Summary Geometry PCM/PTM Related PDB entries

A1CD9

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	sing	1.51Å	1.51Å
C2	C3	doub	1.39Å	1.41Å	Aromatic
C2	C9	sing	1.37Å	1.39Å	Aromatic
C3	C4	sing	1.38Å	1.38Å	Aromatic
C9	C8	doub	1.40Å	1.42Å	Aromatic
C4	C5	doub	1.39Å	1.41Å	Aromatic
C5	C8	sing	1.41Å	1.42Å	Aromatic
C5	N1	sing	1.38Å	1.39Å	Aromatic
C8	C7	sing	1.46Å	1.45Å	Aromatic
N1	C6	sing	1.37Å	1.39Å	Aromatic
C7	C10	sing	1.51Å	1.52Å
C7	C6	doub	1.35Å	1.38Å	Aromatic
C10	N2	sing	1.47Å	1.47Å
C6	C14	sing	1.51Å	1.51Å
N2	C13	sing	1.47Å	1.48Å
N2	C11	sing	1.35Å	1.37Å
C14	C13	sing	1.53Å	1.54Å
C12	C11	sing	1.51Å	1.52Å
C11	O1	doub	1.21Å	1.22Å
N1	H1	sing	0.97Å	1.00Å
C4	H2	sing	1.08Å	1.08Å
C10	H3	sing	1.09Å	1.10Å
C10	H4	sing	1.09Å	1.10Å
C13	H5	sing	1.09Å	1.10Å
C13	H6	sing	1.09Å	1.10Å
C1	H7	sing	1.09Å	1.10Å
C1	H8	sing	1.09Å	1.10Å
C1	H9	sing	1.09Å	1.10Å
C3	H10	sing	1.08Å	1.08Å
C9	H11	sing	1.08Å	1.08Å
C12	H12	sing	1.09Å	1.10Å
C12	H13	sing	1.09Å	1.10Å
C12	H14	sing	1.09Å	1.10Å
C14	H15	sing	1.09Å	1.10Å
C14	H16	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	C2	C3	119.7°	119.8°
C1	C2	C9	121.0°	119.7°
C2	C1	H7	109.5°	109.5°
C2	C1	H8	109.5°	109.5°
C2	C1	H9	109.5°	109.5°
C3	C2	C9	119.2°	120.5°
C2	C3	C4	122.4°	120.7°
C2	C3	H10	118.8°	119.6°
C2	C9	C8	120.6°	119.9°
C2	C9	H11	119.7°	120.1°
C3	C4	C5	117.7°	119.8°
C3	C4	H2	121.1°	120.1°
C4	C3	H10	118.8°	119.7°
C9	C8	C5	118.0°	119.8°
C9	C8	C7	135.3°	134.4°
C8	C9	H11	119.7°	120.0°
C4	C5	C8	122.0°	119.3°
C4	C5	N1	130.4°	133.4°
C5	C4	H2	121.1°	120.1°
C8	C5	N1	107.6°	107.2°
C5	C8	C7	106.8°	105.8°
C5	N1	C6	109.3°	110.0°
C5	N1	H1	125.4°	125.0°
C8	C7	C10	130.6°	128.1°
C8	C7	C6	107.4°	107.5°
N1	C6	C7	109.0°	109.5°
N1	C6	C14	124.6°	126.5°
C6	N1	H1	125.4°	125.1°
C10	C7	C6	122.0°	124.4°
C7	C10	N2	109.8°	107.3°
C7	C10	H3	109.4°	109.8°
C7	C10	H4	109.4°	109.8°
C7	C6	C14	126.3°	124.0°
C10	N2	C13	119.1°	118.1°
C10	N2	C11	123.1°	120.9°
N2	C10	H3	109.4°	109.9°
N2	C10	H4	109.4°	109.9°
C6	C14	C13	109.2°	109.0°
C6	C14	H15	109.5°	109.6°
