Summary Geometry PCM/PTM Related PDB entries

JNR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C10	C9	doub	1.38Å	1.38Å	Aromatic
C10	C11	sing	1.38Å	1.39Å	Aromatic
C9	C8	sing	1.38Å	1.39Å	Aromatic
C11	C12	doub	1.38Å	1.39Å	Aromatic
C8	C7	doub	1.40Å	1.40Å	Aromatic
C12	C7	sing	1.40Å	1.39Å	Aromatic
C7	C6	sing	1.48Å	1.51Å
N1	C1	doub	1.30Å	1.32Å
C1	N3	sing	1.37Å	1.32Å
C1	N2	sing	1.37Å	1.32Å
N4	C6	sing	1.35Å	1.34Å
N4	C5	sing	1.47Å	1.47Å
C6	O1	doub	1.22Å	1.23Å
N3	C2	sing	1.47Å	1.44Å
C3	C2	sing	1.53Å	1.51Å
C3	C4	sing	1.53Å	1.52Å
C5	C4	sing	1.53Å	1.53Å
C5	C13	sing	1.51Å	1.54Å
O3	C13	doub	1.21Å	1.23Å
C13	O2	sing	1.34Å	1.23Å
N1	H1	sing	0.97Å	1.00Å
C2	H3	sing	1.09Å	1.10Å
C2	H4	sing	1.09Å	1.10Å
C3	H5	sing	1.09Å	1.10Å
C3	H6	sing	1.09Å	1.10Å
C4	H7	sing	1.09Å	1.10Å
C4	H8	sing	1.09Å	1.10Å
C5	H9	sing	1.09Å	1.10Å
N2	H10	sing	0.97Å	1.00Å
N2	H11	sing	0.97Å	1.00Å
N3	H12	sing	0.97Å	1.00Å
N4	H13	sing	0.97Å	1.00Å
C8	H14	sing	1.08Å	1.08Å
C9	H15	sing	1.08Å	1.08Å
C10	H16	sing	1.08Å	1.08Å
C11	H17	sing	1.08Å	1.08Å
C12	H18	sing	1.08Å	1.08Å
O2	H2	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C9	C10	C11	120.0°	120.3°
C10	C9	C8	119.6°	120.1°
C10	C9	H15	120.2°	120.0°
C9	C10	H16	120.0°	119.8°
C10	C11	C12	120.5°	120.1°
C11	C10	H16	120.0°	119.9°
C10	C11	H17	119.8°	119.9°
C9	C8	C7	120.9°	119.8°
C9	C8	H14	119.5°	120.1°
C8	C9	H15	120.2°	119.9°
C11	C12	C7	120.2°	119.8°
C12	C11	H17	119.7°	120.0°
C11	C12	H18	120.0°	120.1°
C8	C7	C12	118.8°	119.7°
C8	C7	C6	120.0°	120.1°
C7	C8	H14	119.5°	120.1°
C12	C7	C6	121.3°	120.1°
C7	C12	H18	119.9°	120.1°
C7	C6	N4	113.5°	120.0°
C7	C6	O1	119.9°	120.0°
N1	C1	N3	119.3°	120.0°
N1	C1	N2	120.6°	120.0°
C1	N1	H1	112.0°	120.0°
N3	C1	N2	120.0°	120.0°
C1	N3	C2	124.4°	120.0°
C1	N3	H12	117.8°	120.1°
C1	N2	H10	120.0°	120.0°
C1	N2	H11	120.0°	120.1°
C6	N4	C5	133.2°	120.0°
N4	C6	O1	126.4°	120.0°
C6	N4	H13	113.4°	120.0°
N4	C5	C4	113.2°	109.4°
N4	C5	C13	117.6°	109.5°
N4	C5	H9	103.9°	109.4°
C5	N4	H13	113.4°	120.0°
