Summary Geometry PCM/PTM Related PDB entries

CJI

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O9	RH3	sing	2.30Å	2.11Å
RH3	O12	sing	2.33Å	2.08Å
RH3	O14	sing	2.30Å	2.09Å
RH3	N1	sing	2.10Å	2.10Å
O12	C1	doub	1.25Å	1.24Å
O15	RH4	sing	2.30Å	2.11Å
RH4	O11	sing	2.29Å	2.09Å
RH4	O10	sing	2.29Å	2.12Å
O11	C1	sing	1.25Å	1.24Å
C1	C2	sing	1.50Å	1.53Å
N1	C3	sing	1.35Å	1.35Å	Aromatic
N1	C5	sing	1.37Å	1.31Å	Aromatic
N2	C3	doub	1.35Å	1.34Å	Aromatic
N2	C4	sing	1.37Å	1.33Å	Aromatic
C4	C5	doub	1.34Å	1.35Å	Aromatic
O9	HO9	sing	0.86Å	0.95Å
O14	H1	sing	0.86Å	0.95Å
O15	H2	sing	0.86Å	0.95Å
O10	H3	sing	0.86Å	0.95Å
C2	H5	sing	0.97Å	1.10Å
C2	H6	sing	0.97Å	1.10Å
C2	H7	sing	0.97Å	1.10Å
C3	H8	sing	0.94Å	1.08Å
C4	H9	sing	0.94Å	1.08Å
C5	H10	sing	0.94Å	1.08Å
RH3	RH4	sing	2.40Å	2.43Å
H4	O9	sing	0.86Å	0.95Å
H11	O10	sing	0.86Å	0.95Å
H12	O14	sing	0.86Å	0.95Å
H13	O15	sing	0.86Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O9	RH3	O12	85.3°	91.3°
O9	RH3	O14	95.7°	89.5°
O9	RH3	N1	178.9°	179.0°
RH3	O9	HO9	109.5°	109.5°
O9	RH3	RH4	80.8°	52.3°
RH3	O9	H4	109.4°	109.5°
O12	RH3	O14	178.8°	179.1°
O12	RH3	N1	93.9°	88.9°
RH3	O12	C1	124.2°	111.1°
O12	RH3	RH4	83.1°	80.0°
O14	RH3	N1	85.2°	90.2°
RH3	O14	H1	109.5°	109.5°
O14	RH3	RH4	96.3°	100.5°
RH3	O14	H12	109.4°	109.5°
RH3	N1	C3	137.5°	127.9°
RH3	N1	C5	113.9°	126.8°
N1	RH3	RH4	98.5°	128.8°
O12	C1	O11	126.1°	123.9°
O12	C1	C2	116.0°	118.3°
O15	RH4	O11	84.4°	89.9°
O15	RH4	O10	93.8°	90.0°
RH4	O15	H2	109.5°	109.5°
O15	RH4	RH3	85.2°	144.6°
RH4	O15	H13	109.4°	109.5°
O11	RH4	O10	172.3°	179.8°
RH4	O11	C1	115.4°	109.1°
O11	RH4	RH3	90.9°	91.1°
RH4	O10	H3	109.5°	109.5°
O10	RH4	RH3	81.6°	89.1°
RH4	O10	H11	109.5°	109.5°
O11	C1	C2	117.9°	117.8°
C1	C2	H5	109.5°	109.7°
C1	C2	H6	109.5°	109.6°
C1	C2	H7	109.5°	109.6°
C3	N1	C5	108.5°	105.3°
N1	C3	N2	107.4°	111.4°
N1	C3	H8	126.3°	124.3°
N1	C5	C4	108.3°	109.1°
N1	C5	H10	125.8°	125.3°
C3	N2	C4	108.1°	105.3°
N2	C3	H8	126.3°	124.3°
N2	C4	C5	107.6°	109.0°
N2	C4	H9	126.2°	125.4°
C5	C4	H9	126.2°	125.6°
C4	C5	H10	125.9°	125.6°
HO9	O9	H4	109.5°	107.3°
H1	O14	H12	109.5°	107.5°
H2	O15	H13	109.5°	107.4°
H3	O10	H11	109.4°	107.4°
H5	C2	H6	109.5°	109.3°
H5	C2	H7	109.4°	109.3°
H6	C2	H7	109.5°	109.3°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O9	RH3	O12	O14	142.4°	179.6°
O9	RH3	O12	N1	179.3°	179.0°
O9	RH3	O12	RH4	81.2°	51.3°
O9	RH3	O14	N1	179.3°	179.0°
O9	RH3	O14	RH4	81.3°	51.4°
O9	RH3	N1	RH4	44.1°	179.8°
O9	RH3	O12	C1	82.2°	5.4°
O9	RH3	RH4	O15	0.2°	12.8°
O9	RH3	RH4	O11	84.4°	78.5°
O9	RH3	RH4	O10	94.4°	101.5°
O9	RH3	N1	C3	41.9°	134.2°
O9	RH3	N1	C5	141.8°	46.2°
RH3	O9	HO9	H4	120.0°	118.7°
O9	RH3	O14	H1	180.0°	108.6°
O9	RH3	O14	H12	60.0°	8.9°
