Summary Geometry PCM/PTM Related PDB entries

J9H

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C4	C3	sing	1.46Å	1.39Å
C4	C4A	sing	1.50Å	1.38Å
C3	C2	doub	1.38Å	1.39Å
C5	C4A	doub	1.39Å	1.39Å	Aromatic
C5	C6	sing	1.35Å	1.39Å	Aromatic
C4A	C1A	sing	1.39Å	1.39Å	Aromatic
C2	C2A	sing	1.50Å	1.51Å
C2	N1	sing	1.34Å	1.36Å
C6	C6A	doub	1.43Å	1.38Å	Aromatic
C1A	N1	sing	1.40Å	1.37Å
C1A	C10	doub	1.42Å	1.39Å	Aromatic
C22	C21	doub	1.40Å	1.50Å
N1	PT	sing	2.05Å	1.67Å
C6A	C10	sing	1.41Å	1.39Å	Aromatic
C6A	C7	sing	1.40Å	1.39Å	Aromatic
C10	N10	sing	1.36Å	1.39Å	Aromatic
PT	N10	sing	2.07Å	2.20Å
C7	C8	doub	1.36Å	1.39Å	Aromatic
N10	C9	doub	1.34Å	1.35Å	Aromatic
C8	C9	sing	1.41Å	1.39Å	Aromatic
C9	C9A	sing	1.50Å	1.50Å
PT	C22	sing	1.93Å	2.85Å
C9A	H1	sing	0.97Å	1.10Å
C9A	H2	sing	0.97Å	1.10Å
C9A	H3	sing	0.97Å	1.10Å
C8	H4	sing	0.94Å	1.08Å
C7	H5	sing	0.95Å	1.08Å
C5	H6	sing	0.95Å	1.08Å
C6	H7	sing	0.93Å	1.08Å
C2A	H8	sing	0.97Å	1.10Å
C2A	H9	sing	0.97Å	1.10Å
C2A	H10	sing	0.97Å	1.10Å
C3	H11	sing	0.94Å	1.08Å
C4	H12	sing	0.99Å	1.10Å
C4	H13	sing	0.99Å	1.10Å
CP	H14	sing	0.94Å	1.10Å
CP	H15	sing	0.94Å	1.10Å
CP	H16	sing	0.95Å	1.10Å
C21	PT	sing	1.92Å	3.10Å
CP	PT	sing	1.95Å	3.06Å
H17	C21	sing	0.98Å	1.10Å
H18	C21	sing	0.98Å	1.10Å
H19	C22	sing	0.98Å	1.10Å
H20	C22	sing	0.98Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C3	C4	C4A	119.1°	115.6°
C4	C3	C2	120.2°	121.2°
C4	C3	H11	119.9°	117.7°
C3	C4	H12	107.0°	109.8°
C3	C4	H13	107.0°	109.8°
C4	C4A	C5	119.8°	121.1°
C4	C4A	C1A	119.5°	118.8°
C4A	C4	H12	107.0°	108.7°
C4A	C4	H13	107.0°	108.7°
C3	C2	C2A	118.4°	120.8°
C3	C2	N1	120.4°	121.2°
C2	C3	H11	119.9°	121.1°
C4A	C5	C6	120.1°	121.0°
C5	C4A	C1A	120.7°	120.1°
C4A	C5	H6	120.0°	119.4°
C5	C6	C6A	119.7°	120.7°
C6	C5	H6	119.9°	119.6°
C5	C6	H7	120.1°	119.8°
C4A	C1A	N1	121.0°	121.0°
C4A	C1A	C10	118.8°	120.2°
C2A	C2	N1	121.3°	118.0°
C2	C2A	H8	109.5°	109.8°
C2	C2A	H9	109.4°	109.9°
C2	C2A	H10	109.5°	109.5°
C2	N1	C1A	119.8°	122.2°
C2	N1	PT	126.8°	127.5°
C6	C6A	C10	120.1°	119.2°
C6	C6A	C7	120.1°	123.7°
C6A	C6	H7	120.1°	119.5°
N1	C1A	C10	120.2°	118.7°
