Summary Geometry PCM/PTM Related PDB entries

TBY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C11	C10	sing	1.52Å	1.53Å
C11	C12	sing	1.52Å	1.51Å
C10	SN1	sing	2.14Å	2.14Å
SN1	C2	sing	2.14Å	2.14Å
SN1	C6	sing	2.14Å	2.15Å
C2	C3	sing	1.51Å	1.52Å
C3	C4	sing	1.52Å	1.53Å
C4	C5	sing	1.52Å	1.51Å
C6	C7	sing	1.52Å	1.52Å
C7	C8	sing	1.52Å	1.52Å
C8	C9	sing	1.52Å	1.50Å
C12	C13	sing	1.52Å	1.51Å
C11	H11	sing	0.98Å	1.10Å
C11	H11A	sing	0.98Å	1.10Å
C10	H10	sing	0.94Å	1.10Å
C10	H10A	sing	0.94Å	1.10Å
C2	H2	sing	0.95Å	1.10Å
C2	H2A	sing	0.95Å	1.10Å
C3	H3	sing	0.98Å	1.10Å
C3	H3A	sing	0.98Å	1.10Å
C4	H4	sing	0.98Å	1.10Å
C4	H4A	sing	0.98Å	1.10Å
C5	H5	sing	0.98Å	1.10Å
C5	H5A	sing	0.98Å	1.10Å
C5	H5B	sing	0.98Å	1.10Å
C6	H6	sing	0.95Å	1.10Å
C6	H6A	sing	0.95Å	1.10Å
C7	H7	sing	0.98Å	1.10Å
C7	H7A	sing	0.98Å	1.10Å
C8	H8	sing	0.98Å	1.10Å
C8	H8A	sing	0.98Å	1.10Å
C9	H9	sing	0.98Å	1.10Å
C9	H9A	sing	0.98Å	1.10Å
C9	H9B	sing	0.98Å	1.10Å
C12	H12	sing	0.98Å	1.10Å
C12	H12A	sing	0.98Å	1.10Å
C13	H13	sing	0.98Å	1.10Å
C13	H13A	sing	0.98Å	1.10Å
C13	H13B	sing	0.98Å	1.10Å
CL1	SN1	sing	2.41Å	34.99Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C10	C11	C12	109.7°	114.4°
C11	C10	SN1	112.2°	110.0°
C10	C11	H11	109.4°	108.8°
C10	C11	H11A	109.4°	108.8°
C11	C10	H10	108.8°	110.2°
C11	C10	H10A	108.8°	110.1°
C11	C12	C13	111.3°	116.9°
C12	C11	H11	109.4°	108.9°
C12	C11	H11A	109.4°	108.8°
C11	C12	H12	109.0°	107.8°
C11	C12	H12A	109.0°	108.0°
C10	SN1	C2	107.7°	117.6°
C10	SN1	C6	97.0°	115.5°
SN1	C10	H10	108.8°	108.4°
SN1	C10	H10A	108.8°	108.5°
C10	SN1	CL1	119.6°	101.3°
C2	SN1	C6	126.8°	115.7°
SN1	C2	C3	108.5°	108.3°
SN1	C2	H2	109.7°	111.5°
SN1	C2	H2A	109.7°	107.3°
C2	SN1	CL1	114.7°	101.3°
SN1	C6	C7	110.0°	109.8°
SN1	C6	H6	109.3°	108.4°
SN1	C6	H6A	109.3°	108.7°
C6	SN1	CL1	90.3°	101.3°
C2	C3	C4	108.8°	114.7°
C3	C2	H2	109.7°	109.9°
C3	C2	H2A	109.7°	110.4°
C2	C3	H3	109.6°	108.8°
C2	C3	H3A	109.6°	108.8°
C3	C4	C5	110.2°	116.9°
