Summary Geometry PCM/PTM Related PDB entries

E5O

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C2	C1	doub	1.36Å	1.38Å	Aromatic
C2	N5	sing	1.33Å	1.31Å	Aromatic
C1	N4	sing	1.32Å	1.32Å	Aromatic
N5	C3	doub	1.34Å	1.33Å	Aromatic
N4	CU	sing	2.18Å	2.09Å
N4	C4	doub	1.33Å	1.44Å	Aromatic
CU	S	sing	2.19Å	2.40Å
C3	C4	sing	1.40Å	1.51Å	Aromatic
C3	C5	sing	1.50Å	1.46Å
C4	C7	sing	1.48Å	1.52Å
C5	C6	sing	1.51Å	1.47Å
S	C9	sing	1.70Å	1.71Å
N1	C7	doub	1.27Å	1.31Å
N1	N2	sing	1.40Å	1.36Å
C7	C8	sing	1.50Å	1.52Å
N2	C9	doub	1.30Å	1.32Å
C9	N3	sing	1.38Å	1.28Å
N3	C10	sing	1.49Å	1.44Å
N3	C11	sing	1.49Å	1.47Å
C1	H1	sing	0.94Å	1.08Å
C2	H2	sing	0.94Å	1.08Å
C5	H3	sing	0.98Å	1.10Å
C5	H4	sing	0.98Å	1.10Å
C6	H5	sing	0.97Å	1.10Å
C6	H6	sing	0.97Å	1.10Å
C6	H7	sing	0.97Å	1.10Å
C8	H8	sing	0.97Å	1.10Å
C8	H9	sing	0.97Å	1.10Å
C8	H10	sing	0.97Å	1.10Å
C10	H11	sing	0.97Å	1.10Å
C10	H12	sing	0.97Å	1.10Å
C10	H13	sing	0.98Å	1.10Å
C11	H14	sing	0.97Å	1.10Å
C11	H15	sing	0.97Å	1.10Å
C11	H16	sing	0.98Å	1.10Å
CU	N1	sing	1.97Å	2.50Å
CU	BR1	sing	2.40Å	12.57Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	C2	N5	122.8°	121.9°
C2	C1	N4	120.2°	121.4°
C2	C1	H1	119.9°	119.6°
C1	C2	H2	118.6°	119.4°
C2	N5	C3	121.8°	118.2°
N5	C2	H2	118.6°	118.8°
C1	N4	CU	113.7°	125.8°
C1	N4	C4	121.8°	117.8°
N4	C1	H1	119.9°	119.0°
N5	C3	C4	119.5°	119.1°
N5	C3	C5	106.7°	117.1°
CU	N4	C4	124.5°	78.6°
N4	CU	S	142.3°	167.3°
N4	CU	N1	70.0°	94.5°
N4	CU	BR1	124.1°	92.3°
N4	C4	C3	113.8°	121.6°
N4	C4	C7	115.9°	111.5°
CU	S	C9	109.2°	108.8°
S	CU	N1	72.3°	74.1°
S	CU	BR1	64.4°	99.1°
C4	C3	C5	133.7°	123.8°
C3	C4	C7	130.3°	126.9°
C3	C5	C6	126.8°	113.1°
C3	C5	H3	105.0°	109.1°
C3	C5	H4	105.0°	109.3°
C4	C7	N1	112.4°	112.1°
C4	C7	C8	133.2°	120.7°
C6	C5	H3	104.9°	109.0°
C6	C5	H4	105.0°	109.8°
C5	C6	H5	109.5°	109.5°
C5	C6	H6	109.5°	109.6°
C5	C6	H7	109.5°	109.5°
S	C9	N2	120.2°	111.1°
S	C9	N3	124.9°	126.7°
C7	N1	N2	124.6°	133.3°
N1	C7	C8	114.4°	127.2°
C7	N1	CU	117.2°	88.0°
N1	N2	C9	120.2°	113.8°