N3	C2	C3	108.6°	109.5°
N3	C2	H3	109.7°	109.5°
N3	C2	H4	109.7°	109.5°
C2	N3	H12	117.8°	119.9°
C2	C3	C4	109.4°	109.5°
C3	C2	H3	109.7°	109.4°
C3	C2	H4	109.7°	109.5°
C2	C3	H5	109.5°	109.5°
C2	C3	H6	109.5°	109.4°
C3	C4	C5	113.9°	109.5°
C4	C3	H5	109.5°	109.5°
C4	C3	H6	109.5°	109.5°
C3	C4	H7	108.4°	109.5°
C3	C4	H8	108.4°	109.5°
C4	C5	C13	113.4°	109.5°
C5	C4	H7	108.4°	109.5°
C5	C4	H8	108.3°	109.4°
C4	C5	H9	103.3°	109.5°
C5	C13	O3	115.8°	120.0°
C5	C13	O2	117.8°	120.0°
C13	C5	H9	103.2°	109.5°
O3	C13	O2	125.1°	120.0°
C13	O2	H2	109.5°	117.1°
H3	C2	H4	109.5°	109.4°
H5	C3	H6	109.5°	109.4°
H7	C4	H8	109.5°	109.4°
H10	N2	H11	120.0°	119.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C9	C10	C11	H16	180.0°	179.9°
C10	C9	C8	H15	180.0°	179.9°
C9	C10	C11	C12	0.5°	0.3°
C10	C9	C8	C7	1.9°	0.0°
C10	C9	C8	H14	178.1°	179.9°
C9	C10	C11	H17	179.5°	180.0°
C11	C10	C9	C8	0.3°	0.0°
C10	C11	C12	H17	180.0°	179.7°
C10	C11	C12	C7	0.2°	0.6°
C11	C10	C9	H15	179.7°	180.0°
C10	C11	C12	H18	179.8°	180.0°
C9	C8	C7	H14	180.0°	180.0°
C9	C8	C7	C12	2.7°	0.3°
C9	C8	C7	C6	177.8°	180.0°
C8	C9	C10	H16	179.7°	180.0°
C11	C12	C7	C8	1.8°	0.6°
C11	C12	C7	H18	180.0°	179.4°
C11	C12	C7	C6	178.6°	179.7°
C12	C11	C10	H16	179.4°	179.6°
C8	C7	C12	C6	179.5°	179.7°
C8	C7	C6	N4	33.9°	180.0°
C8	C7	C6	O1	150.0°	0.0°
C7	C8	C9	H15	178.0°	180.0°
C8	C7	C12	H18	178.2°	180.0°
C12	C7	C6	N4	145.6°	0.3°
C12	C7	C6	O1	30.5°	179.7°
C12	C7	C8	H14	177.3°	179.7°
C7	C12	C11	H17	179.8°	179.7°
C7	C6	N4	O1	175.8°	180.0°
C7	C6	N4	C5	159.9°	180.0°
C7	C6	N4	H13	20.1°	0.0°
C6	C7	C8	H14	2.2°	0.1°
C6	C7	C12	H18	1.4°	0.4°
N1	C1	N3	N2	178.0°	179.9°
N1	C1	N3	C2	169.6°	180.0°
N1	C1	N2	H10	178.0°	0.1°
N1	C1	N2	H11	2.0°	180.0°
N1	C1	N3	H12	10.4°	0.0°
C1	N3	C2	H12	180.0°	180.0°
C1	N3	C2	C3	175.8°	180.0°
N3	C1	N1	H1	178.0°	180.0°
C1	N3	C2	H3	64.3°	60.0°
C1	N3	C2	H4	56.0°	60.0°
N3	C1	N2	H10	0.0°	180.0°
N3	C1	N2	H11	180.0°	0.1°
N2	C1	N3	C2	12.3°	0.0°
N2	C1	N1	H1	0.0°	0.1°
