°	122.5°
C11	S2	C12	95.3°	92.2°
S2	C12	C13	109.5°	109.7°
S2	C12	C18	129.0°	130.6°
C13	C12	C18	121.5°	119.8°
C12	C13	C15	119.6°	118.8°
C12	C13	C14	111.5°	111.8°
C12	C18	C17	118.2°	120.2°
C12	C18	H7	120.9°	119.9°
C15	C13	C14	129.0°	129.3°
C13	C15	C16	119.1°	120.4°
C13	C15	H4	120.4°	119.8°
C13	C14	H3	122.5°	122.5°
C15	C16	C17	120.9°	120.6°
C16	C15	H4	120.4°	119.8°
C15	C16	H5	119.6°	119.7°
C16	C17	C18	120.7°	120.2°
C16	C17	H6	119.6°	119.9°
C17	C16	H5	119.6°	119.7°
C18	C17	H6	119.7°	119.9°
C17	C18	H7	120.9°	119.9°
O2	C2	H9	109.5°	109.4°
O2	C2	H8	109.5°	109.5°
O2	C2	H10	109.4°	109.4°
C3	C4	C5	119.7°	120.0°
C3	C4	H12	120.2°	120.0°
C4	C3	H11	118.1°	120.0°
C4	C5	O3	121.6°	120.0°
C4	C5	N1	122.3°	120.0°
C5	C4	H12	120.2°	120.0°
O3	C5	N1	116.0°	120.0°
C5	N1	C6	116.0°	120.0°
C9	C6	N1	115.2°	109.6°
C9	C6	C7	103.4°	108.7°
C6	C9	S1	101.8°	105.1°
C9	C6	H13	107.2°	109.7°
C6	C9	H19	111.4°	110.3°
C6	C9	H18	111.3°	110.3°
N1	C6	C7	115.2°	109.6°
N1	C6	H13	108.1°	109.6°
C6	C7	C8	103.1°	106.6°
C7	C6	H13	107.2°	109.6°
C6	C7	H14	111.0°	110.0°
C6	C7	H15	111.0°	110.0°
C7	C8	S1	105.1°	102.6°
C8	C7	H14	111.0°	110.0°
C8	C7	H15	111.0°	110.1°
C7	C8	H16	110.6°	110.8°
C7	C8	H17	110.5°	110.7°
C8	S1	C9	96.6°	97.0°
C8	S1	O4	108.7°	109.4°
C8	S1	O5	110.9°	109.3°
S1	C8	H16	110.6°	110.8°
S1	C8	H17	110.6°	110.8°
C9	S1	O4	110.3°	109.4°
C9	S1	O5	110.5°	109.3°
S1	C9	H19	111.4°	110.3°
S1	C9	H18	111.4°	110.3°
O4	S1	O5	117.8°	120.0°
H14	C7	H15	109.5°	110.1°
H16	C8	H17	109.5°	110.8°
H2	C10	H1	109.5°	109.5°
H9	C2	H8	109.5°	109.5°
H9	C2	H10	109.5°	109.5°
H8	C2	H10	109.5°	109.5°
H19	C9	H18	109.4°	110.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O2	C1	O1	C3	179.1°	180.0°
O2	C1	C3	C4	161.4°	111.6°
C1	O2	C2	H9	180.0°	60.1°
C1	O2	C2	H8	60.0°	60.0°
C1	O2	C2	H10	60.0°	180.0°
O2	C1	C3	H11	18.6°	68.4°
O1	C1	O2	C2	4.2°	0.0°
O1	C1	C3	C4	19.4°	68.3°
O1	C1	C3	H11	160.6°	111.7°
C3	C1	O2	C2	176.6°	180.0°
C1	C3	C4	H11	180.0°	180.0°
C1	C3	C4	C5	14.0°	44.6°
C1	C3	C4	H12	166.0°	135.4°
C11	C10	N1	H2	121.3°	120.0°
C11	C10	N1	H1	121.3°	120.0°
