Summary Geometry PCM/PTM Related PDB entries

4KV

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C7	C8	doub	1.38Å	1.35Å	Aromatic
C7	C6	sing	1.38Å	1.39Å	Aromatic
C8	C9	sing	1.38Å	1.42Å	Aromatic
O3	C6	sing	1.37Å	1.42Å
C6	C5	doub	1.39Å	1.37Å	Aromatic
C9	C4	doub	1.41Å	1.40Å	Aromatic
C5	C4	sing	1.40Å	1.37Å	Aromatic
C4	C3	sing	1.50Å	1.48Å
C3	O1	sing	1.25Å	1.27Å
C3	C2	doub	1.47Å	1.43Å
O1	PT1	sing	2.01Å	2.00Å
C2	C1	sing	1.46Å	1.38Å
PT1	S3	sing	2.22Å	2.16Å
PT1	S1	sing	2.21Å	2.22Å
C1	S1	doub	1.68Å	1.68Å
C1	S2	sing	1.76Å	1.78Å
C12	S3	sing	1.78Å	1.76Å
S3	O2	doub	1.50Å	1.49Å
S3	C13	sing	1.77Å	1.78Å
S2	C10	sing	1.81Å	1.79Å
C10	C11	sing	1.50Å	1.53Å
C5	H2	sing	0.94Å	1.08Å
C7	H3	sing	0.95Å	1.08Å
C8	H4	sing	0.94Å	1.08Å
C10	H5	sing	0.98Å	1.10Å
C10	H6	sing	0.98Å	1.10Å
C12	H7	sing	0.97Å	1.10Å
C12	H8	sing	0.97Å	1.10Å
C12	H9	sing	0.97Å	1.10Å
C13	H10	sing	0.97Å	1.10Å
C13	H11	sing	0.97Å	1.10Å
C13	H12	sing	0.97Å	1.10Å
C2	H13	sing	0.94Å	1.08Å
C9	H14	sing	0.94Å	1.08Å
C11	H15	sing	0.97Å	1.10Å
C11	H16	sing	0.97Å	1.10Å
C11	H17	sing	0.97Å	1.10Å
O3	H18	sing	0.86Å	0.95Å
PT1	CL1	sing	2.31Å	17.14Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C8	C7	C6	119.8°	119.6°
C7	C8	C9	119.9°	120.8°
C8	C7	H3	120.1°	120.3°
C7	C8	H4	120.0°	119.5°
C7	C6	O3	121.3°	117.5°
C7	C6	C5	121.3°	120.1°
C6	C7	H3	120.1°	120.1°
C8	C9	C4	119.4°	120.9°
C9	C8	H4	120.1°	119.7°
C8	C9	H14	120.3°	119.1°
O3	C6	C5	117.3°	122.3°
C6	O3	H18	109.5°	113.7°
C6	C5	C4	120.3°	121.2°
C6	C5	H2	119.9°	119.2°
C9	C4	C5	119.3°	117.5°
C9	C4	C3	120.1°	124.1°
C4	C9	H14	120.3°	120.0°
C5	C4	C3	120.7°	118.3°
C4	C5	H2	119.8°	119.6°
C4	C3	O1	113.9°	118.2°
C4	C3	C2	119.0°	122.7°
O1	C3	C2	127.1°	119.1°
C3	O1	PT1	130.1°	116.3°
C3	C2	C1	128.0°	128.0°
C3	C2	H13	116.0°	116.6°
O1	PT1	S3	175.3°	91.7°
O1	PT1	S1	96.5°	85.4°
O1	PT1	CL1	103.7°	175.4°
C2	C1	S1	128.5°	120.4°
C2	C1	S2	111.1°	114.8°
C1	C2	H13	116.0°	115.4°
S3	PT1	S1	88.1°	176.4°
PT1	S3	C12	113.9°	117.8°
PT1	S3	O2	115.1°	112.3°
PT1	S3	C13	108.1°	111.4°
S3	PT1	CL1	73.9°	92.8°
PT1	S1	C1	109.9°	102.5°
S1	PT1	CL1	126.0°	90.0°
S1	C1	S2	118.9°	124.9°
