Summary Geometry PCM/PTM Related PDB entries

VVU

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C2	C1	sing	1.50Å	1.51Å
C1	O1	doub	1.25Å	1.25Å
C1	O2	sing	1.25Å	1.24Å
C4	C3	sing	1.50Å	1.55Å
O1	RH1	sing	2.33Å	2.02Å
O2	RH2	sing	2.31Å	2.00Å
C3	O7	doub	1.25Å	1.23Å
C3	O8	sing	1.25Å	1.22Å
O7	RH1	sing	2.36Å	2.05Å
O8	RH2	sing	2.31Å	2.07Å
RH1	RH2	sing	2.34Å	2.38Å
RH1	O0	sing	2.32Å	2.06Å
RH1	O3	sing	2.30Å	2.07Å
RH2	O9	sing	2.30Å	2.08Å
RH2	O4	sing	2.31Å	2.03Å
O0	C5	doub	1.26Å	1.23Å
C5	O9	sing	1.25Å	1.22Å
C5	C6	sing	1.50Å	1.54Å
O3	C7	doub	1.25Å	1.24Å
O4	C7	sing	1.25Å	1.25Å
C7	C8	sing	1.50Å	1.54Å
C2	H2	sing	0.97Å	1.10Å
C2	H3	sing	0.97Å	1.10Å
C2	H4	sing	0.97Å	1.10Å
C4	H6	sing	0.97Å	1.10Å
C4	H7	sing	0.97Å	1.10Å
C4	H8	sing	0.97Å	1.10Å
C6	H10	sing	0.97Å	1.10Å
C6	H11	sing	0.97Å	1.10Å
C6	H12	sing	0.97Å	1.10Å
C8	H14	sing	0.97Å	1.10Å
C8	H15	sing	0.97Å	1.10Å
C8	H16	sing	0.97Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	C1	O1	119.9°	117.9°
C2	C1	O2	120.7°	117.2°
C1	C2	H2	109.5°	109.7°
C1	C2	H3	109.5°	109.6°
C1	C2	H4	109.5°	109.6°
O1	C1	O2	119.4°	124.9°
C1	O1	RH1	122.9°	112.8°
C1	O2	RH2	124.1°	112.4°
C4	C3	O7	115.5°	118.1°
C4	C3	O8	116.6°	117.4°
C3	C4	H6	109.5°	109.8°
C3	C4	H7	109.5°	109.7°
C3	C4	H8	109.5°	109.6°
O1	RH1	O7	87.2°	91.3°
O1	RH1	RH2	86.6°	85.9°
O1	RH1	O0	88.8°	88.7°
O1	RH1	O3	175.7°	176.0°
O2	RH2	O8	89.0°	91.0°
O2	RH2	RH1	86.8°	90.3°
O2	RH2	O9	87.9°	88.6°
O2	RH2	O4	173.0°	176.1°
O7	C3	O8	127.5°	124.5°
C3	O7	RH1	119.6°	112.0°
C3	O8	RH2	117.7°	110.9°
O7	RH1	RH2	86.8°	87.9°
O7	RH1	O0	174.8°	176.6°
O7	RH1	O3	92.7°	89.4°
O8	RH2	RH1	88.1°	88.2°
O8	RH2	O9	175.3°	175.7°
O8	RH2	O4	92.3°	89.0°
RH2	RH1	O0	89.5°	88.7°
RH2	RH1	O3	89.1°	90.2°
RH1	RH2	O9	88.2°	87.5°
RH1	RH2	O4	86.3°	85.8°
O0	RH1	O3	91.0°	90.3°
RH1	O0	C5	110.3°	114.9°
RH1	O3	C7	117.0°	109.1°
O9	RH2	O4	90.3°	91.1°
RH2	O9	C5	110.6°	114.6°
RH2	O4	C7	121.6°	109.1°
O0	C5	O9	139.8°	125.5°
O0	C5	C6	114.1°	117.7°
O9	C5	C6	105.9°	116.8°
C5	C6	H10	109.5°	109.8°
C5	C6	H11	109.4°	109.6°