C1A	N1	PT	110.9°	109.7°
C1A	C10	C6A	120.5°	118.7°
C1A	C10	N10	119.3°	117.1°
C21	C22	PT	85.0°	68.4°
C22	C21	PT	66.3°	69.0°
C22	C21	H17	118.9°	120.6°
C22	C21	H18	118.9°	120.5°
C21	C22	H19	115.2°	120.7°
C21	C22	H20	115.2°	120.5°
N1	PT	N10	90.0°	82.4°
N1	PT	C22	81.8°	147.0°
N1	PT	C21	108.5°	107.4°
N1	PT	CP	73.3°	93.3°
C10	C6A	C7	119.8°	117.0°
C6A	C10	N10	120.2°	124.2°
C6A	C7	C8	119.0°	119.2°
C6A	C7	H5	120.5°	120.4°
C10	N10	PT	95.4°	111.1°
C10	N10	C9	120.1°	117.1°
PT	N10	C9	142.8°	131.4°
N10	PT	C22	110.5°	109.2°
N10	PT	C21	99.5°	95.1°
N10	PT	CP	84.6°	91.6°
C7	C8	C9	120.4°	120.4°
C7	C8	H4	119.8°	120.1°
C8	C7	H5	120.5°	120.4°
N10	C9	C8	120.5°	122.0°
N10	C9	C9A	119.1°	118.5°
C8	C9	C9A	120.4°	119.5°
C9	C8	H4	119.8°	119.5°
C9	C9A	H1	109.5°	109.9°
C9	C9A	H2	109.5°	109.9°
C9	C9A	H3	109.5°	109.7°
C22	PT	C21	28.8°	42.6°
C22	PT	CP	151.0°	116.4°
PT	C22	H19	115.2°	135.4°
PT	C22	H20	115.2°	71.0°
H1	C9A	H2	109.5°	108.8°
H1	C9A	H3	109.4°	109.2°
H2	C9A	H3	109.5°	109.3°
H8	C2A	H9	109.5°	109.1°
H8	C2A	H10	109.4°	109.3°
H9	C2A	H10	109.5°	109.3°
H12	C4	H13	109.5°	103.6°
H14	CP	H15	109.4°	109.5°
H14	CP	H16	109.5°	109.5°
H14	CP	PT	109.5°	109.5°
H15	CP	H16	109.5°	109.5°
H15	CP	PT	109.5°	109.5°
H16	CP	PT	109.5°	109.4°
C21	PT	CP	175.5°	158.9°
PT	C21	H17	118.9°	70.5°
PT	C21	H18	118.9°	134.4°
H17	C21	H18	109.5°	118.9°
H19	C22	H20	109.4°	118.7°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C3	C4	C4A	H12	121.4°	123.9°
C3	C4	C4A	H13	121.4°	124.0°
C4	C3	C2	H11	180.0°	179.9°
C3	C4	C4A	C5	179.9°	178.9°
C3	C4	C4A	C1A	0.0°	1.4°
C4	C3	C2	C2A	179.8°	179.5°
C4	C3	C2	N1	0.3°	0.1°
C3	C4	H12	H13	115.6°	117.2°
C4A	C4	C3	C2	0.1°	1.3°
C4	C4A	C5	C1A	179.9°	179.7°
C4	C4A	C5	C6	180.0°	179.9°
C4	C4A	C1A	N1	0.1°	0.3°
C4	C4A	C1A	C10	179.9°	180.0°
C4	C4A	C5	H6	0.0°	0.1°
C4A	C4	C3	H11	179.9°	178.8°
C4A	C4	H12	H13	115.7°	115.5°
C3	C2	C2A	N1	179.9°	179.4°
C3	C2	N1	C1A	0.4°	1.1°
C3	C2	N1	PT	160.3°	171.5°
C3	C2	C2A	H8	180.0°	145.5°
C3	C2	C2A	H9	60.0°	25.6°
C3	C2	C2A	H10	60.0°	94.5°
C2	C3	C4	H12	121.3°	124.6°
C2	C3	C4	H13	121.5°	122.1°