C4	C3	H3	109.6°	108.9°
C4	C3	H3A	109.7°	108.5°
C3	C4	H4	109.3°	107.8°
C3	C4	H4A	109.3°	107.9°
C5	C4	H4	109.3°	108.3°
C5	C4	H4A	109.3°	108.2°
C4	C5	H5	109.5°	109.6°
C4	C5	H5A	109.5°	109.6°
C4	C5	H5B	109.4°	109.6°
C6	C7	C8	111.5°	114.5°
C7	C6	H6	109.3°	110.2°
C7	C6	H6A	109.3°	110.1°
C6	C7	H7	109.0°	108.8°
C6	C7	H7A	108.9°	108.9°
C7	C8	C9	107.9°	117.0°
C8	C7	H7	109.0°	108.6°
C8	C7	H7A	109.0°	108.9°
C7	C8	H8	109.9°	107.9°
C7	C8	H8A	109.8°	107.8°
C9	C8	H8	109.8°	108.2°
C9	C8	H8A	109.9°	108.3°
C8	C9	H9	109.5°	109.5°
C8	C9	H9A	109.5°	109.6°
C8	C9	H9B	109.5°	109.6°
C13	C12	H12	109.0°	108.2°
C13	C12	H12A	109.0°	108.1°
C12	C13	H13	109.5°	109.5°
C12	C13	H13A	109.5°	109.6°
C12	C13	H13B	109.5°	109.6°
H11	C11	H11A	109.5°	106.9°
H10	C10	H10A	109.5°	109.6°
H2	C2	H2A	109.5°	109.4°
H3	C3	H3A	109.5°	106.9°
H4	C4	H4A	109.5°	107.4°
H5	C5	H5A	109.5°	109.4°
H5	C5	H5B	109.5°	109.3°
H5A	C5	H5B	109.5°	109.3°
H6	C6	H6A	109.5°	109.6°
H7	C7	H7A	109.4°	106.9°
H8	C8	H8A	109.5°	107.4°
H9	C9	H9A	109.5°	109.4°
H9	C9	H9B	109.4°	109.3°
H9A	C9	H9B	109.5°	109.4°
H12	C12	H12A	109.5°	107.4°
H13	C13	H13A	109.5°	109.4°
H13	C13	H13B	109.4°	109.3°
H13A	C13	H13B	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C10	C11	C12	H11	120.0°	122.0°
C10	C11	C12	H11A	120.0°	121.9°
C11	C10	SN1	H10	120.4°	120.5°
C11	C10	SN1	H10A	120.4°	120.5°
C11	C10	SN1	C2	90.8°	33.9°
C11	C10	SN1	C6	41.5°	176.2°
C10	C11	C12	C13	176.4°	179.0°
C10	C11	H11	H11A	119.9°	117.3°
C11	C10	H10	H10A	118.7°	121.3°
C10	C11	C12	H12	63.3°	59.0°
C10	C11	C12	H12A	56.1°	56.8°
C11	C10	SN1	CL1	135.9°	75.4°
C12	C11	C10	SN1	173.2°	179.2°
C11	C12	C13	H12	120.3°	121.8°
C11	C12	C13	H12A	120.3°	122.1°
C12	C11	H11	H11A	119.9°	117.3°
C12	C11	C10	H10	52.8°	59.8°
C12	C11	C10	H10A	66.3°	61.3°
C11	C12	H12	H12A	119.1°	116.1°
C11	C12	C13	H13	180.0°	179.7°
C11	C12	C13	H13A	60.0°	60.3°
C11	C12	C13	H13B	60.0°	59.8°
C10	SN1	C2	C6	113.5°	142.3°
C10	SN1	C2	CL1	135.9°	109.2°
