Summary Geometry PCM/PTM Related PDB entries

U5J

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C14	C15	doub	1.37Å	1.36Å	Aromatic
C14	C13	sing	1.38Å	1.34Å	Aromatic
C15	C16	sing	1.42Å	1.36Å	Aromatic
C18	C19	sing	1.50Å	1.51Å
C18	O17	sing	1.42Å	1.37Å
O20	C19	doub	1.21Å	1.25Å
C19	O21	sing	1.31Å	1.25Å
C13	C12	doub	1.37Å	1.35Å	Aromatic
C16	O17	sing	1.38Å	1.36Å
C16	C11	doub	1.42Å	1.36Å	Aromatic
C12	C11	sing	1.40Å	1.37Å	Aromatic
C11	C09	sing	1.51Å	1.52Å
C09	O10	doub	1.24Å	1.13Å
C09	N08	sing	1.35Å	1.41Å
N08	C07	sing	1.46Å	1.44Å
C03	C04	sing	1.51Å	1.54Å
C07	C04	sing	1.54Å	1.52Å
O05	C04	sing	1.44Å	1.44Å
O05	C06	sing	1.43Å	1.42Å
C03	HG2	sing	2.08Å	2.79Å
HG2	O01	sing	2.42Å	2.78Å
C13	H1	sing	0.94Å	1.08Å
C15	H2	sing	0.94Å	1.08Å
C03	H3	sing	0.95Å	1.10Å
C04	H4	sing	0.99Å	1.10Å
C06	H5	sing	0.97Å	1.10Å
C06	H6	sing	0.97Å	1.10Å
C06	H7	sing	0.97Å	1.10Å
C07	H8	sing	0.99Å	1.10Å
C07	H9	sing	0.99Å	1.10Å
C12	H10	sing	0.94Å	1.08Å
C14	H11	sing	0.94Å	1.08Å
C18	H12	sing	0.98Å	1.10Å
C18	H13	sing	0.98Å	1.10Å
N08	H14	sing	0.86Å	1.00Å
O01	H15	sing	0.87Å	0.95Å
O21	H16	sing	0.88Å	0.95Å
C03	H17	sing	0.95Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C15	C14	C13	119.8°	120.4°
C14	C15	C16	121.8°	120.2°
C14	C15	H2	119.1°	119.4°
C15	C14	H11	120.1°	119.6°
C14	C13	C12	117.7°	120.1°
C14	C13	H1	121.1°	120.0°
C13	C14	H11	120.1°	120.0°
C15	C16	O17	118.3°	124.4°
C15	C16	C11	119.8°	120.1°
C16	C15	H2	119.1°	120.4°
C19	C18	O17	99.4°	109.8°
C18	C19	O20	121.7°	123.1°
C18	C19	O21	120.8°	112.2°
C19	C18	H12	111.9°	110.0°
C19	C18	H13	111.9°	109.7°
C18	O17	C16	121.8°	128.8°
O17	C18	H12	111.9°	109.6°
O17	C18	H13	111.9°	109.5°
O20	C19	O21	117.4°	124.7°
C19	O21	H16	109.5°	111.9°
C13	C12	C11	124.6°	122.7°
C12	C13	H1	121.1°	119.9°
C13	C12	H10	117.7°	118.5°
O17	C16	C11	121.9°	115.5°
C16	C11	C12	116.3°	116.6°
C16	C11	C09	127.6°	126.2°
C12	C11	C09	116.1°	117.2°
C11	C12	H10	117.7°	118.9°
C11	C09	O10	119.4°	119.4°
C11	C09	N08	130.1°	119.0°
O10	C09	N08	110.4°	121.5°
C09	N08	C07	124.9°	124.4°
C09	N08	H14	117.5°	118.1°
N08	C07	C04	104.3°	112.7°
N08	C07	H8	110.7°	109.9°
N08	C07	H9	110.8°	108.4°
C07	N08	H14	117.6°	117.4°
C03	C04	C07	112.2°	114.1°
C03	C04	O05	104.0°	108.2°
C04	C03	HG2	116.2°	109.5°
C04	C03	H3	107.8°	109.3°
C03	C04	H4	108.7°	108.4°
C04	C03	H17	107.8°	109.9°
C07	C04	O05	112.8°	108.5°
C07	C04	H4	108.9°	108.2°
C04	C07	H8	110.7°	109.4°
C04	C07	H9	110.7°	108.8°
C04	O05	C06	124.1°	121.9°
O05	C04	H4	110.1°	109.3°
O05	C06	H5	109.5°	109.4°
O05	C06	H6	109.5°	109.7°
O05	C06	H7	109.5°	109.8°
C03	HG2	O01	120.0°	119.9°
HG2	C03	H3	107.8°	109.5°
HG2	C03	H17	107.8°	109.6°
HG2	O01	H15	109.5°	109.4°
H3	C03	H17	109.5°	109.0°
H5	C06	H6	109.4°	109.1°
H5	C06	H7	109.4°	109.1°
H6	C06	H7	109.4°	109.7°
H8	C07	H9	109.5°	107.5°
H12	C18	H13	109.5°	108.2°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C15	C14	C13	H11	180.0°	180.0°
C14	C15	C16	H2	180.0°	179.9°
C15	C14	C13	C12	0.1°	0.1°
C14	C15	C16	O17	179.1°	179.8°
C14	C15	C16	C11	0.8°	0.4°
C15	C14	C13	H1	179.9°	180.0°
C13	C14	C15	C16	0.6°	0.1°
