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Summary Geometry Related PDB entries

EM2

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1P	P	doub	1.48Å	1.51Å
C6	N1	doub	1.32Å	1.35Å	Aromatic
C6	C5	sing	1.38Å	1.40Å	Aromatic
N1	C2	sing	1.33Å	1.36Å	Aromatic
P	O3P	sing	1.61Å	1.51Å
P	O4P	sing	1.61Å	1.61Å
P	O2P	sing	1.61Å	1.52Å
C5A	O4P	sing	1.43Å	1.43Å
C5A	C5	sing	1.51Å	1.51Å
C5	C4	doub	1.40Å	1.50Å	Aromatic
C2	C2A	sing	1.43Å	1.28Å
C2	C3	doub	1.40Å	1.48Å	Aromatic
C2A	C1	trip	1.17Å	1.28Å
C4	C3	sing	1.40Å	1.48Å	Aromatic
C4	C4A	sing	1.47Å	1.51Å
C3	O3	sing	1.36Å	1.36Å
O3	H1	sing	0.97Å	0.95Å
C4A	H2	sing	1.08Å	1.08Å
C6	H5	sing	1.08Å	1.08Å
C5A	H6	sing	1.09Å	1.10Å
C5A	H7	sing	1.09Å	1.10Å
O2P	H8	sing	0.97Å	0.95Å
O3P	H9	sing	0.97Å	0.95Å
C1	H10	sing	1.05Å	1.06Å
C4A	O1	doub	1.21Å	1.48Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1P	P	O3P	110.5°	109.5°
O1P	P	O4P	108.9°	109.5°
O1P	P	O2P	109.0°	109.5°
N1	C6	C5	122.4°	121.3°
C6	N1	C2	123.6°	122.1°
N1	C6	H5	118.8°	119.4°
C6	C5	C5A	118.9°	120.4°
C6	C5	C4	119.2°	119.3°
C5	C6	H5	118.8°	119.3°
N1	C2	C2A	121.4°	119.7°
N1	C2	C3	119.8°	120.6°
O3P	P	O4P	109.6°	109.5°
O3P	P	O2P	109.3°	109.5°
P	O3P	H9	109.5°	114.0°
O4P	P	O2P	109.6°	109.4°
P	O4P	C5A	119.6°	122.9°
P	O2P	H8	109.5°	114.0°
O4P	C5A	C5	109.8°	109.4°
O4P	C5A	H6	109.4°	109.5°
O4P	C5A	H7	109.4°	109.5°
C5A	C5	C4	122.0°	120.4°
C5	C5A	H6	109.4°	109.4°
C5	C5A	H7	109.4°	109.5°
C5	C4	C3	116.7°	118.1°
C5	C4	C4A	124.0°	120.9°
C2A	C2	C3	118.8°	119.7°
C2	C2A	C1	179.4°	180.0°
C2	C3	C4	118.3°	118.7°
C2	C3	O3	120.3°	120.7°
C2A	C1	H10	180.0°	180.0°
C3	C4	C4A	119.3°	121.0°
C4	C3	O3	121.3°	120.6°
C4	C4A	H2	121.7°	120.0°
C4	C4A	O1	116.6°	120.1°
C3	O3	H1	109.5°	114.0°
H2	C4A	O1	121.7°	120.0°
H6	C5A	H7	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1P	P	O3P	O4P	120.0°	120.0°
O1P	P	O3P	O2P	120.0°	120.1°
O1P	P	O4P	O2P	119.2°	120.0°
O1P	P	O4P	C5A	52.3°	55.0°
O1P	P	O2P	H8	0.0°	60.0°
O1P	P	O3P	H9	0.0°	180.0°
N1	C6	C5	H5	180.0°	179.9°
N1	C6	C5	C5A	179.3°	180.0°
N1	C6	C5	C4	0.2°	0.1°
C6	N1	C2	C2A	179.8°	180.0°
C6	N1	C2	C3	0.1°	0.0°
C5	C6	N1	C2	0.1°	0.1°
C6	C5	C5A	O4P	104.6°	0.1°
C6	C5	C5A	C4	179.5°	179.9°
C6	C5	C4	C3	0.2°	0.1°
C6	C5	C4	C4A	179.3°	180.0°
C6	C5	C5A	H6	135.3°	120.1°
C6	C5	C5A	H7	15.4°	120.0°
N1	C2	C2A	C3	179.9°	180.0°
N1	C2	C2A	C1	97.6°	1.7°
N1	C2	C3	C4	0.1°	0.0°
N1	C2	C3	O3	179.6°	180.0°
C2	N1	C6	H5	179.9°	180.0°
O3P	P	O4P	O2P	119.9°	119.9°
O3P	P	O4P	C5A	173.2°	65.0°
O3P	P	O2P	H8	120.8°	60.1°
P	O4P	C5A	C5	178.9°	180.0°
P	O4P	C5A	H6	58.9°	60.0°
P	O4P	C5A	H7	61.1°	60.0°
O4P	P	O2P	H8	119.1°	180.0°
O4P	P	O3P	H9	120.0°	60.0°
O2P	P	O4P	C5A	66.9°	175.0°
O2P	P	O3P	H9	120.0°	60.0°
O4P	C5A	C5	H6	120.1°	120.0°
O4P	C5A	C5	H7	120.0°	120.0°
O4P	C5A	C5	C4	74.9°	180.0°
O4P	C5A	H6	H7	119.8°	120.0°
C5A	C5	C4	C3	179.3°	180.0°
C5A	C5	C4	C4A	0.2°	0.1°
C5A	C5	C6	H5	0.7°	0.1°
C5	C5A	H6	H7	119.8°	120.0°
C5	C4	C3	C2	0.1°	0.0°
C5	C4	C3	C4A	179.1°	180.0°
C5	C4	C3	O3	179.8°	180.0°
C5	C4	C4A	H2	35.4°	180.0°
C4	C5	C6	H5	179.7°	180.0°
C4	C5	C5A	H6	45.2°	60.0°
C4	C5	C5A	H7	165.1°	59.9°
C5	C4	C4A	O1	144.6°	0.0°
C2A	C2	C3	C4	179.8°	180.0°
C2A	C2	C3	O3	0.5°	0.0°
C2	C2A	C1	H10	89.4°	4.3°
C3	C2	C2A	C1	82.3°	178.3°
C2	C3	C4	O3	179.7°	180.0°
C2	C3	C4	C4A	179.2°	180.0°
C2	C3	O3	H1	164.2°	90.0°
C4	C3	O3	H1	15.5°	90.0°
C3	C4	C4A	H2	143.7°	0.0°
C3	C4	C4A	O1	36.3°	180.0°
C4A	C4	C3	O3	1.1°	0.0°
C4	C4A	H2	O1	180.0°	180.0°

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PDB entries from 2024-07-17

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