N2	N1	CU	118.0°	125.0°
C7	C8	H8	109.5°	109.6°
C7	C8	H9	109.5°	109.5°
C7	C8	H10	109.5°	109.5°
N2	C9	N3	114.8°	122.2°
C9	N3	C10	121.2°	123.0°
C9	N3	C11	125.5°	123.2°
C10	N3	C11	113.3°	113.8°
N3	C10	H11	109.5°	110.4°
N3	C10	H12	109.5°	109.6°
N3	C10	H13	109.5°	109.6°
N3	C11	H14	109.5°	110.5°
N3	C11	H15	109.5°	109.6°
N3	C11	H16	109.5°	109.6°
H3	C5	H4	109.5°	106.3°
H5	C6	H6	109.5°	109.5°
H5	C6	H7	109.5°	109.4°
H6	C6	H7	109.4°	109.4°
H8	C8	H9	109.5°	109.4°
H8	C8	H10	109.5°	109.4°
H9	C8	H10	109.5°	109.5°
H11	C10	H12	109.5°	109.0°
H11	C10	H13	109.5°	108.9°
H12	C10	H13	109.5°	109.3°
H14	C11	H15	109.5°	108.9°
H14	C11	H16	109.5°	108.9°
H15	C11	H16	109.5°	109.2°
N1	CU	BR1	100.6°	173.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	C2	N5	H2	180.0°	179.4°
C2	C1	N4	H1	180.0°	177.7°
C1	C2	N5	C3	0.7°	0.6°
C2	C1	N4	CU	178.6°	94.2°
C2	C1	N4	C4	1.2°	1.8°
N5	C2	C1	N4	0.4°	1.7°
C2	N5	C3	C4	1.0°	0.2°
C2	N5	C3	C5	179.7°	180.0°
N5	C2	C1	H1	179.6°	179.3°
C1	N4	CU	C4	177.4°	116.2°
C1	N4	CU	S	177.3°	115.7°
C1	N4	C4	C3	0.8°	0.9°
C1	N4	C4	C7	179.5°	178.3°
N4	C1	C2	H2	179.6°	178.9°
C1	N4	CU	N1	179.1°	141.7°
C1	N4	CU	BR1	91.4°	37.4°
N5	C3	C4	N4	0.2°	0.1°
N5	C3	C4	C5	179.1°	179.7°
N5	C3	C4	C7	179.3°	179.2°
N5	C3	C5	C6	179.6°	94.1°
C3	N5	C2	H2	179.2°	180.0°
N5	C3	C5	H3	58.1°	27.4°
N5	C3	C5	H4	57.3°	143.3°
N4	CU	S	N1	1.8°	27.0°
N4	CU	S	BR1	113.4°	152.7°
CU	N4	C4	C3	178.0°	123.6°
CU	N4	C4	C7	2.4°	57.1°
N4	CU	S	C9	0.5°	42.3°
N4	CU	N1	C7	1.0°	14.5°
N4	CU	N1	N2	176.3°	159.0°
CU	N4	C1	H1	1.3°	83.5°
N4	CU	N1	BR1	122.6°	172.3°
C4	N4	CU	S	0.1°	0.5°
N4	C4	C3	C7	179.6°	179.1°
N4	C4	C3	C5	179.3°	179.8°
N4	C4	C7	N1	1.2°	98.2°
N4	C4	C7	C8	179.7°	84.7°
C4	N4	C1	H1	178.8°	179.4°
C4	N4	CU	N1	1.7°	25.5°
C4	N4	CU	BR1	91.2°	153.6°
S	CU	N1	C7	177.9°	171.2°
S	CU	N1	N2	2.6°	26.8°
CU	S	C9	N2	2.6°	6.2°
CU	S	C9	N3	177.5°	174.0°
S	CU	N1	BR1	58.6°	2.0°
C4	C3	C5	C6	1.2°	86.2°
C3	C4	C7	N1	179.2°	82.7°
C3	C4	C7	C8	0.2°	94.5°
C4	C3	C5	H3	121.1°	152.3°
C4	C3	C5	H4	123.5°	36.4°
