Summary Geometry PCM/PTM Related PDB entries

JI6

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C1	doub	1.26Å	1.24Å
O4	C10	sing	1.43Å	1.48Å
C10	C11	sing	1.51Å	1.58Å
C10	C9	sing	1.54Å	1.57Å
C1	O2	sing	1.26Å	1.35Å
C1	C9	sing	1.54Å	1.52Å
O2	CU	sing	1.97Å	2.03Å
C9	N1	sing	1.47Å	1.49Å
N1	CU	sing	1.94Å	1.98Å
N1	C8	doub	1.27Å	1.28Å
CU	O3	sing	2.06Å	1.99Å
C8	C7	sing	1.45Å	1.50Å
O3	C2	sing	1.27Å	1.37Å
C7	C2	sing	1.40Å	1.42Å	Aromatic
C7	C6	doub	1.40Å	1.43Å	Aromatic
C2	C3	doub	1.42Å	1.43Å	Aromatic
C6	C5	sing	1.38Å	1.44Å	Aromatic
C3	C4	sing	1.39Å	1.44Å	Aromatic
C5	C4	doub	1.38Å	1.44Å	Aromatic
C3	H1	sing	0.94Å	1.08Å
C4	H2	sing	0.94Å	1.08Å
O4	H3	sing	0.87Å	0.95Å
C5	H4	sing	0.94Å	1.08Å
C6	H5	sing	0.94Å	1.08Å
C11	H6	sing	0.97Å	1.10Å
C11	H7	sing	0.97Å	1.10Å
C11	H8	sing	0.97Å	1.10Å
C10	H9	sing	0.99Å	1.10Å
C8	H10	sing	0.95Å	1.08Å
C9	H11	sing	1.00Å	1.10Å
O5	CU	sing	1.96Å	21.33Å
H12	O5	sing	0.86Å	0.00Å
H13	O5	sing	0.86Å	0.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C1	O2	121.6°	124.5°
O1	C1	C9	119.2°	118.2°
O4	C10	C11	109.7°	107.3°
O4	C10	C9	106.5°	112.3°
C10	O4	H3	109.5°	111.8°
O4	C10	H9	110.5°	108.5°
C11	C10	C9	111.9°	114.0°
C10	C11	H6	109.5°	109.8°
C10	C11	H7	109.5°	109.4°
C10	C11	H8	109.5°	109.7°
C11	C10	H9	109.0°	107.0°
C10	C9	C1	106.1°	112.3°
C10	C9	N1	111.0°	113.6°
C9	C10	H9	109.2°	107.6°
C10	C9	H11	110.1°	107.6°
O2	C1	C9	119.2°	117.3°
C1	O2	CU	113.7°	107.0°
C1	C9	N1	107.7°	108.8°
C1	C9	H11	110.7°	106.8°
O2	CU	N1	82.7°	83.8°
O2	CU	O3	172.6°	107.7°
O2	CU	O5	25.2°	152.2°
C9	N1	CU	116.0°	105.3°
C9	N1	C8	116.8°	133.2°
N1	C9	H11	111.2°	107.4°
CU	N1	C8	123.9°	73.6°
N1	CU	O3	91.8°	115.6°
N1	CU	O5	59.6°	98.0°
N1	C8	C7	123.8°	122.3°
N1	C8	H10	118.1°	119.4°
CU	O3	C2	122.4°	100.9°
O3	CU	O5	147.8°	96.6°
C8	C7	C2	124.6°	113.9°
C8	C7	C6	114.9°	123.7°
C7	C8	H10	118.1°	118.3°
O3	C2	C7	122.9°	116.5°
O3	C2	C3	116.1°	126.0°
C2	C7	C6	120.5°	121.5°
C7	C2	C3	121.0°	116.6°
C7	C6	C5	119.8°	119.8°
C7	C6	H5	120.1°	119.8°
C2	C3	C4	118.3°	120.9°
C2	C3	H1	120.9°	119.1°
C6	C5	C4	118.7°	119.6°
C6	C5	H4	120.6°	120.1°
C5	C6	H5	120.1°	120.3°
C3	C4	C5	121.7°	120.9°
C4	C3	H1	120.9°	119.9°
C3	C4	H2	119.1°	119.4°
C5	C4	H2	119.2°	119.7°
C4	C5	H4	120.6°	120.3°
H6	C11	H7	109.5°	109.2°
H6	C11	H8	109.4°	109.4°
H7	C11	H8	109.5°	109.3°
CU	O5	H12	90.0°	109.5°
CU	O5	H13	90.0°	109.5°
H12	O5	H13	90.0°	107.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C1	C9	C10	68.4°	57.8°
O1	C1	O2	C9	179.5°	177.5°
O1	C1	O2	CU	177.8°	147.6°
O1	C1	C9	N1	172.8°	175.6°
O1	C1	C9	H11	51.0°	59.9°
O4	C10	C11	C9	118.0°	125.0°
O4	C10	C11	H9	121.2°	116.2°
O4	C10	C9	H9	119.3°	119.3°
O4	C10	C9	C1	55.2°	70.6°
O4	C10	C9	N1	61.5°	53.5°
O4	C10	C11	H6	180.0°	177.4°
O4	C10	C11	H7	60.0°	57.6°
O4	C10	C11	H8	60.0°	62.3°