O12	RH3	O14	N1	36.9°	1.5°
O12	RH3	O14	RH4	61.1°	128.2°
O12	RH3	N1	RH4	83.6°	76.2°
O12	RH3	RH4	O15	86.2°	112.4°
O12	RH3	RH4	O11	1.9°	21.0°
O12	RH3	RH4	O10	179.3°	159.0°
RH3	O12	C1	O11	6.0°	59.2°
RH3	O12	C1	C2	173.5°	121.1°
O12	RH3	N1	C3	2.4°	122.2°
O12	RH3	N1	C5	178.7°	57.4°
O12	RH3	O9	HO9	180.0°	83.7°
O12	RH3	O14	H1	37.6°	71.8°
O12	RH3	O9	H4	60.0°	158.9°
O12	RH3	O14	H12	157.6°	170.6°
O14	RH3	N1	RH4	95.7°	103.8°
O14	RH3	O12	C1	60.3°	174.2°
O14	RH3	RH4	O15	94.9°	68.3°
O14	RH3	RH4	O11	179.1°	159.6°
O14	RH3	RH4	O10	0.3°	20.4°
O14	RH3	N1	C3	178.4°	57.8°
O14	RH3	N1	C5	2.0°	122.6°
O14	RH3	O9	HO9	0.7°	96.4°
RH3	O14	H1	H12	120.0°	118.8°
O14	RH3	O9	H4	120.7°	21.1°
N1	RH3	O12	C1	97.1°	175.6°
N1	RH3	RH4	O15	179.1°	167.2°
N1	RH3	RH4	O11	94.8°	101.5°
N1	RH3	RH4	O10	86.4°	78.6°
RH3	N1	C3	C5	176.5°	179.6°
RH3	N1	C3	N2	177.7°	179.6°
RH3	N1	C5	C4	179.2°	179.6°
N1	RH3	O9	HO9	140.4°	19.9°
N1	RH3	O14	H1	0.7°	70.4°
RH3	N1	C3	H8	2.3°	0.4°
RH3	N1	C5	H10	0.8°	0.4°
N1	RH3	O9	H4	99.6°	97.5°
N1	RH3	O14	H12	120.7°	172.1°
O12	C1	O11	RH4	7.9°	32.6°
O12	C1	O11	C2	179.5°	179.7°
O12	C1	C2	H5	0.0°	1.2°
O12	C1	C2	H6	120.0°	121.2°
O12	C1	C2	H7	120.0°	118.8°
C1	O12	RH3	RH4	0.9°	45.9°
O15	RH4	O11	O10	76.3°	33.7°
O15	RH4	O11	RH3	85.1°	144.6°
O15	RH4	O10	RH3	84.6°	144.6°
O15	RH4	O11	C1	90.5°	151.8°
RH4	O15	H2	H13	120.0°	118.8°
O15	RH4	O10	H3	180.0°	174.4°
O15	RH4	O10	H11	60.0°	68.1°
O11	RH4	O10	RH3	9.0°	178.3°
RH4	O11	C1	C2	171.7°	147.7°
O11	RH4	O15	H2	180.0°	92.9°
O11	RH4	O10	H3	104.4°	152.0°
O11	RH4	O10	H11	15.6°	34.5°
O11	RH4	O15	H13	60.0°	149.6°
O10	RH4	O11	C1	14.2°	174.5°
O10	RH4	O15	H2	7.5°	87.2°
RH4	O10	H3	H11	120.0°	118.8°
O10	RH4	O15	H13	112.5°	30.3°
O11	C1	C2	H5	179.6°	178.6°
O11	C1	C2	H6	59.6°	58.5°
O11	C1	C2	H7	60.4°	61.5°
C1	O11	RH4	RH3	5.4°	7.2°
C1	C2	H5	H6	120.0°	120.3°
C1	C2	H5	H7	120.0°	120.2°
C1	C2	H6	H7	120.0°	120.2°
N1	C3	N2	H8	180.0°	179.9°
N1	C3	N2	C4	0.3°	0.1°
C3	N1	C5	C4	1.8°	0.0°
C3	N1	C5	H10	178.2°	179.9°
C3	N1	RH3	RH4	86.0°	45.9°
C5	N1	C3	N2	1.3°	0.1°
N1	C5	C4	N2	1.6°	0.0°
N1	C5	C4	H10	180.0°	180.0°
C5	N1	C3	H8	178.7°	180.0°
N1	C5	C4	H9	178.4°	180.0°
C5	N1	RH3	RH4	97.7°	133.6°
C3	N2	C4	C5	0.8°	0.0°
C3	N2	C4	H9	179.2°	180.0°
N2	C4	C5	H9	180.0°	180.0°
C4	N2	C3	H8	179.7°	180.0°
N2	C4	C5	H10	178.4°	180.0°
HO9	O9	RH3	RH4	96.2°	159.9°
H1	O14	RH3	RH4	98.7°	160.0°
H2	O15	RH4	RH3	88.7°	1.2°
H3	O10	RH4	RH3	95.4°	29.7°
H5	C2	H6	H7	120.0°	119.5°
H9	C4	C5	H10	1.6°	0.0°
RH4	RH3	O9	H4	143.8°	82.7°
RH3	RH4	O10	H11	24.6°	147.2°
RH4	RH3	O14	H12	141.3°	42.4°
RH3	RH4	O15	H13	31.3°	118.6°

Release date:	2022-06-08
Definition date:	2021-12-14
Last modified:	2026-09-16
Release status:	REL
Processing site:	PDBE
Derived from:	7QHR