C5	C6	H12	109.5°	109.6°
O3	C7	O4	126.0°	123.9°
O3	C7	C8	119.1°	118.3°
O4	C7	C8	114.9°	117.8°
C7	C8	H14	109.5°	109.8°
C7	C8	H15	109.5°	109.7°
C7	C8	H16	109.4°	109.6°
H2	C2	H3	109.4°	109.2°
H2	C2	H4	109.5°	109.3°
H3	C2	H4	109.5°	109.3°
H6	C4	H7	109.4°	109.3°
H6	C4	H8	109.5°	109.2°
H7	C4	H8	109.4°	109.3°
H10	C6	H11	109.5°	109.3°
H10	C6	H12	109.5°	109.3°
H11	C6	H12	109.5°	109.3°
H14	C8	H15	109.5°	109.2°
H14	C8	H16	109.4°	109.2°
H15	C8	H16	109.5°	109.3°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	C1	O1	O2	179.7°	179.6°
C2	C1	O1	RH1	176.0°	134.0°
C2	C1	O2	RH2	178.4°	146.5°
C1	C2	H2	H3	120.0°	120.2°
C1	C2	H2	H4	120.0°	120.3°
C1	C2	H3	H4	120.0°	120.2°
O1	C1	O2	RH2	2.0°	33.9°
C1	O1	RH1	O7	90.8°	57.4°
C1	O1	RH1	RH2	3.8°	30.4°
C1	O1	RH1	O0	85.8°	119.2°
C1	O1	RH1	O3	1.9°	42.9°
O1	C1	C2	H2	0.0°	0.5°
O1	C1	C2	H3	120.0°	120.4°
O1	C1	C2	H4	120.0°	119.6°
O2	C1	O1	RH1	4.3°	46.4°
C1	O2	RH2	O8	87.4°	84.1°
C1	O2	RH2	RH1	0.7°	4.1°
C1	O2	RH2	O9	89.0°	91.7°
C1	O2	RH2	O4	13.9°	6.7°
O2	C1	C2	H2	179.7°	179.2°
O2	C1	C2	H3	59.7°	59.2°
O2	C1	C2	H4	60.3°	60.7°
C4	C3	O7	O8	172.1°	179.9°
C4	C3	O7	RH1	179.0°	141.1°
C4	C3	O8	RH2	178.8°	129.6°
C3	C4	H6	H7	120.0°	120.3°
C3	C4	H6	H8	120.0°	120.2°
C3	C4	H7	H8	120.0°	120.2°
O1	RH1	RH2	O2	1.8°	10.4°
O1	RH1	O7	C3	83.6°	79.1°
O1	RH1	O7	RH2	86.7°	85.8°
O1	RH1	O7	O0	40.4°	91.1°
O1	RH1	O7	O3	175.7°	176.1°
O1	RH1	RH2	O8	87.4°	101.4°
O1	RH1	RH2	O0	88.8°	88.8°
O1	RH1	RH2	O3	179.9°	179.1°
O1	RH1	O0	O3	175.7°	176.2°
O1	RH1	RH2	O9	89.8°	78.2°
O1	RH1	RH2	O4	179.8°	169.5°
O1	RH1	O0	C5	82.2°	85.7°
O1	RH1	O3	C7	2.3°	22.3°
O2	RH2	O8	C3	83.9°	58.6°
O2	RH2	RH1	O7	89.2°	81.1°
O2	RH2	O8	RH1	86.9°	90.2°
O2	RH2	O8	O9	49.2°	84.6°
O2	RH2	O8	O4	173.1°	176.1°
O2	RH2	RH1	O9	88.0°	88.5°
O2	RH2	RH1	O4	178.4°	179.8°
O2	RH2	RH1	O0	87.0°	99.2°
O2	RH2	RH1	O3	178.1°	170.5°
O2	RH2	O9	O4	173.2°	176.1°
O2	RH2	O9	C5	80.4°	117.2°
O2	RH2	O4	C7	12.9°	36.2°
O7	C3	O8	RH2	6.8°	50.5°
C3	O7	RH1	RH2	3.1°	6.7°
C3	O7	RH1	O0	43.2°	12.0°
C3	O7	RH1	O3	92.1°	97.0°