C1	N2	H10	H11	180.0°	179.9°
N2	C1	N3	H12	167.7°	179.9°
C6	N4	C5	H13	180.0°	180.0°
C6	N4	C5	C4	91.6°	155.0°
C6	N4	C5	C13	43.9°	85.0°
C6	N4	C5	H9	157.1°	35.1°
C5	N4	C6	O1	24.4°	0.0°
N4	C5	C4	C3	17.4°	65.0°
N4	C5	C4	C13	137.3°	120.0°
N4	C5	C4	H9	111.7°	119.9°
N4	C5	C13	H9	113.6°	120.0°
N4	C5	C13	O3	60.4°	0.1°
N4	C5	C13	O2	132.1°	180.0°
N4	C5	C4	H7	138.1°	55.1°
N4	C5	C4	H8	103.2°	175.0°
O1	C6	N4	H13	155.6°	180.0°
N3	C2	C3	H3	119.9°	120.0°
N3	C2	C3	H4	119.9°	120.0°
N3	C2	C3	C4	156.0°	180.0°
N3	C2	H3	H4	120.4°	120.0°
N3	C2	C3	H5	36.0°	60.0°
N3	C2	C3	H6	84.0°	60.0°
C2	C3	C4	H5	120.0°	120.0°
C2	C3	C4	H6	120.0°	120.0°
C2	C3	C4	C5	163.5°	180.0°
C3	C2	H3	H4	120.4°	120.0°
C2	C3	H5	H6	120.1°	119.9°
C2	C3	C4	H7	75.9°	60.0°
C2	C3	C4	H8	42.9°	60.0°
C3	C2	N3	H12	4.2°	0.0°
C3	C4	C5	H7	120.6°	120.1°
C3	C4	C5	H8	120.7°	120.0°
C3	C4	C5	C13	119.9°	175.0°
C4	C3	C2	H3	84.1°	60.0°
C4	C3	C2	H4	36.2°	59.9°
C4	C3	H5	H6	120.0°	120.0°
C3	C4	H7	H8	118.0°	120.0°
C3	C4	C5	H9	129.1°	54.9°
C4	C5	C13	H9	111.0°	120.0°
C4	C5	C13	O3	164.3°	119.9°
C4	C5	C13	O2	3.2°	60.0°
C5	C4	C3	H5	43.5°	60.0°
C5	C4	C3	H6	76.5°	60.0°
C5	C4	H7	H8	118.0°	119.9°
C4	C5	N4	H13	88.4°	25.0°
C5	C13	O3	O2	166.5°	179.9°
C13	C5	C4	H7	0.7°	65.0°
C13	C5	C4	H8	119.4°	55.0°
C13	C5	N4	H13	136.2°	95.0°
C5	C13	O2	H2	166.2°	180.0°
O3	C13	C5	H9	53.3°	120.0°
O3	C13	O2	H2	0.0°	0.1°
O2	C13	C5	H9	114.2°	60.1°
H3	C2	C3	H5	155.9°	60.1°
H3	C2	C3	H6	35.9°	180.0°
H3	C2	N3	H12	115.7°	120.0°
H4	C2	C3	H5	83.8°	180.0°
H4	C2	C3	H6	156.1°	60.1°
H4	C2	N3	H12	124.0°	120.0°
H5	C3	C4	H7	164.2°	180.0°
H5	C3	C4	H8	77.1°	60.0°
H6	C3	C4	H7	44.1°	60.0°
H6	C3	C4	H8	162.9°	180.0°
H7	C4	C5	H9	110.3°	175.0°
H8	C4	C5	H9	8.4°	65.1°
H9	C5	N4	H13	22.9°	145.0°
H14	C8	C9	H15	1.9°	0.0°
H15	C9	C10	H16	0.3°	0.1°
H16	C10	C11	H17	0.6°	0.0°
H17	C11	C12	H18	0.2°	0.4°

Release date:	2024-08-14
Definition date:	2022-08-24
Last modified:	2025-10-06
Release status:	REL
Processing site:	PDBJ
Derived from:	7XXQ