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Summary Geometry Related PDB entries

A1C39

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O6	P1	doub	1.48Å	1.68Å
O2	C4	doub	1.21Å	1.28Å
O5	C2	doub	1.21Å	1.28Å
O4	C6	doub	1.21Å	1.28Å
O7	P1	sing	1.61Å	1.71Å
C2	C1	sing	1.51Å	1.51Å
C2	C3	sing	1.51Å	1.51Å
P1	O1	sing	1.61Å	1.71Å
P1	C1	sing	1.82Å	1.87Å
C4	C3	sing	1.51Å	1.50Å
C4	C5	sing	1.51Å	1.51Å
C6	C3	sing	1.51Å	1.51Å
C6	O3	sing	1.34Å	1.29Å
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
O1	H3	sing	0.97Å	0.95Å
C3	H4	sing	1.09Å	1.10Å
C5	H5	sing	1.09Å	1.10Å
C5	H6	sing	1.09Å	1.10Å
C5	H7	sing	1.09Å	1.10Å
O3	H8	sing	0.97Å	0.95Å
O7	H9	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O6	P1	O7	91.6°	109.5°
O6	P1	O1	108.5°	109.4°
O6	P1	C1	93.6°	109.5°
O2	C4	C3	116.9°	120.0°
O2	C4	C5	122.0°	120.0°
O5	C2	C1	120.8°	120.0°
O5	C2	C3	120.2°	120.0°
O4	C6	C3	116.5°	120.0°
O4	C6	O3	122.5°	120.0°
O7	P1	O1	111.4°	109.5°
O7	P1	C1	127.1°	109.5°
P1	O7	H9	109.5°	114.0°
C1	C2	C3	118.9°	120.0°
C2	C1	P1	111.5°	109.5°
C2	C1	H1	109.0°	109.5°
C2	C1	H2	109.0°	109.5°
C2	C3	C4	100.8°	109.5°
C2	C3	C6	111.8°	109.5°
C2	C3	H4	112.2°	109.5°
O1	P1	C1	116.4°	109.5°
P1	O1	H3	109.5°	114.0°
P1	C1	H1	109.0°	109.5°
P1	C1	H2	109.0°	109.5°
C3	C4	C5	121.1°	120.0°
C4	C3	C6	107.0°	109.5°
C4	C3	H4	112.3°	109.4°
C4	C5	H5	109.5°	109.4°
C4	C5	H6	109.5°	109.4°
C4	C5	H7	109.5°	109.5°
C3	C6	O3	121.0°	120.0°
C6	C3	H4	112.1°	109.5°
C6	O3	H8	109.5°	117.0°
H1	C1	H2	109.5°	109.5°
H5	C5	H6	109.5°	109.5°
H5	C5	H7	109.5°	109.5°
H6	C5	H7	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O6	P1	O7	O1	110.6°	120.0°
O6	P1	O7	C1	95.8°	120.1°
O6	P1	C1	C2	49.7°	55.0°
O6	P1	O1	C1	103.9°	120.0°
O6	P1	C1	H1	170.0°	65.0°
O6	P1	C1	H2	70.6°	175.0°
O6	P1	O1	H3	0.0°	180.0°
O6	P1	O7	H9	0.0°	60.0°
O2	C4	C3	C2	42.7°	95.0°
O2	C4	C3	C5	179.9°	180.0°
O2	C4	C3	C6	74.3°	25.0°
O2	C4	C3	H4	162.3°	145.1°
O2	C4	C5	H5	0.0°	0.0°
O2	C4	C5	H6	120.0°	120.0°
O2	C4	C5	H7	120.0°	119.9°
O5	C2	C1	C3	177.1°	180.0°
O5	C2	C1	P1	82.0°	0.0°
O5	C2	C3	C4	81.5°	90.0°
O5	C2	C3	C6	31.9°	30.0°
O5	C2	C1	H1	157.7°	120.0°
O5	C2	C1	H2	38.3°	120.0°
O5	C2	C3	H4	158.9°	150.0°
O4	C6	C3	C2	56.1°	0.0°
O4	C6	C3	C4	53.4°	120.0°
O4	C6	C3	O3	178.9°	180.0°
O4	C6	C3	H4	176.9°	120.0°
O4	C6	O3	H8	0.0°	0.0°
O7	P1	C1	C2	144.4°	175.0°
O7	P1	O1	C1	156.7°	120.0°
O7	P1	C1	H1	95.3°	55.0°
O7	P1	C1	H2	24.1°	65.0°
O7	P1	O1	H3	99.3°	60.0°
C2	C1	P1	O1	63.1°	65.0°
C2	C1	P1	H1	120.3°	120.0°
C2	C1	P1	H2	120.3°	120.0°
C1	C2	C3	C4	95.7°	90.0°
C1	C2	C3	C6	150.9°	150.0°
C2	C1	H1	H2	119.1°	120.0°
C1	C2	C3	H4	24.0°	30.0°
C3	C2	C1	P1	95.2°	180.0°
C2	C3	C4	C6	116.9°	120.0°
C2	C3	C4	H4	119.6°	120.0°
C2	C3	C4	C5	137.2°	85.0°
C2	C3	C6	H4	127.0°	120.0°
C2	C3	C6	O3	125.0°	180.0°
C3	C2	C1	H1	25.1°	60.0°
C3	C2	C1	H2	144.5°	60.0°
O1	P1	C1	H1	57.2°	175.0°
O1	P1	C1	H2	176.6°	55.0°
O1	P1	O7	H9	110.6°	60.0°
P1	C1	H1	H2	119.1°	120.0°
C1	P1	O1	H3	104.0°	60.0°
C1	P1	O7	H9	95.8°	180.0°
C4	C3	C6	H4	123.5°	120.0°
C4	C3	C6	O3	125.5°	60.0°
C3	C4	C5	H5	179.9°	180.0°
C3	C4	C5	H6	60.1°	60.0°
C3	C4	C5	H7	59.9°	60.0°
C5	C4	C3	C6	105.8°	155.0°
C5	C4	C3	H4	17.6°	35.0°
C4	C5	H5	H6	120.0°	120.0°
C4	C5	H5	H7	120.0°	119.9°
C4	C5	H6	H7	120.0°	120.0°
C3	C6	O3	H8	178.9°	180.0°
O3	C6	C3	H4	2.0°	60.0°
H5	C5	H6	H7	120.0°	120.0°

253795

PDB entries from 2026-05-20

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