C10	C11	C14	S2	179.0°	179.8°
C10	C11	S2	C12	176.5°	179.9°
C10	C11	C14	C13	175.8°	180.0°
C11	C10	N1	C5	115.6°	90.0°
C11	C10	N1	C6	68.4°	90.3°
C11	C10	H2	H1	115.9°	120.0°
C10	C11	C14	H3	4.2°	0.0°
N1	C10	C11	C14	104.1°	90.0°
N1	C10	C11	S2	74.8°	89.8°
C10	N1	C5	C4	6.6°	178.3°
C10	N1	C5	O3	170.3°	1.6°
C10	N1	C5	C6	176.2°	179.7°
C10	N1	C6	C9	57.2°	126.5°
C10	N1	C6	C7	63.1°	114.3°
C10	N1	C6	H13	177.1°	6.0°
N1	C10	H2	H1	115.9°	120.0°
C14	C11	S2	C12	4.3°	0.0°
C11	C14	C13	C12	3.7°	0.3°
C11	C14	C13	C15	176.8°	180.0°
C11	C14	C13	H3	180.0°	180.0°
C14	C11	C10	H2	17.2°	30.0°
C14	C11	C10	H1	134.6°	150.0°
C11	S2	C12	C13	2.2°	0.1°
C11	S2	C12	C18	177.9°	179.8°
S2	C11	C14	C13	5.2°	0.2°
S2	C11	C10	H2	163.9°	150.2°
S2	C11	C10	H1	46.5°	30.2°
S2	C11	C14	H3	174.8°	179.8°
S2	C12	C13	C18	179.9°	180.0°
S2	C12	C13	C15	179.9°	180.0°
S2	C12	C13	C14	0.3°	0.3°
S2	C12	C18	C17	179.8°	179.4°
S2	C12	C18	H7	0.2°	0.4°
C12	C13	C15	C14	179.4°	179.6°
C12	C13	C15	C16	0.0°	0.4°
C13	C12	C18	C17	0.1°	0.6°
C12	C13	C15	H4	180.0°	179.7°
C12	C13	C14	H3	176.3°	179.7°
C13	C12	C18	H7	179.9°	179.6°
C18	C12	C13	C15	0.0°	0.0°
C18	C12	C13	C14	179.6°	179.7°
C12	C18	C17	C16	0.1°	0.9°
C12	C18	C17	H7	180.0°	179.1°
C12	C18	C17	H6	179.9°	180.0°
C13	C15	C16	H4	180.0°	179.9°
C13	C15	C16	C17	0.0°	0.1°
C15	C13	C14	H3	3.2°	0.1°
C13	C15	C16	H5	179.9°	180.0°
C14	C13	C15	C16	179.4°	180.0°
C14	C13	C15	H4	0.6°	0.1°
C15	C16	C17	H5	180.0°	179.9°
C15	C16	C17	C18	0.0°	0.6°
C15	C16	C17	H6	180.0°	179.7°
C16	C17	C18	H6	180.0°	179.1°
C17	C16	C15	H4	179.9°	180.0°
C16	C17	C18	H7	179.9°	179.9°
C18	C17	C16	H5	180.0°	179.3°
O2	C2	H9	H8	120.0°	120.0°
O2	C2	H9	H10	120.0°	119.9°
O2	C2	H8	H10	120.0°	119.9°
C3	C4	C5	H12	180.0°	180.0°
C3	C4	C5	O3	76.3°	8.7°
C3	C4	C5	N1	100.5°	171.2°
C4	C5	O3	N1	177.0°	180.0°
C4	C5	N1	C6	177.2°	1.3°
C5	C4	C3	H11	166.0°	135.4°
O3	C5	N1	C6	5.9°	178.7°
O3	C5	C4	H12	103.7°	171.2°
C5	N1	C6	C9	119.1°	53.2°
C5	N1	C6	C7	120.6°	66.0°
N1	C5	C4	H12	79.5°	8.8°
C5	N1	C6	H13	0.8°	173.7°
C5	N1	C10	H2	123.1°	150.0°
C5	N1	C10	H1	5.7°	30.0°