C10	SN1	C6	CL1	119.9°	108.4°
C10	SN1	C2	C3	17.3°	71.8°
C10	SN1	C6	C7	149.5°	176.2°
SN1	C10	C11	H11	53.2°	58.8°
SN1	C10	C11	H11A	66.7°	57.4°
SN1	C10	H10	H10A	118.7°	118.3°
C10	SN1	C2	H2	137.1°	49.3°
C10	SN1	C2	H2A	102.6°	169.0°
C10	SN1	C6	H6	90.4°	55.8°
C10	SN1	C6	H6A	29.4°	63.3°
C2	SN1	C6	CL1	121.8°	108.5°
SN1	C2	C3	H2	119.9°	122.1°
SN1	C2	C3	H2A	119.8°	117.2°
SN1	C2	C3	C4	80.3°	170.2°
C2	SN1	C6	C7	92.2°	40.7°
C2	SN1	C10	H10	148.8°	86.7°
C2	SN1	C10	H10A	29.6°	154.4°
SN1	C2	H2	H2A	120.4°	118.5°
SN1	C2	C3	H3	159.8°	47.9°
SN1	C2	C3	H3A	39.6°	68.1°
C2	SN1	C6	H6	27.9°	161.1°
C2	SN1	C6	H6A	147.7°	79.8°
C6	SN1	C2	C3	96.3°	70.5°
SN1	C6	C7	H6	120.1°	119.4°
SN1	C6	C7	H6A	120.1°	119.7°
SN1	C6	C7	C8	126.2°	178.9°
C6	SN1	C10	H10	78.9°	55.7°
C6	SN1	C10	H10A	161.9°	63.3°
C6	SN1	C2	H2	23.6°	168.5°
C6	SN1	C2	H2A	143.9°	48.7°
SN1	C6	H6	H6A	119.7°	118.5°
SN1	C6	C7	H7	5.9°	59.4°
SN1	C6	C7	H7A	113.4°	56.8°
C2	C3	C4	H3	119.9°	122.2°
C2	C3	C4	H3A	119.9°	121.8°
C2	C3	C4	C5	174.4°	178.5°
C3	C2	H2	H2A	120.5°	121.3°
C2	C3	H3	H3A	120.3°	117.3°
C2	C3	C4	H4	54.3°	59.3°
C2	C3	C4	H4A	65.5°	56.4°
C3	C2	SN1	CL1	153.1°	178.9°
C3	C4	C5	H4	120.1°	122.0°
C3	C4	C5	H4A	120.1°	122.0°
C4	C3	C2	H2	39.6°	67.8°
C4	C3	C2	H2A	159.9°	53.0°
C4	C3	H3	H3A	120.3°	117.0°
C3	C4	H4	H4A	119.7°	116.0°
C3	C4	C5	H5	180.0°	178.6°
C3	C4	C5	H5A	60.0°	58.6°
C3	C4	C5	H5B	60.0°	61.4°
C5	C4	C3	H3	65.7°	56.3°
C5	C4	C3	H3A	54.5°	59.7°
C5	C4	H4	H4A	119.7°	116.6°
C4	C5	H5	H5A	120.0°	120.2°
C4	C5	H5	H5B	120.0°	120.1°
C4	C5	H5A	H5B	120.0°	120.2°
C6	C7	C8	H7	120.3°	121.8°
C6	C7	C8	H7A	120.3°	122.1°
C6	C7	C8	C9	130.6°	178.8°
C7	C6	H6	H6A	119.7°	121.3°
C6	C7	H7	H7A	119.0°	117.4°
C6	C7	C8	H8	109.6°	56.6°
C6	C7	C8	H8A	10.8°	59.1°
C7	C6	SN1	CL1	29.6°	67.8°
C7	C8	C9	H8	119.8°	122.0°
C7	C8	C9	H8A	119.8°	121.9°
C8	C7	C6	H6	113.7°	59.6°
C8	C7	C6	H6A	6.1°	61.4°
C8	C7	H7	H7A	119.1°	117.4°
C7	C8	H8	H8A	120.7°	115.9°
C7	C8	C9	H9	180.0°	179.9°