O7	C3	C4	H6	0.0°	0.9°
O7	C3	C4	H7	120.0°	120.9°
O7	C3	C4	H8	120.0°	119.0°
O8	C3	O7	RH1	7.0°	39.0°
C3	O8	RH2	RH1	3.0°	31.6°
C3	O8	RH2	O9	34.7°	26.0°
C3	O8	RH2	O4	89.2°	117.4°
O8	C3	C4	H6	173.0°	179.2°
O8	C3	C4	H7	53.0°	59.1°
O8	C3	C4	H8	67.0°	60.9°
O7	RH1	RH2	O8	0.0°	9.9°
O7	RH1	RH2	O0	176.2°	179.7°
O7	RH1	RH2	O3	92.7°	89.4°
O7	RH1	O0	O3	135.3°	85.0°
O7	RH1	RH2	O9	177.2°	169.7°
O7	RH1	RH2	O4	92.4°	99.0°
O7	RH1	O0	C5	41.8°	5.5°
O7	RH1	O3	C7	86.3°	78.1°
O8	RH2	RH1	O9	177.1°	179.6°
O8	RH2	RH1	O4	92.5°	89.1°
O8	RH2	RH1	O0	176.2°	169.8°
O8	RH2	RH1	O3	92.8°	79.5°
O8	RH2	O9	O4	124.0°	91.4°
O8	RH2	O9	C5	31.2°	32.5°
O8	RH2	O4	C7	88.2°	54.6°
RH2	RH1	O0	O3	89.1°	90.2°
RH1	RH2	O9	O4	86.3°	85.7°
RH2	RH1	O0	C5	4.4°	0.3°
RH1	RH2	O9	C5	6.5°	26.8°
RH2	RH1	O3	C7	0.5°	9.8°
RH1	RH2	O4	C7	0.3°	33.7°
O0	RH1	RH2	O9	1.0°	10.6°
O0	RH1	RH2	O4	91.4°	80.7°
RH1	O0	C5	O9	15.5°	23.8°
RH1	O0	C5	C6	170.3°	156.9°
O0	RH1	O3	C7	90.0°	98.5°
O3	RH1	RH2	O9	90.1°	101.0°
O3	RH1	RH2	O4	0.3°	9.7°
O3	RH1	O0	C5	93.5°	90.5°
RH1	O3	C7	O4	0.4°	46.5°
RH1	O3	C7	C8	179.8°	133.5°
RH2	O9	C5	O0	16.5°	36.4°
RH2	O9	C5	C6	168.9°	144.4°
O9	RH2	O4	C7	87.9°	121.1°
O4	RH2	O9	C5	92.8°	58.9°
RH2	O4	C7	O3	0.0°	58.2°
RH2	O4	C7	C8	179.8°	121.8°
O0	C5	O9	C6	174.6°	179.3°
O0	C5	C6	H10	0.0°	1.5°
O0	C5	C6	H11	120.0°	121.6°
O0	C5	C6	H12	120.0°	118.4°
O9	C5	C6	H10	176.2°	179.2°
O9	C5	C6	H11	63.9°	59.1°
O9	C5	C6	H12	56.1°	60.9°
C5	C6	H10	H11	120.0°	120.3°
C5	C6	H10	H12	120.0°	120.2°
C5	C6	H11	H12	120.0°	120.1°
O3	C7	O4	C8	179.8°	180.0°
O3	C7	C8	H14	0.0°	1.1°
O3	C7	C8	H15	120.0°	121.1°
O3	C7	C8	H16	120.0°	118.9°
O4	C7	C8	H14	179.9°	178.8°
O4	C7	C8	H15	59.8°	58.8°
O4	C7	C8	H16	60.2°	61.2°
C7	C8	H14	H15	120.0°	120.3°
C7	C8	H14	H16	120.0°	120.3°
C7	C8	H15	H16	120.0°	120.2°
H2	C2	H3	H4	120.0°	119.6°
H6	C4	H7	H8	120.0°	119.5°
H10	C6	H11	H12	120.0°	119.5°
H14	C8	H15	H16	120.0°	119.5°

Release date:	2023-06-14
Definition date:	2023-04-12
Last modified:	2026-09-16
Release status:	REL
Processing site:	PDBE
Derived from:	8OQE