C6	C14	H16	109.6°	109.5°
C13	N2	C11	117.8°	120.9°
N2	C13	C14	112.7°	109.1°
N2	C13	H5	108.6°	109.5°
N2	C13	H6	108.7°	109.6°
N2	C11	C12	122.9°	120.0°
N2	C11	O1	120.6°	120.0°
C14	C13	H5	108.7°	109.5°
C14	C13	H6	108.6°	109.5°
C13	C14	H15	109.5°	109.6°
C13	C14	H16	109.5°	109.5°
C12	C11	O1	116.6°	120.0°
C11	C12	H12	109.5°	109.5°
C11	C12	H13	109.5°	109.5°
C11	C12	H14	109.5°	109.5°
H3	C10	H4	109.5°	110.0°
H5	C13	H6	109.5°	109.5°
H7	C1	H8	109.4°	109.5°
H7	C1	H9	109.4°	109.4°
H8	C1	H9	109.5°	109.4°
H12	C12	H13	109.4°	109.5°
H12	C12	H14	109.5°	109.4°
H13	C12	H14	109.5°	109.5°
H15	C14	H16	109.5°	109.6°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	C2	C3	C9	176.6°	179.9°
C1	C2	C3	C4	176.8°	180.0°
C1	C2	C9	C8	178.4°	180.0°
C2	C1	H7	H8	120.0°	120.1°
C2	C1	H7	H9	120.0°	120.0°
C2	C1	H8	H9	120.0°	120.0°
C1	C2	C3	H10	3.2°	0.0°
C1	C2	C9	H11	1.6°	0.0°
C2	C3	C4	H10	180.0°	180.0°
C3	C2	C9	C8	1.8°	0.0°
C2	C3	C4	C5	1.9°	0.0°
C2	C3	C4	H2	178.1°	180.0°
C3	C2	C1	H7	91.7°	90.0°
C3	C2	C1	H8	148.4°	150.0°
C3	C2	C1	H9	28.3°	30.0°
C3	C2	C9	H11	178.2°	179.9°
C9	C2	C3	C4	0.2°	0.0°
C2	C9	C8	H11	180.0°	180.0°
C2	C9	C8	C5	1.4°	0.0°
C2	C9	C8	C7	177.3°	179.8°
C9	C2	C1	H7	91.8°	90.1°
C9	C2	C1	H8	28.2°	30.0°
C9	C2	C1	H9	148.3°	149.9°
C9	C2	C3	H10	179.8°	180.0°
C3	C4	C5	H2	180.0°	180.0°
C3	C4	C5	C8	2.3°	0.0°
C3	C4	C5	N1	178.5°	179.9°
C9	C8	C5	C4	0.8°	0.0°
C9	C8	C5	C7	179.0°	179.8°
C9	C8	C5	N1	179.9°	179.9°
C9	C8	C7	C10	2.7°	0.1°
C9	C8	C7	C6	179.1°	179.7°
C4	C5	C8	N1	179.3°	180.0°
C4	C5	C8	C7	179.8°	179.8°
C4	C5	N1	C6	179.6°	179.8°
C4	C5	N1	H1	0.4°	0.0°
C5	C4	C3	H10	178.1°	180.0°
C8	C5	N1	C6	1.2°	0.1°
C5	C8	C7	C10	176.1°	179.9°
C5	C8	C7	C6	0.4°	0.5°
C8	C5	N1	H1	178.8°	179.9°
C8	C5	C4	H2	177.6°	180.0°
C5	C8	C9	H11	178.6°	180.0°
N1	C5	C8	C7	0.9°	0.2°
C5	N1	C6	H1	180.0°	179.8°
C5	N1	C6	C7	1.0°	0.4°
C5	N1	C6	C14	176.6°	179.3°
N1	C5	C4	H2	1.5°	0.1°
C8	C7	C6	N1	0.4°	0.6°
C8	C7	C10	C6	176.0°	179.6°
C8	C7	C10	N2	165.0°	168.6°
C8	C7	C6	C14	177.2°	179.2°
C8	C7	C10	H3	74.9°	71.9°