C5	C3	C4	C7	0.2°	1.1°
C3	C5	C6	H3	122.3°	121.5°
C3	C5	C6	H4	122.3°	122.3°
C3	C5	H3	H4	112.2°	117.8°
C3	C5	C6	H5	180.0°	179.5°
C3	C5	C6	H6	60.0°	59.5°
C3	C5	C6	H7	60.0°	60.5°
C4	C7	N1	C8	179.2°	176.9°
C4	C7	N1	N2	175.1°	171.3°
C4	C7	C8	H8	180.0°	4.0°
C4	C7	C8	H9	60.0°	116.0°
C4	C7	C8	H10	60.0°	123.9°
C4	C7	N1	CU	0.1°	49.6°
C6	C5	H3	H4	112.2°	118.3°
C5	C6	H5	H6	120.0°	120.1°
C5	C6	H5	H7	120.0°	120.0°
C5	C6	H6	H7	120.0°	120.0°
S	C9	N2	N1	0.4°	12.0°
S	C9	N2	N3	179.9°	179.8°
S	C9	N3	C10	0.8°	179.3°
S	C9	N3	C11	179.9°	1.0°
C9	S	CU	N1	2.3°	15.3°
C9	S	CU	BR1	113.9°	165.0°
C7	N1	N2	CU	174.9°	127.0°
C7	N1	N2	C9	176.9°	158.2°
N1	C7	C8	H8	1.0°	179.4°
N1	C7	C8	H9	120.9°	60.6°
N1	C7	C8	H10	119.1°	59.4°
C7	N1	CU	BR1	123.5°	173.2°
N2	N1	C7	C8	4.2°	5.6°
N1	N2	C9	N3	179.6°	167.8°
N2	N1	CU	BR1	61.2°	28.8°
C7	C8	H8	H9	120.0°	120.1°
C7	C8	H8	H10	120.0°	120.1°
C7	C8	H9	H10	120.0°	120.1°
C8	C7	N1	CU	179.1°	133.5°
N2	C9	N3	C10	179.2°	1.0°
N2	C9	N3	C11	0.0°	178.8°
C9	N2	N1	CU	2.0°	31.2°
C9	N3	C10	C11	179.2°	179.8°
C9	N3	C10	H11	180.0°	1.0°
C9	N3	C10	H12	60.0°	119.1°
C9	N3	C10	H13	60.0°	121.0°
C9	N3	C11	H14	180.0°	0.8°
C9	N3	C11	H15	60.0°	119.3°
C9	N3	C11	H16	60.0°	120.9°
N3	C10	H11	H12	120.0°	120.5°
N3	C10	H11	H13	120.0°	120.4°
N3	C10	H12	H13	120.0°	120.2°
C10	N3	C11	H14	0.8°	179.0°
C10	N3	C11	H15	119.2°	61.0°
C10	N3	C11	H16	120.8°	58.9°
C11	N3	C10	H11	0.8°	179.2°
C11	N3	C10	H12	120.8°	60.7°
C11	N3	C10	H13	119.2°	59.2°
N3	C11	H14	H15	120.0°	120.4°
N3	C11	H14	H16	120.0°	120.5°
N3	C11	H15	H16	120.0°	120.1°
H1	C1	C2	H2	0.4°	1.3°
H3	C5	C6	H5	57.7°	59.0°
H3	C5	C6	H6	177.7°	179.0°
H3	C5	C6	H7	62.3°	61.0°
H4	C5	C6	H5	57.7°	57.2°
H4	C5	C6	H6	62.3°	62.9°
H4	C5	C6	H7	177.7°	177.1°
H5	C6	H6	H7	120.0°	119.9°
H8	C8	H9	H10	120.0°	119.8°
H11	C10	H12	H13	120.0°	118.9°
H14	C11	H15	H16	120.0°	118.9°

Release date:	2020-10-21
Definition date:	2019-10-18
Last modified:	2026-09-16
Release status:	REL
Processing site:	PDBJ
Derived from:	6L4K