Summary Geometry PCM/PTM Related PDB entries

A1JID

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C3	C1	sing	1.53Å	1.53Å
C4	C1	sing	1.53Å	1.53Å
C1	O1	sing	1.45Å	1.43Å
C1	C2	sing	1.53Å	1.54Å
O1	C22	sing	1.34Å	1.44Å
C22	C16	sing	1.51Å	1.50Å
C22	O5	doub	1.21Å	1.23Å
O23	C14	doub	1.22Å	1.22Å
C16	N15	sing	1.46Å	1.45Å
S07	C08	sing	1.76Å	1.77Å
C14	N15	sing	1.35Å	1.34Å
C14	C13	sing	1.47Å	1.51Å
C08	C13	doub	1.40Å	1.42Å	Aromatic
C08	C09	sing	1.39Å	1.41Å	Aromatic
C13	C12	sing	1.40Å	1.41Å	Aromatic
C09	C10	doub	1.38Å	1.41Å	Aromatic
C12	C11	doub	1.38Å	1.40Å	Aromatic
C10	C11	sing	1.39Å	1.40Å	Aromatic
C10	H1	sing	1.08Å	1.08Å
S07	H2	sing	1.35Å	1.30Å
C09	H3	sing	1.08Å	1.08Å
C11	H4	sing	1.08Å	1.08Å
C12	H5	sing	1.08Å	1.08Å
N15	H6	sing	0.97Å	1.00Å
C16	H7	sing	1.09Å	1.10Å
C16	H8	sing	1.09Å	1.10Å
C2	H9	sing	1.09Å	1.10Å
C2	H10	sing	1.09Å	1.10Å
C2	H11	sing	1.09Å	1.10Å
C3	H12	sing	1.09Å	1.10Å
C3	H13	sing	1.09Å	1.10Å
C3	H14	sing	1.09Å	1.10Å
C4	H15	sing	1.09Å	1.10Å
C4	H16	sing	1.09Å	1.10Å
C4	H17	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C3	C1	C4	109.7°	109.5°
C3	C1	O1	106.5°	109.4°
C3	C1	C2	111.5°	109.5°
C1	C3	H12	109.5°	109.5°
C1	C3	H13	109.5°	109.5°
C1	C3	H14	109.5°	109.5°
C4	C1	O1	107.2°	109.5°
C4	C1	C2	111.2°	109.5°
C1	C4	H15	109.5°	109.5°
C1	C4	H16	109.5°	109.4°
C1	C4	H17	109.5°	109.5°
O1	C1	C2	110.5°	109.5°
C1	O1	C22	123.3°	117.0°
C1	C2	H9	109.5°	109.4°
C1	C2	H10	109.4°	109.5°
C1	C2	H11	109.5°	109.5°
O1	C22	C16	119.6°	120.0°
O1	C22	O5	119.6°	120.0°
C16	C22	O5	120.8°	120.0°
C22	C16	N15	106.5°	109.4°
C22	C16	H7	110.2°	109.5°
C22	C16	H8	110.2°	109.4°
O23	C14	N15	120.2°	120.0°
O23	C14	C13	117.7°	120.0°
C16	N15	C14	121.7°	120.0°
C16	N15	H6	119.1°	120.0°
N15	C16	H7	110.2°	109.5°
N15	C16	H8	110.2°	109.5°
S07	C08	C13	124.1°	120.2°
S07	C08	C09	118.5°	120.2°
C08	S07	H2	102.0°	103.0°
N15	C14	C13	122.0°	120.0°
C14	N15	H6	119.1°	120.0°
C14	C13	C08	119.2°	120.2°
C14	C13	C12	120.3°	120.2°
C13	C08	C09	117.4°	119.6°
C08	C13	C12	120.5°	119.5°
C08	C09	C10	121.6°	120.0°
C08	C09	H3	119.2°	119.9°
C13	C12	C11	121.0°	119.9°
C13	C12	H5	119.5°	120.0°
C09	C10	C11	120.2°	120.4°
C09	C10	H1	119.9°	119.7°
C10	C09	H3	119.2°	120.0°
C12	C11	C10	119.2°	120.4°
C12	C11	H4	120.4°	119.8°
C11	C12	H5	119.5°	120.0°
C11	C10	H1	119.9°	119.8°
C10	C11	H4	120.4°	119.8°
H7	C16	H8	109.5°	109.5°
H9	C2	H10	109.5°	109.5°
H9	C2	H11	109.5°	109.5°
H10	C2	H11	109.5°	109.5°
H12	C3	H13	109.5°	109.4°
H12	C3	H14	109.5°	109.5°
H13	C3	H14	109.4°	109.4°
H15	C4	H16	109.4°	109.5°
H15	C4	H17	109.4°	109.5°
H16	C4	H17	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C3	C1	C4	O1	115.3°	120.0°
C3	C1	C4	C2	123.8°	120.0°
C3	C1	O1	C2	121.3°	120.0°
C3	C1	O1	C22	168.5°	180.0°
C3	C1	C2	H9	180.0°	60.0°
C3	C1	C2	H10	60.0°	60.0°
C3	C1	C2	H11	60.0°	180.0°
C1	C3	H12	H13	120.0°	120.0°
C1	C3	H12	H14	120.0°	120.0°