C8	C7	C10	H4	45.0°	49.1°
C7	C8	C9	H11	2.7°	0.2°
N1	C6	C7	C10	177.2°	179.8°
N1	C6	C7	C14	177.5°	179.7°
N1	C6	C14	C13	169.2°	162.0°
N1	C6	C14	H15	70.8°	78.1°
N1	C6	C14	H16	49.3°	42.2°
C7	C10	N2	H3	120.1°	119.4°
C7	C10	N2	H4	120.1°	119.4°
C10	C7	C6	C14	0.4°	0.5°
C7	C10	N2	C13	39.7°	43.8°
C7	C10	N2	C11	142.6°	136.2°
C7	C10	H3	H4	119.9°	121.0°
C6	C7	C10	N2	10.9°	11.0°
C7	C6	C14	C13	13.6°	18.3°
C7	C6	N1	H1	179.0°	179.8°
C6	C7	C10	H3	109.1°	108.5°
C6	C7	C10	H4	131.0°	130.4°
C7	C6	C14	H15	106.4°	101.6°
C7	C6	C14	H16	133.6°	138.1°
C10	N2	C13	C11	177.8°	180.0°
C10	N2	C13	C14	56.4°	64.3°
C10	N2	C11	C12	12.1°	180.0°
C10	N2	C11	O1	169.5°	0.0°
N2	C10	H3	H4	119.8°	121.1°
C10	N2	C13	H5	64.0°	55.6°
C10	N2	C13	H6	176.9°	175.8°
C6	C14	C13	N2	38.6°	45.8°
C6	C14	C13	H15	120.0°	119.9°
C6	C14	C13	H16	120.0°	119.8°
C14	C6	N1	H1	3.4°	0.5°
C6	C14	C13	H5	81.8°	74.1°
C6	C14	C13	H6	159.1°	165.7°
C6	C14	H15	H16	120.1°	120.3°
N2	C13	C14	H5	120.5°	119.9°
N2	C13	C14	H6	120.5°	119.9°
C13	N2	C11	C12	165.6°	0.0°
C13	N2	C11	O1	12.7°	180.0°
C13	N2	C10	H3	80.3°	75.6°
C13	N2	C10	H4	159.8°	163.2°
N2	C13	H5	H6	118.5°	120.2°
N2	C13	C14	H15	81.3°	74.2°
N2	C13	C14	H16	158.6°	165.5°
C11	N2	C13	C14	125.8°	115.7°
N2	C11	C12	O1	178.4°	180.0°
C11	N2	C10	H3	97.3°	104.4°
C11	N2	C10	H4	22.5°	16.8°
C11	N2	C13	H5	113.8°	124.4°
C11	N2	C13	H6	5.3°	4.2°
N2	C11	C12	H12	178.4°	89.9°
N2	C11	C12	H13	58.4°	150.0°
N2	C11	C12	H14	61.6°	30.0°
C14	C13	H5	H6	118.5°	120.2°
C13	C14	H15	H16	120.1°	120.2°
C11	C12	H12	H13	120.0°	120.1°
C11	C12	H12	H14	120.0°	120.0°
C11	C12	H13	H14	120.0°	120.1°
O1	C11	C12	H12	0.0°	90.0°
O1	C11	C12	H13	120.0°	30.0°
O1	C11	C12	H14	120.0°	150.0°
H2	C4	C3	H10	1.9°	0.0°
H5	C13	C14	H15	158.2°	165.9°
H5	C13	C14	H16	38.1°	45.6°
H6	C13	C14	H15	39.2°	45.8°
H6	C13	C14	H16	80.9°	74.5°
H7	C1	H8	H9	120.0°	119.9°
H12	C12	H13	H14	120.0°	119.9°

Release date:	2026-06-24
Definition date:	2025-05-27
Last modified:	2026-06-19
Release status:	REL
Processing site:	RCSB
Derived from:	9OT4