C4A	C5	C6	H6	180.0°	179.8°
C4A	C5	C6	C6A	0.2°	0.3°
C5	C4A	C1A	N1	179.8°	179.9°
C5	C4A	C1A	C10	0.0°	0.2°
C4A	C5	C6	H7	179.8°	179.9°
C5	C4A	C4	H12	58.7°	54.9°
C5	C4A	C4	H13	58.5°	57.1°
C6	C5	C4A	C1A	0.0°	0.4°
C5	C6	C6A	H7	180.0°	179.6°
C5	C6	C6A	C10	0.2°	0.1°
C5	C6	C6A	C7	179.9°	179.8°
C4A	C1A	N1	C2	0.4°	0.9°
C4A	C1A	N1	C10	179.7°	179.7°
C4A	C1A	N1	PT	163.2°	172.9°
C4A	C1A	C10	C6A	0.0°	0.1°
C4A	C1A	C10	N10	179.8°	179.6°
C1A	C4A	C5	H6	179.9°	179.8°
C1A	C4A	C4	H12	121.3°	125.3°
C1A	C4A	C4	H13	121.4°	122.6°
C2A	C2	N1	C1A	179.7°	178.3°
C2A	C2	N1	PT	19.6°	7.9°
C2	C2A	H8	H9	120.0°	120.5°
C2	C2A	H8	H10	120.0°	120.1°
C2	C2A	H9	H10	120.0°	120.2°
C2A	C2	C3	H11	0.2°	0.6°
C2	N1	C1A	PT	163.6°	171.9°
C2	N1	C1A	C10	179.9°	178.7°
C2	N1	PT	N10	179.8°	179.2°
C2	N1	PT	C22	69.5°	65.3°
N1	C2	C2A	H8	0.1°	35.1°
N1	C2	C2A	H9	119.9°	155.0°
N1	C2	C2A	H10	120.1°	84.9°
N1	C2	C3	H11	179.7°	180.0°
C2	N1	PT	C21	80.2°	86.2°
C2	N1	PT	CP	95.4°	89.6°
C6	C6A	C10	C1A	0.1°	0.0°
C6	C6A	C10	C7	179.8°	180.0°
C6	C6A	C10	N10	179.9°	179.6°
C6	C6A	C7	C8	179.9°	179.8°
C6	C6A	C7	H5	0.1°	0.1°
C6A	C6	C5	H6	179.8°	179.9°
N1	C1A	C10	C6A	179.7°	179.8°
N1	C1A	C10	N10	0.1°	0.1°
C1A	N1	PT	N10	18.1°	7.8°
C1A	N1	PT	C22	92.7°	106.1°
C1A	N1	PT	C21	81.9°	85.2°
C1A	N1	PT	CP	102.4°	99.0°
C10	C1A	N1	PT	16.5°	6.8°
C1A	C10	C6A	N10	179.8°	179.6°
C1A	C10	C6A	C7	180.0°	179.9°
C1A	C10	N10	PT	11.7°	6.6°
C1A	C10	N10	C9	179.9°	179.3°
C22	C21	PT	N1	22.6°	163.3°
C21	C22	PT	N10	71.5°	76.0°
C21	C22	PT	H19	115.5°	112.5°
C21	C22	PT	H20	115.5°	135.6°
C22	C21	PT	H17	111.1°	135.7°
C22	C21	PT	H18	111.1°	112.6°
C22	C21	PT	CP	91.3°	5.1°
C22	C21	H17	H18	141.3°	179.9°
C21	C22	H19	H20	131.7°	178.8°
N1	PT	N10	C10	16.9°	8.0°
N1	PT	N10	C22	81.3°	148.2°
N1	PT	N10	C21	108.8°	106.9°
N1	PT	N10	CP	73.3°	93.1°
N1	PT	N10	C9	179.9°	179.0°
N1	PT	C22	CP	31.0°	151.8°
N1	PT	CP	H14	180.0°	136.0°
N1	PT	CP	H15	60.0°	16.0°
N1	PT	CP	H16	60.0°	104.0°
N1	PT	C21	CP	113.9°	168.4°
N1	PT	C21	H17	88.5°	27.6°
N1	PT	C21	H18	133.7°	84.1°
N1	PT	C22	H19	86.1°	142.7°
N1	PT	C22	H20	42.9°	105.3°
C6A	C10	N10	PT	168.1°	173.0°