C1	C3	H13	H14	120.0°	120.0°
C3	C1	C4	H15	180.0°	180.0°
C3	C1	C4	H16	60.0°	60.0°
C3	C1	C4	H17	60.0°	60.0°
C4	C1	O1	C2	121.4°	120.0°
C4	C1	O1	C22	74.1°	60.0°
C4	C1	C2	H9	57.3°	180.0°
C4	C1	C2	H10	177.3°	60.0°
C4	C1	C2	H11	62.8°	60.0°
C4	C1	C3	H12	180.0°	60.0°
C4	C1	C3	H13	60.0°	60.0°
C4	C1	C3	H14	60.0°	180.0°
C1	C4	H15	H16	120.0°	119.9°
C1	C4	H15	H17	120.0°	120.0°
C1	C4	H16	H17	120.0°	120.0°
C1	O1	C22	C16	159.9°	180.0°
C1	O1	C22	O5	19.8°	0.0°
O1	C1	C2	H9	61.7°	59.9°
O1	C1	C2	H10	58.3°	180.0°
O1	C1	C2	H11	178.2°	60.0°
O1	C1	C3	H12	64.3°	60.0°
O1	C1	C3	H13	55.8°	180.0°
O1	C1	C3	H14	175.7°	60.0°
O1	C1	C4	H15	64.7°	60.0°
O1	C1	C4	H16	175.3°	180.0°
O1	C1	C4	H17	55.3°	60.0°
C2	C1	O1	C22	47.3°	60.0°
C1	C2	H9	H10	120.0°	120.0°
C1	C2	H9	H11	120.0°	120.0°
C1	C2	H10	H11	120.0°	120.0°
C2	C1	C3	H12	56.4°	180.0°
C2	C1	C3	H13	176.4°	60.0°
C2	C1	C3	H14	63.7°	60.0°
C2	C1	C4	H15	56.2°	60.0°
C2	C1	C4	H16	63.8°	60.0°
C2	C1	C4	H17	176.2°	180.0°
O1	C22	C16	O5	179.6°	180.0°
O1	C22	C16	N15	178.9°	180.0°
O1	C22	C16	H7	59.4°	60.0°
O1	C22	C16	H8	61.5°	60.0°
C22	C16	N15	H7	119.5°	120.0°
C22	C16	N15	H8	119.6°	120.0°
C22	C16	N15	C14	89.8°	180.0°
C22	C16	N15	H6	90.2°	0.0°
C22	C16	H7	H8	121.4°	120.0°
O5	C22	C16	N15	1.5°	0.0°
O5	C22	C16	H7	121.0°	120.0°
O5	C22	C16	H8	118.1°	120.0°
O23	C14	N15	C16	1.8°	0.0°
O23	C14	N15	C13	177.1°	180.0°
O23	C14	C13	C08	14.6°	0.0°
O23	C14	C13	C12	165.2°	179.3°
O23	C14	N15	H6	178.2°	180.0°
C16	N15	C14	H6	180.0°	180.0°
C16	N15	C14	C13	175.4°	180.0°
N15	C16	H7	H8	121.3°	120.0°
S07	C08	C13	C14	0.8°	0.7°
S07	C08	C13	C09	178.7°	179.3°
S07	C08	C13	C12	179.0°	180.0°
S07	C08	C09	C10	179.4°	179.8°
S07	C08	C09	H3	0.6°	0.2°
N15	C14	C13	C08	162.6°	180.0°
N15	C14	C13	C12	17.6°	0.7°
C14	N15	C16	H7	29.7°	60.0°
C14	N15	C16	H8	150.6°	60.0°
C14	C13	C08	C12	179.8°	179.3°
C14	C13	C08	C09	179.5°	180.0°
C14	C13	C12	C11	179.0°	179.8°
C14	C13	C12	H5	1.0°	0.2°
C13	C14	N15	H6	4.6°	0.0°
C13	C08	C09	C10	1.8°	0.5°
C08	C13	C12	C11	1.2°	0.5°
C13	C08	S07	H2	5.3°	90.0°
C13	C08	C09	H3	178.2°	179.5°
C08	C13	C12	H5	178.8°	179.5°
C09	C08	C13	C12	0.3°	0.7°
C08	C09	C10	H3	180.0°	180.0°
C08	C09	C10	C11	1.8°	0.0°
C08	C09	C10	H1	178.2°	179.8°
C09	C08	S07	H2	173.4°	89.3°
C13	C12	C11	H5	180.0°	180.0°
C13	C12	C11	C10	1.2°	0.0°
C13	C12	C11	H4	178.8°	180.0°
C09	C10	C11	C12	0.3°	0.2°
C09	C10	C11	H1	180.0°	179.8°
C09	C10	C11	H4	179.7°	179.7°
C12	C11	C10	H4	180.0°	180.0°
C12	C11	C10	H1	179.8°	180.0°
C11	C10	C09	H3	178.2°	180.0°
C10	C11	C12	H5	178.8°	180.0°
H1	C10	C09	H3	1.8°	0.2°
H1	C10	C11	H4	0.2°	0.0°
H4	C11	C12	H5	1.2°	0.0°
H6	N15	C16	H7	150.3°	120.0°
H6	N15	C16	H8	29.4°	119.9°
H9	C2	H10	H11	120.0°	120.0°
H12	C3	H13	H14	120.0°	120.0°
H15	C4	H16	H17	120.0°	120.0°

Release date:	2026-06-17
Definition date:	2025-06-26
Last modified:	2026-06-12
Release status:	REL
Processing site:	PDBE
Derived from:	9REY