C1	S2	C10	110.7°	110.4°
C12	S3	O2	105.7°	107.1°
C12	S3	C13	107.3°	99.8°
S3	C12	H7	109.5°	109.4°
S3	C12	H8	109.5°	109.4°
S3	C12	H9	109.5°	109.3°
O2	S3	C13	106.1°	107.4°
S3	C13	H10	109.5°	109.3°
S3	C13	H11	109.5°	109.4°
S3	C13	H12	109.5°	109.3°
S2	C10	C11	108.2°	110.6°
S2	C10	H5	109.8°	110.0°
S2	C10	H6	109.8°	109.6°
C11	C10	H5	109.8°	109.6°
C11	C10	H6	109.8°	109.2°
C10	C11	H15	109.5°	109.5°
C10	C11	H16	109.5°	109.4°
C10	C11	H17	109.5°	109.5°
H5	C10	H6	109.5°	107.9°
H7	C12	H8	109.5°	109.6°
H7	C12	H9	109.4°	109.6°
H8	C12	H9	109.5°	109.6°
H10	C13	H11	109.5°	109.6°
H10	C13	H12	109.5°	109.6°
H11	C13	H12	109.5°	109.6°
H15	C11	H16	109.4°	109.5°
H15	C11	H17	109.5°	109.5°
H16	C11	H17	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C8	C7	C6	H3	180.0°	180.0°
C7	C8	C9	H4	180.0°	179.5°
C8	C7	C6	O3	179.0°	179.9°
C8	C7	C6	C5	0.8°	0.0°
C7	C8	C9	C4	0.7°	1.5°
C7	C8	C9	H14	179.3°	179.3°
C6	C7	C8	C9	1.0°	0.4°
C7	C6	O3	C5	179.9°	180.0°
C7	C6	C5	C4	0.4°	0.7°
C7	C6	C5	H2	179.7°	180.0°
C6	C7	C8	H4	179.0°	179.9°
C7	C6	O3	H18	180.0°	180.0°
C8	C9	C4	H14	180.0°	177.8°
C8	C9	C4	C5	0.2°	2.1°
C8	C9	C4	C3	179.1°	179.5°
C9	C8	C7	H3	179.0°	179.6°
O3	C6	C5	C4	179.5°	179.3°
O3	C6	C5	H2	0.5°	0.1°
O3	C6	C7	H3	1.0°	0.1°
C6	C5	C4	C9	0.0°	1.7°
C6	C5	C4	H2	180.0°	179.3°
C6	C5	C4	C3	179.2°	179.3°
C5	C6	C7	H3	179.2°	180.0°
C5	C6	O3	H18	0.1°	0.1°
C9	C4	C5	C3	179.3°	177.6°
C9	C4	C3	O1	34.7°	165.0°
C9	C4	C3	C2	145.9°	17.8°
C9	C4	C5	H2	180.0°	179.0°
C4	C9	C8	H4	179.3°	179.0°
C5	C4	C3	O1	146.0°	17.6°
C5	C4	C3	C2	33.4°	159.6°
C5	C4	C9	H14	179.8°	179.9°
C4	C3	O1	C2	179.3°	177.3°
C4	C3	O1	PT1	179.8°	130.7°
C4	C3	C2	C1	179.5°	178.5°
C3	C4	C5	H2	0.7°	1.4°
C4	C3	C2	H13	0.5°	3.0°
C3	C4	C9	H14	0.9°	2.7°
O1	C3	C2	C1	0.2°	4.3°
C3	O1	PT1	S3	171.7°	103.9°
C3	O1	PT1	S1	0.6°	74.0°
O1	C3	C2	H13	179.8°	174.2°
C3	O1	PT1	CL1	128.9°	64.5°
C2	C3	O1	PT1	0.5°	52.0°
C3	C2	C1	H13	180.0°	178.6°
C3	C2	C1	S1	0.4°	0.0°
C3	C2	C1	S2	165.8°	179.8°
O1	PT1	S3	S1	171.1°	36.6°
O1	PT1	S3	CL1	60.5°	179.1°
O1	PT1	S1	CL1	112.2°	179.2°
O1	PT1	S1	C1	0.6°	56.2°
O1	PT1	S3	C12	12.1°	155.0°