C10	C6A	C7	C8	0.0°	0.1°
C6A	C10	N10	C9	0.3°	1.1°
C10	C6A	C7	H5	179.9°	179.8°
C10	C6A	C6	H7	179.7°	179.7°
C7	C6A	C10	N10	0.2°	0.5°
C6A	C7	C8	H5	180.0°	179.7°
C6A	C7	C8	C9	0.1°	0.0°
C6A	C7	C8	H4	179.9°	179.9°
C7	C6A	C6	H7	0.1°	0.2°
C10	N10	PT	C9	163.2°	173.0°
C10	N10	C9	C8	0.1°	1.2°
C10	N10	C9	C9A	179.6°	179.5°
C10	N10	PT	C22	64.4°	140.2°
C10	N10	PT	C21	91.9°	99.0°
C10	N10	PT	CP	90.2°	101.1°
PT	N10	C9	C8	160.5°	171.4°
PT	N10	C9	C9A	19.8°	7.9°
N10	PT	C22	CP	117.9°	101.9°
N10	PT	CP	H14	88.4°	53.5°
N10	PT	CP	H15	151.7°	66.6°
N10	PT	CP	H16	31.7°	173.5°
N10	PT	C21	CP	152.9°	108.0°
N10	PT	C21	H17	4.7°	111.2°
N10	PT	C21	H18	133.1°	0.5°
N10	PT	C22	H19	173.0°	36.4°
N10	PT	C22	H20	44.0°	148.4°
C7	C8	C9	N10	0.1°	0.7°
C7	C8	C9	H4	180.0°	179.8°
C7	C8	C9	C9A	179.8°	180.0°
N10	C9	C8	C9A	179.7°	179.3°
C9	N10	PT	C22	98.8°	32.8°
N10	C9	C9A	H1	89.9°	149.4°
N10	C9	C9A	H2	150.1°	29.7°
N10	C9	C9A	H3	30.1°	90.5°
N10	C9	C8	H4	179.9°	179.4°
C9	N10	PT	C21	71.3°	74.1°
C9	N10	PT	CP	106.6°	85.9°
C8	C9	C9A	H1	89.9°	31.3°
C8	C9	C9A	H2	30.2°	151.0°
C8	C9	C9A	H3	150.2°	88.9°
C9	C8	C7	H5	179.9°	179.7°
C9	C9A	H1	H2	120.0°	120.4°
C9	C9A	H1	H3	120.0°	120.4°
C9	C9A	H2	H3	120.0°	120.5°
C9A	C9	C8	H4	0.2°	0.1°
C22	PT	CP	H14	147.9°	59.0°
C22	PT	CP	H15	27.9°	179.0°
C22	PT	CP	H16	92.1°	61.1°
PT	C22	H19	H20	131.7°	91.5°
H1	C9A	H2	H3	120.0°	119.1°
H4	C8	C7	H5	0.1°	0.1°
H6	C5	C6	H7	0.2°	0.2°
H8	C2A	H9	H10	120.0°	119.4°
H11	C3	C4	H12	58.7°	55.4°
H11	C3	C4	H13	58.6°	57.8°
H14	CP	H15	H16	120.0°	120.1°
H14	CP	H15	PT	120.0°	120.0°
H14	CP	H16	PT	120.0°	120.0°
H14	CP	PT	C21	64.8°	55.1°
H15	CP	H16	PT	120.0°	120.0°
H15	CP	PT	C21	55.2°	175.1°
H16	CP	PT	C21	175.2°	64.9°
PT	C21	H17	H18	141.4°	130.7°
CP	PT	C21	H17	157.6°	140.8°
CP	PT	C21	H18	19.8°	107.5°
CP	PT	C22	H19	55.1°	65.5°
CP	PT	C22	H20	73.9°	46.5°
H17	C21	C22	H19	133.3°	179.1°
H17	C21	C22	H20	4.4°	0.3°
H18	C21	C22	H19	4.4°	0.9°
H18	C21	C22	H20	133.3°	179.8°

Release date:	2019-02-27
Definition date:	2019-02-12
Last modified:	2026-09-16
Release status:	REL
Processing site:	RCSB
Derived from:	6QE9