C7	C8	C9	H9A	60.0°	60.1°
C7	C8	C9	H9B	60.0°	60.0°
C9	C8	C7	H7	10.3°	59.4°
C9	C8	C7	H7A	109.1°	56.7°
C9	C8	H8	H8A	120.7°	116.6°
C8	C9	H9	H9A	120.0°	120.1°
C8	C9	H9	H9B	120.0°	120.1°
C8	C9	H9A	H9B	120.0°	120.2°
C13	C12	C11	H11	56.4°	57.0°
C13	C12	C11	H11A	63.6°	59.1°
C13	C12	H12	H12A	119.2°	116.6°
C12	C13	H13	H13A	120.0°	120.1°
C12	C13	H13	H13B	120.0°	120.1°
C12	C13	H13A	H13B	120.0°	120.2°
H11	C11	C10	H10	67.2°	178.2°
H11	C11	C10	H10A	173.6°	60.8°
H11	C11	C12	H12	176.6°	179.1°
H11	C11	C12	H12A	63.9°	65.2°
H11A	C11	C10	H10	172.9°	62.1°
H11A	C11	C10	H10A	53.7°	176.9°
H11A	C11	C12	H12	56.7°	62.9°
H11A	C11	C12	H12A	176.1°	178.7°
H10	C10	SN1	CL1	15.5°	164.1°
H10A	C10	SN1	CL1	103.7°	45.2°
H2	C2	C3	H3	80.3°	170.0°
H2	C2	C3	H3A	159.5°	53.9°
H2	C2	SN1	CL1	87.0°	60.0°
H2A	C2	C3	H3	40.0°	69.3°
H2A	C2	C3	H3A	80.2°	174.7°
H2A	C2	SN1	CL1	33.3°	59.8°
H3	C3	C4	H4	174.2°	178.5°
H3	C3	C4	H4A	54.4°	65.8°
H3A	C3	C4	H4	65.6°	62.5°
H3A	C3	C4	H4A	174.6°	178.2°
H4	C4	C5	H5	59.9°	59.4°
H4	C4	C5	H5A	179.9°	179.4°
H4	C4	C5	H5B	60.1°	60.6°
H4A	C4	C5	H5	59.9°	56.7°
H4A	C4	C5	H5A	60.1°	63.4°
H4A	C4	C5	H5B	179.9°	176.6°
H5	C5	H5A	H5B	120.0°	119.7°
H6	C6	C7	H7	126.0°	178.7°
H6	C6	C7	H7A	6.6°	62.5°
H6	C6	SN1	CL1	149.7°	52.6°
H6A	C6	C7	H7	114.2°	60.3°
H6A	C6	C7	H7A	126.5°	176.5°
H6A	C6	SN1	CL1	90.5°	171.7°
H7	C7	C8	H8	130.0°	178.4°
H7	C7	C8	H8A	109.5°	62.7°
H7A	C7	C8	H8	10.7°	65.5°
H7A	C7	C8	H8A	131.2°	178.8°
H8	C8	C9	H9	60.2°	57.9°
H8	C8	C9	H9A	179.8°	177.8°
H8	C8	C9	H9B	59.8°	62.0°
H8A	C8	C9	H9	60.3°	58.2°
H8A	C8	C9	H9A	59.8°	61.8°
H8A	C8	C9	H9B	179.8°	178.1°
H9	C9	H9A	H9B	120.0°	119.7°
H12	C12	C13	H13	59.7°	57.9°
H12	C12	C13	H13A	179.7°	177.9°
H12	C12	C13	H13B	60.2°	62.1°
H12A	C12	C13	H13	59.7°	58.2°
H12A	C12	C13	H13A	60.3°	61.8°
H12A	C12	C13	H13B	179.7°	178.2°
H13	C13	H13A	H13B	120.0°	119.7°

Definition date:	2008-09-05
Last modified:	2026-07-31
Release status:	REL
Processing site:	RCSB
Derived from:	3E94