O4	C10	C9	H11	175.0°	172.3°
C11	C10	C9	H9	120.8°	118.4°
C11	C10	C9	C1	175.1°	167.1°
C11	C10	C9	N1	58.4°	68.8°
C11	C10	O4	H3	180.0°	164.9°
C10	C11	H6	H7	120.0°	120.0°
C10	C11	H6	H8	120.0°	120.4°
C10	C11	H7	H8	120.0°	120.1°
C11	C10	C9	H11	65.1°	50.0°
C10	C9	C1	O2	111.1°	124.6°
C10	C9	C1	N1	118.9°	126.6°
C10	C9	C1	H11	119.4°	117.7°
C10	C9	N1	H11	122.8°	118.9°
C10	C9	N1	CU	106.3°	153.1°
C10	C9	N1	C8	93.3°	71.3°
C9	C10	O4	H3	58.8°	69.1°
C9	C10	C11	H6	62.0°	57.6°
C9	C10	C11	H7	58.0°	177.5°
C9	C10	C11	H8	178.0°	62.7°
O2	C1	C9	N1	7.8°	2.1°
C1	O2	CU	N1	2.2°	37.4°
C1	O2	CU	O3	40.0°	152.3°
O2	C1	C9	H11	129.5°	117.8°
C1	O2	CU	O5	19.8°	58.0°
C9	C1	O2	CU	2.7°	29.9°
C1	C9	N1	H11	121.5°	115.2°
C1	C9	N1	CU	9.3°	27.2°
C1	C9	N1	C8	151.0°	54.6°
C1	C9	C10	H9	64.1°	48.7°
O2	CU	N1	C9	6.8°	34.8°
O2	CU	N1	O3	175.1°	106.7°
O2	CU	N1	O5	10.6°	152.0°
O2	CU	N1	C8	152.0°	96.5°
O2	CU	O3	O5	16.0°	166.3°
O2	CU	O3	C2	73.9°	132.2°
O2	CU	O5	H12	90.0°	2.1°
O2	CU	O5	H13	90.0°	119.7°
C9	N1	CU	C8	158.8°	131.3°
C9	N1	CU	O3	168.3°	141.5°
C9	N1	C8	C7	179.5°	177.7°
N1	C9	C10	H9	179.2°	172.7°
C9	N1	C8	H10	0.5°	4.0°
C9	N1	CU	O5	3.8°	117.2°
N1	CU	O3	O5	25.8°	102.2°
CU	N1	C8	C7	21.8°	81.9°
N1	CU	O3	C2	32.1°	40.7°
CU	N1	C8	H10	158.2°	99.8°
CU	N1	C9	H11	130.8°	88.1°
N1	CU	O5	H12	90.0°	93.9°
N1	CU	O5	H13	90.0°	148.5°
C8	N1	CU	O3	32.9°	10.2°
N1	C8	C7	H10	180.0°	178.3°
N1	C8	C7	C2	1.3°	114.9°
N1	C8	C7	C6	178.0°	75.8°
C8	N1	C9	H11	29.6°	169.8°
C8	N1	CU	O5	162.7°	111.5°
CU	O3	C2	C7	21.0°	31.0°
CU	O3	C2	C3	157.7°	137.8°
O3	CU	O5	H12	90.0°	148.9°
O3	CU	O5	H13	90.0°	31.3°
C8	C7	C2	O3	1.4°	10.9°
C8	C7	C2	C6	179.2°	169.6°
C8	C7	C2	C3	179.9°	179.1°
C8	C7	C6	C5	179.7°	176.2°
C8	C7	C6	H5	0.3°	6.7°
O3	C2	C7	C3	178.7°	169.9°
O3	C2	C7	C6	177.8°	179.5°
O3	C2	C3	C4	178.2°	175.7°
O3	C2	C3	H1	1.8°	6.7°
C2	O3	CU	O5	57.9°	61.5°
C2	C7	C6	C5	0.4°	7.7°
C7	C2	C3	C4	0.6°	6.9°
C7	C2	C3	H1	179.4°	175.6°
C2	C7	C6	H5	179.6°	175.3°
C2	C7	C8	H10	178.7°	66.8°
C6	C7	C2	C3	0.9°	9.5°
C7	C6	C5	H5	180.0°	177.1°
C7	C6	C5	C4	0.4°	2.7°
C7	C6	C5	H4	179.6°	177.4°
C6	C7	C8	H10	2.0°	102.5°
C2	C3	C4	H1	180.0°	177.5°
C2	C3	C4	C5	0.2°	2.3°
C2	C3	C4	H2	179.8°	177.6°
C6	C5	C4	C3	0.7°	0.1°
C6	C5	C4	H4	180.0°	180.0°
C6	C5	C4	H2	179.3°	179.9°
C3	C4	C5	H2	180.0°	180.0°
C3	C4	C5	H4	179.4°	179.9°
C5	C4	C3	H1	179.8°	179.9°
C4	C5	C6	H5	179.6°	179.7°
H1	C3	C4	H2	0.2°	0.1°
H2	C4	C5	H4	0.7°	0.1°
H3	O4	C10	H9	59.7°	49.7°
H4	C5	C6	H5	0.4°	0.3°
H6	C11	H7	H8	120.0°	119.7°
H6	C11	C10	H9	58.8°	61.2°
H7	C11	C10	H9	178.8°	58.7°
H8	C11	C10	H9	61.2°	178.6°
H9	C10	C9	H11	55.7°	68.5°
CU	O5	H12	H13	90.0°	118.8°

Release date:	2023-05-10
Definition date:	2022-08-16
Last modified:	2026-09-16
Release status:	REL
Processing site:	PDBJ
Derived from:	7YRK