Summary Geometry PCM/PTM Related PDB entries

A1BI9

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C5	C4	doub	1.38Å	1.38Å	Aromatic
C5	C6	sing	1.38Å	1.41Å	Aromatic
C4	C3	sing	1.40Å	1.39Å	Aromatic
O2	B1	sing	1.37Å	1.48Å
B1	C6	sing	1.56Å	1.67Å
B1	O3	sing	1.37Å	1.48Å
O1	C2	doub	1.22Å	1.23Å
C6	C8	doub	1.38Å	1.40Å	Aromatic
C3	C2	sing	1.48Å	1.51Å
C3	C9	doub	1.40Å	1.40Å	Aromatic
C2	N1	sing	1.35Å	1.37Å
C8	C9	sing	1.38Å	1.39Å	Aromatic
C8	CL1	sing	1.74Å	1.74Å
N1	C1	sing	1.47Å	1.48Å
N1	C10	sing	1.40Å	1.43Å
C15	C10	doub	1.39Å	1.41Å	Aromatic
C15	C14	sing	1.38Å	1.38Å	Aromatic
C10	C11	sing	1.39Å	1.41Å	Aromatic
C14	C13	doub	1.38Å	1.38Å	Aromatic
C11	C12	doub	1.38Å	1.39Å	Aromatic
C13	C12	sing	1.38Å	1.38Å	Aromatic
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C1	H3	sing	1.09Å	1.10Å
C4	H4	sing	1.08Å	1.08Å
C5	H5	sing	1.08Å	1.08Å
O2	H6	sing	0.97Å	0.95Å
O3	H7	sing	0.97Å	0.95Å
C9	H8	sing	1.08Å	1.08Å
C11	H9	sing	1.08Å	1.08Å
C12	H10	sing	1.08Å	1.08Å
C13	H11	sing	1.08Å	1.08Å
C14	H12	sing	1.08Å	1.08Å
C15	H13	sing	1.08Å	1.08Å
B1	O4	sing	1.37Å	1.39Å
O4	H15	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C4	C5	C6	121.8°	120.1°
C5	C4	C3	119.9°	119.9°
C5	C4	H4	120.1°	120.0°
C4	C5	H5	119.1°	119.9°
C5	C6	B1	119.1°	119.8°
C5	C6	C8	117.7°	120.3°
C6	C5	H5	119.1°	120.0°
C4	C3	C2	115.3°	120.2°
C4	C3	C9	119.2°	119.7°
C3	C4	H4	120.1°	120.1°
O2	B1	C6	113.8°	109.5°
O2	B1	O3	106.0°	109.6°
B1	O2	H6	109.5°	114.0°
O2	B1	O4	113.7°	109.5°
C6	B1	O3	114.3°	109.5°
B1	C6	C8	123.1°	119.8°
C6	B1	O4	108.7°	109.4°
B1	O3	H7	109.5°	114.0°
O3	B1	O4	99.6°	109.4°
O1	C2	C3	119.4°	120.0°
O1	C2	N1	120.7°	120.0°
C6	C8	C9	120.8°	120.1°
C6	C8	CL1	118.8°	120.0°
C2	C3	C9	125.4°	120.2°
C3	C2	N1	119.9°	120.0°
C3	C9	C8	120.3°	119.9°
C3	C9	H8	119.8°	120.0°
C2	N1	C1	120.0°	120.0°
C2	N1	C10	123.9°	120.0°
C9	C8	CL1	120.3°	120.0°
C8	C9	H8	119.9°	120.1°
C1	N1	C10	116.1°	120.0°
N1	C1	H1	109.5°	109.5°
N1	C1	H2	109.4°	109.5°
N1	C1	H3	109.5°	109.4°
N1	C10	C15	121.1°	120.1°
N1	C10	C11	120.5°	120.1°
C10	C15	C14	120.1°	119.9°
C15	C10	C11	118.4°	119.9°
C10	C15	H13	119.9°	120.0°
C15	C14	C13	120.9°	120.1°
C15	C14	H12	119.6°	120.0°
C14	C15	H13	119.9°	120.1°
C10	C11	C12	120.2°	119.9°
C10	C11	H9	119.9°	120.0°
C14	C13	C12	119.9°	120.1°
C14	C13	H11	120.1°	120.0°
C13	C14	H12	119.6°	119.9°
C11	C12	C13	120.5°	120.1°
C12	C11	H9	119.9°	120.1°
C11	C12	H10	119.7°	119.9°
C13	C12	H10	119.7°	119.9°
C12	C13	H11	120.1°	119.9°
H1	C1	H2	109.5°	109.5°
H1	C1	H3	109.5°	109.5°
H2	C1	H3	109.5°	109.5°
B1	O4	H15	109.5°	114.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C4	C5	C6	H5	180.0°	179.9°
C5	C4	C3	H4	180.0°	179.9°
C4	C5	C6	B1	178.2°	180.0°
C4	C5	C6	C8	2.3°	0.0°
C5	C4	C3	C2	178.2°	180.0°
C5	C4	C3	C9	5.0°	0.3°