O1	PT1	S3	O2	110.3°	29.9°
O1	PT1	S3	C13	131.3°	90.6°
C2	C1	S1	PT1	0.6°	34.9°
C2	C1	S1	S2	164.4°	179.7°
C2	C1	S2	C10	173.7°	177.9°
S3	PT1	S1	CL1	68.6°	142.5°
S3	PT1	S1	C1	179.9°	19.5°
PT1	S3	C12	O2	127.4°	127.6°
PT1	S3	C12	C13	119.7°	120.6°
PT1	S3	O2	C13	119.5°	122.8°
PT1	S3	C12	H7	180.0°	58.6°
PT1	S3	C12	H8	60.0°	178.6°
PT1	S3	C12	H9	60.0°	61.4°
PT1	S3	C13	H10	180.0°	54.8°
PT1	S3	C13	H11	60.0°	174.8°
PT1	S3	C13	H12	60.0°	65.1°
PT1	S1	C1	S2	165.0°	144.8°
S1	PT1	S3	C12	176.8°	168.4°
S1	PT1	S3	O2	60.9°	66.5°
S1	PT1	S3	C13	57.6°	54.0°
S1	C1	S2	C10	6.7°	1.8°
S1	C1	C2	H13	179.6°	178.6°
C1	S1	PT1	CL1	111.6°	123.0°
C1	S2	C10	C11	173.7°	82.7°
C1	S2	C10	H5	66.5°	38.4°
C1	S2	C10	H6	53.9°	156.8°
S2	C1	C2	H13	14.2°	1.7°
C12	S3	O2	C13	113.8°	106.4°
S3	C12	H7	H8	120.0°	119.9°
S3	C12	H7	H9	120.0°	119.8°
S3	C12	H8	H9	120.0°	119.8°
C12	S3	C13	H10	56.6°	180.0°
C12	S3	C13	H11	176.7°	60.0°
C12	S3	C13	H12	63.4°	60.1°
C12	S3	PT1	CL1	48.4°	25.9°
O2	S3	C12	H7	52.6°	173.8°
O2	S3	C12	H8	172.6°	53.7°
O2	S3	C12	H9	67.3°	66.3°
O2	S3	C13	H10	56.0°	68.5°
O2	S3	C13	H11	64.0°	51.5°
O2	S3	C13	H12	176.0°	171.6°
O2	S3	PT1	CL1	170.8°	151.0°
C13	S3	C12	H7	60.3°	62.0°
C13	S3	C12	H8	59.7°	58.0°
C13	S3	C12	H9	179.7°	178.0°
S3	C13	H10	H11	120.0°	119.9°
S3	C13	H10	H12	120.0°	119.7°
S3	C13	H11	H12	120.0°	119.9°
C13	S3	PT1	CL1	70.8°	88.5°
S2	C10	C11	H5	119.8°	121.3°
S2	C10	C11	H6	119.8°	120.7°
S2	C10	H5	H6	120.6°	119.5°
S2	C10	C11	H15	180.0°	180.0°
S2	C10	C11	H16	60.0°	60.0°
S2	C10	C11	H17	60.0°	60.0°
C11	C10	H5	H6	120.6°	118.8°
C10	C11	H15	H16	120.0°	120.0°
C10	C11	H15	H17	120.0°	120.0°
C10	C11	H16	H17	120.0°	120.0°
H3	C7	C8	H4	1.0°	0.1°
H4	C8	C9	H14	0.7°	1.2°
H5	C10	C11	H15	60.2°	58.7°
H5	C10	C11	H16	179.8°	178.6°
H5	C10	C11	H17	59.8°	61.4°
H6	C10	C11	H15	60.2°	59.3°
H6	C10	C11	H16	59.8°	60.7°
H6	C10	C11	H17	179.8°	179.3°
H7	C12	H8	H9	120.0°	120.3°
H10	C13	H11	H12	120.0°	120.3°
H15	C11	H16	H17	120.0°	120.0°

Release date:	2015-09-02
Definition date:	2015-04-01
Last modified:	2026-07-31
Release status:	REL
Processing site:	EBI
Derived from:	4Z3M