C14	C13	C12	H1	180.0°	179.9°
C14	C13	C12	C11	0.6°	0.3°
C13	C14	C15	H2	179.4°	180.0°
C14	C13	C12	H10	179.3°	180.0°
C15	C16	O17	C18	8.9°	0.3°
C15	C16	O17	C11	178.3°	179.5°
C15	C16	C11	C12	0.3°	0.6°
C15	C16	C11	C09	179.9°	179.8°
C16	C15	C14	H11	179.4°	179.9°
C19	C18	O17	H12	118.3°	120.9°
C19	C18	O17	H13	118.3°	120.6°
C18	C19	O20	O21	176.8°	179.8°
C19	C18	O17	C16	164.9°	173.6°
C19	C18	H12	H13	124.7°	119.8°
C18	C19	O21	H16	176.8°	179.9°
O17	C18	C19	O20	121.5°	81.5°
O17	C18	C19	O21	55.1°	98.3°
C18	O17	C16	C11	169.4°	179.7°
O17	C18	H12	H13	124.7°	119.4°
O20	C19	C18	H12	3.2°	157.8°
O20	C19	C18	H13	120.2°	38.9°
O20	C19	O21	H16	0.0°	0.3°
O21	C19	C18	H12	173.5°	22.4°
O21	C19	C18	H13	63.2°	141.2°
C13	C12	C11	C16	0.4°	0.6°
C13	C12	C11	H10	180.0°	179.7°
C13	C12	C11	C09	179.4°	179.8°
C12	C13	C14	H11	179.9°	179.9°
O17	C16	C11	C12	178.5°	179.9°
O17	C16	C11	C09	1.6°	0.8°
O17	C16	C15	H2	0.9°	0.3°
C16	O17	C18	H12	76.8°	52.7°
C16	O17	C18	H13	46.5°	65.8°
C16	C11	C12	C09	179.9°	179.2°
C16	C11	C09	O10	144.4°	174.6°
C16	C11	C09	N08	38.7°	6.3°
C11	C16	C15	H2	179.2°	179.7°
C16	C11	C12	H10	179.5°	179.7°
C12	C11	C09	O10	35.4°	6.3°
C12	C11	C09	N08	141.4°	172.9°
C11	C12	C13	H1	179.4°	179.8°
C11	C09	O10	N08	177.4°	179.1°
C11	C09	N08	C07	179.3°	178.2°
C09	C11	C12	H10	0.6°	0.5°
C11	C09	N08	H14	0.7°	4.0°
O10	C09	N08	C07	2.2°	2.7°
O10	C09	N08	H14	177.8°	175.1°
C09	N08	C07	H14	180.0°	177.8°
C09	N08	C07	C04	175.4°	129.3°
C09	N08	C07	H8	56.2°	7.0°
C09	N08	C07	H9	65.4°	110.2°
N08	C07	C04	C03	75.1°	96.5°
N08	C07	C04	H8	119.1°	122.6°
N08	C07	C04	H9	119.2°	120.3°
N08	C07	C04	O05	42.0°	142.8°
N08	C07	C04	H4	164.6°	24.3°
N08	C07	H8	H9	122.4°	117.8°
C03	C04	C07	O05	117.1°	120.7°
C03	C04	C07	H4	120.4°	120.8°
C03	C04	O05	H4	116.3°	117.9°
C03	C04	O05	C06	140.5°	121.2°
C04	C03	HG2	H3	121.0°	119.9°
C04	C03	HG2	H17	121.0°	120.6°
C04	C03	HG2	O01	175.4°	42.5°
C04	C03	H3	H17	116.9°	120.1°
C03	C04	C07	H8	44.1°	26.1°
C03	C04	C07	H9	165.7°	143.2°
C07	C04	O05	H4	121.9°	117.8°
C07	C04	O05	C06	97.6°	114.5°
C07	C04	C03	HG2	20.4°	57.1°
C07	C04	C03	H3	100.6°	177.0°
C04	C07	H8	H9	122.4°	118.0°
C04	C07	N08	H14	4.6°	53.0°
C07	C04	C03	H17	141.4°	63.4°
O05	C04	C03	HG2	101.8°	177.9°
O05	C04	C03	H3	137.2°	62.1°
C04	O05	C06	H5	180.0°	179.6°
C04	O05	C06	H6	60.0°	60.0°
C04	O05	C06	H7	60.0°	60.7°
O05	C04	C07	H8	161.1°	94.6°
O05	C04	C07	H9	77.2°	22.5°
O05	C04	C03	H17	19.1°	57.5°
C06	O05	C04	H4	24.3°	3.3°
O05	C06	H5	H6	120.0°	120.0°
O05	C06	H5	H7	120.0°	120.1°
O05	C06	H6	H7	120.0°	120.7°
HG2	C03	H3	H17	117.0°	120.0°
HG2	C03	C04	H4	140.9°	63.6°
C03	HG2	O01	H15	180.0°	6.1°
O01	HG2	C03	H3	63.6°	77.4°
O01	HG2	C03	H17	54.4°	163.1°
H1	C13	C12	H10	0.7°	0.1°
H1	C13	C14	H11	0.1°	0.0°
H2	C15	C14	H11	0.6°	0.0°
H3	C03	C04	H4	19.9°	56.3°
H4	C04	C07	H8	76.3°	146.9°
H4	C04	C07	H9	45.4°	96.0°
H4	C04	C03	H17	98.1°	176.0°
H5	C06	H6	H7	119.9°	119.5°
H8	C07	N08	H14	123.7°	175.2°
H9	C07	N08	H14	114.6°	67.5°

Release date:	2021-04-07
Definition date:	2020-04-23
Last modified:	2026-07-31
Release status:	REL
Processing site:	RCSB
Derived from:	6WNM