C6	C5	C4	C3	3.7°	0.0°
C5	C6	B1	O2	124.5°	30.1°
C5	C6	B1	C8	179.5°	180.0°
C5	C6	B1	O3	113.5°	90.0°
C5	C6	C8	C9	2.2°	0.2°
C5	C6	C8	CL1	180.0°	180.0°
C6	C5	C4	H4	176.3°	179.9°
C5	C6	B1	O4	3.2°	150.0°
C4	C3	C2	O1	52.7°	156.1°
C4	C3	C2	C9	176.5°	179.7°
C4	C3	C2	N1	128.4°	23.9°
C4	C3	C9	C8	5.0°	0.5°
C3	C4	C5	H5	176.3°	180.0°
C4	C3	C9	H8	175.0°	179.7°
O2	B1	C6	O3	122.0°	120.1°
O2	B1	C6	O4	127.7°	120.0°
O2	B1	O3	O4	118.2°	120.0°
O2	B1	C6	C8	56.0°	150.0°
O2	B1	O3	H7	180.0°	60.0°
O2	B1	O4	H15	180.0°	59.9°
C6	B1	O3	O4	115.7°	119.9°
B1	C6	C8	C9	178.3°	179.7°
B1	C6	C8	CL1	0.5°	0.1°
B1	C6	C5	H5	1.8°	0.0°
C6	B1	O2	H6	180.0°	180.0°
C6	B1	O3	H7	53.8°	60.0°
C6	B1	O4	H15	52.2°	60.0°
O3	B1	C6	C8	66.0°	89.9°
O3	B1	O2	H6	53.5°	59.9°
O3	B1	O4	H15	67.7°	180.0°
O1	C2	C3	N1	178.9°	179.9°
O1	C2	C3	C9	123.8°	23.7°
O1	C2	N1	C1	7.1°	173.7°
O1	C2	N1	C10	176.0°	6.3°
C6	C8	C9	C3	3.6°	0.5°
C6	C8	C9	CL1	177.7°	179.8°
C8	C6	C5	H5	177.7°	180.0°
C6	C8	C9	H8	176.4°	179.8°
C8	C6	B1	O4	176.3°	30.0°
C2	C3	C9	C8	178.6°	179.8°
C3	C2	N1	C1	171.7°	6.4°
C3	C2	N1	C10	5.1°	173.6°
C2	C3	C4	H4	1.8°	0.1°
C2	C3	C9	H8	1.4°	0.0°
C9	C3	C2	N1	55.1°	156.4°
C3	C9	C8	H8	180.0°	179.7°
C3	C9	C8	CL1	178.6°	179.7°
C9	C3	C4	H4	175.0°	179.8°
C2	N1	C1	C10	177.1°	180.0°
C2	N1	C10	C15	60.5°	7.1°
C2	N1	C10	C11	120.5°	172.6°
C2	N1	C1	H1	180.0°	96.0°
C2	N1	C1	H2	60.0°	24.0°
C2	N1	C1	H3	60.0°	144.0°
CL1	C8	C9	H8	1.4°	0.0°
C1	N1	C10	C15	122.5°	173.0°
C1	N1	C10	C11	56.4°	7.4°
N1	C1	H1	H2	120.0°	120.0°
N1	C1	H1	H3	120.0°	119.9°
N1	C1	H2	H3	120.0°	120.0°
N1	C10	C15	C11	179.0°	179.7°
N1	C10	C15	C14	178.7°	179.7°
N1	C10	C11	C12	179.9°	180.0°
C10	N1	C1	H1	2.9°	84.1°
C10	N1	C1	H2	117.1°	155.9°
C10	N1	C1	H3	122.9°	35.9°
N1	C10	C11	H9	0.0°	0.0°
N1	C10	C15	H13	1.3°	0.0°
C10	C15	C14	H13	180.0°	179.7°
C10	C15	C14	C13	0.3°	0.6°
C15	C10	C11	C12	0.9°	0.3°
C15	C10	C11	H9	179.0°	179.7°
C10	C15	C14	H12	179.7°	179.7°
C14	C15	C10	C11	0.3°	0.6°
C15	C14	C13	H12	180.0°	179.7°
C15	C14	C13	C12	1.0°	0.3°
C15	C14	C13	H11	179.0°	179.7°
C10	C11	C12	H9	180.0°	180.0°
C10	C11	C12	C13	2.2°	0.0°
C10	C11	C12	H10	177.8°	180.0°
C11	C10	C15	H13	179.7°	179.7°
C14	C13	C12	C11	2.2°	0.0°
C14	C13	C12	H11	180.0°	179.9°
C14	C13	C12	H10	177.8°	180.0°
C13	C14	C15	H13	179.7°	179.7°
C11	C12	C13	H10	180.0°	180.0°
C11	C12	C13	H11	177.8°	179.9°
C13	C12	C11	H9	177.8°	180.0°
C12	C13	C14	H12	179.1°	180.0°
H1	C1	H2	H3	120.0°	120.0°
H4	C4	C5	H5	3.7°	0.2°
H6	O2	B1	O4	54.9°	60.1°
H7	O3	B1	O4	61.8°	180.0°
H9	C11	C12	H10	2.2°	0.0°
H10	C12	C13	H11	2.2°	0.0°
H11	C13	C14	H12	0.9°	0.1°
H12	C14	C15	H13	0.3°	0.0°

Release date:	2026-06-24
Definition date:	2024-12-05
Last modified:	2026-06-19
Release status:	REL
Processing site:	RCSB
Derived from:	9EIM