C9	C6	N1	C7	120.3°	119.2°
C9	C6	N1	H13	119.9°	120.5°
C9	C6	C7	H13	113.1°	119.8°
C9	C6	C7	C8	57.6°	47.2°
C6	C9	S1	C8	20.8°	2.2°
C6	C9	S1	H19	118.8°	118.9°
C6	C9	S1	H18	118.8°	118.9°
C6	C9	S1	O4	91.9°	111.3°
C6	C9	S1	O5	136.1°	115.5°
C9	C6	C7	H14	176.5°	166.5°
C9	C6	C7	H15	61.4°	72.1°
C6	C9	H19	H18	123.5°	122.2°
N1	C6	C7	H13	120.3°	120.3°
N1	C6	C7	C8	175.8°	167.1°
N1	C6	C9	S1	173.7°	147.8°
N1	C6	C7	H14	56.9°	73.7°
N1	C6	C7	H15	65.2°	47.7°
C6	N1	C10	H2	52.9°	29.7°
C6	N1	C10	H1	170.3°	149.7°
N1	C6	C9	H19	54.9°	28.8°
N1	C6	C9	H18	67.6°	93.4°
C6	C7	C8	H14	119.0°	119.2°
C6	C7	C8	H15	119.0°	119.3°
C6	C7	C8	S1	40.4°	42.4°
C7	C6	C9	S1	47.1°	28.0°
C6	C7	H14	H15	123.0°	121.4°
C6	C7	C8	H16	78.9°	75.9°
C6	C7	C8	H17	159.7°	160.7°
C7	C6	C9	H19	71.7°	91.0°
C7	C6	C9	H18	165.8°	146.8°
C7	C8	S1	H16	119.3°	118.3°
C7	C8	S1	H17	119.3°	118.2°
C7	C8	S1	C9	11.5°	23.2°
C7	C8	S1	O4	125.5°	136.7°
C7	C8	S1	O5	103.5°	90.2°
C8	C7	C6	H13	55.5°	72.6°
C8	C7	H14	H15	123.0°	121.5°
C7	C8	H16	H17	122.0°	123.4°
C8	S1	C9	O4	112.7°	113.4°
C8	S1	C9	O5	115.3°	113.4°
C8	S1	O4	O5	127.1°	127.4°
S1	C8	C7	H14	159.4°	161.7°
S1	C8	C7	H15	78.6°	76.8°
S1	C8	H16	H17	122.0°	123.5°
C8	S1	C9	H19	98.0°	116.8°
C8	S1	C9	H18	139.6°	121.0°
C9	S1	O4	O5	128.1°	127.5°
S1	C9	C6	H13	66.0°	91.8°
C9	S1	C8	H16	107.9°	95.1°
C9	S1	C8	H17	130.8°	141.4°
S1	C9	H19	H18	123.6°	122.2°
O4	S1	C8	H16	6.2°	18.3°
O4	S1	C8	H17	115.2°	105.1°
O4	S1	C9	H19	149.3°	129.8°
O4	S1	C9	H18	26.9°	7.6°
O5	S1	C8	H16	137.2°	151.5°
O5	S1	C8	H17	15.8°	28.0°
O5	S1	C9	H19	17.3°	3.4°
O5	S1	C9	H18	105.1°	125.6°
H12	C4	C3	H11	14.0°	44.6°
H13	C6	C7	H14	63.4°	46.7°
H13	C6	C7	H15	174.5°	168.1°
H13	C6	C9	H19	175.2°	149.3°
H13	C6	C9	H18	52.8°	27.1°
H14	C7	C8	H16	40.0°	43.4°
H14	C7	C8	H17	81.3°	80.0°
H15	C7	C8	H16	162.1°	164.9°
H15	C7	C8	H17	40.7°	41.4°
H4	C15	C16	H5	0.1°	0.1°
H6	C17	C16	H5	0.0°	0.2°
H6	C17	C18	H7	0.1°	0.9°
H9	C2	H8	H10	120.0°	120.0°

Release date:	2026-03-11
Definition date:	2024-09-09
Last modified:	2026-03-06
Release status:	REL
Processing site:	PDBC
Derived from:	9JF6