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Summary Geometry Related PDB entries

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Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O2	C7	doub	1.21Å	1.25Å
N1	C6	doub	1.29Å	1.25Å
N1	C2	sing	1.36Å	1.33Å
C6	C5	sing	1.50Å	1.50Å
C7	C2	sing	1.48Å	1.48Å
C7	O1	sing	1.35Å	1.24Å
C2	C3	doub	1.36Å	1.34Å
C5	O9	sing	1.43Å	1.44Å
C5	C4	sing	1.53Å	1.52Å
C3	C4	sing	1.51Å	1.51Å
C3	C8	sing	1.47Å	1.45Å
O3	C8	doub	1.22Å	1.25Å
C8	O4	sing	1.35Å	1.25Å
O1	H1	sing	0.97Å	0.95Å
C6	H2	sing	1.08Å	1.08Å
C5	H4	sing	1.09Å	1.10Å
O9	H5	sing	0.97Å	0.95Å
C4	H6	sing	1.09Å	1.10Å
C4	H7	sing	1.09Å	1.10Å
O4	H9	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O2	C7	C2	122.6°	120.0°
O2	C7	O1	116.9°	120.0°
C6	N1	C2	126.2°	121.8°
N1	C6	C5	122.0°	121.2°
N1	C6	H2	119.0°	119.4°
N1	C2	C7	115.4°	119.6°
N1	C2	C3	119.1°	120.7°
C6	C5	O9	110.1°	109.5°
C6	C5	C4	111.4°	109.5°
C5	C6	H2	119.0°	119.5°
C6	C5	H4	108.4°	109.5°
C2	C7	O1	120.4°	120.0°
C7	C2	C3	125.4°	119.6°
C7	O1	H1	109.5°	117.0°
C2	C3	C4	122.4°	119.6°
C2	C3	C8	121.4°	120.2°
O9	C5	C4	109.4°	109.4°
O9	C5	H4	109.3°	109.4°
C5	O9	H5	109.5°	114.0°
C5	C4	C3	113.0°	109.0°
C4	C5	H4	108.2°	109.5°
C5	C4	H6	108.6°	109.6°
C5	C4	H7	108.6°	109.5°
C4	C3	C8	116.2°	120.2°
C3	C4	H6	108.6°	109.7°
C3	C4	H7	108.6°	109.5°
C3	C8	O3	118.2°	120.0°
C3	C8	O4	119.1°	120.0°
O3	C8	O4	122.7°	119.9°
C8	O4	H9	109.5°	117.0°
H6	C4	H7	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O2	C7	C2	N1	35.4°	87.7°
O2	C7	C2	O1	175.9°	179.9°
O2	C7	C2	C3	148.1°	92.0°
O2	C7	O1	H1	0.0°	0.1°
N1	C6	C5	H2	180.0°	180.0°
C6	N1	C2	C7	172.0°	161.1°
C6	N1	C2	C3	4.7°	19.2°
N1	C6	C5	O9	148.2°	86.2°
N1	C6	C5	C4	26.7°	33.8°
N1	C6	C5	H4	92.2°	153.8°
C2	N1	C6	C5	16.7°	0.1°
N1	C2	C7	C3	176.5°	179.7°
N1	C2	C7	O1	140.5°	92.2°
N1	C2	C3	C4	5.4°	0.8°
N1	C2	C3	C8	174.4°	179.5°
C2	N1	C6	H2	163.3°	179.9°
C6	C5	O9	C4	122.7°	120.0°
C6	C5	O9	H4	119.0°	120.0°
C6	C5	C4	H4	119.1°	120.1°
C6	C5	C4	C3	25.0°	46.2°
C6	C5	O9	H5	180.0°	60.0°
C6	C5	C4	H6	95.5°	166.3°
C6	C5	C4	H7	145.5°	73.6°
C7	C2	C3	C4	170.9°	179.5°
C7	C2	C3	C8	9.3°	0.2°
C2	C7	O1	H1	176.1°	180.0°
O1	C7	C2	C3	36.0°	88.1°
C2	C3	C4	C5	17.0°	32.2°
C2	C3	C4	C8	179.8°	179.7°
C2	C3	C8	O3	52.9°	5.3°
C2	C3	C8	O4	127.6°	174.7°
C2	C3	C4	H6	103.5°	152.3°
C2	C3	C4	H7	137.5°	87.5°
O9	C5	C4	H4	119.0°	119.9°
O9	C5	C4	C3	147.0°	73.8°
O9	C5	C6	H2	31.7°	93.8°
O9	C5	C4	H6	26.5°	46.3°
O9	C5	C4	H7	92.5°	166.5°
C5	C4	C3	H6	120.5°	120.0°
C5	C4	C3	H7	120.5°	119.8°
C5	C4	C3	C8	162.8°	147.5°
C4	C5	C6	H2	153.3°	146.2°
C4	C5	O9	H5	57.3°	180.0°
C5	C4	H6	H7	118.4°	120.2°
C4	C3	C8	O3	127.0°	174.4°
C4	C3	C8	O4	52.5°	5.6°
C3	C4	C5	H4	94.1°	166.2°
C3	C4	H6	H7	118.4°	120.2°
C3	C8	O3	O4	179.5°	180.0°
C8	C3	C4	H6	76.7°	27.4°
C8	C3	C4	H7	42.3°	92.8°
C3	C8	O4	H9	179.5°	180.0°
O3	C8	O4	H9	0.0°	0.0°
H2	C6	C5	H4	87.8°	26.2°
H4	C5	O9	H5	61.0°	60.0°
H4	C5	C4	H6	145.4°	73.7°
H4	C5	C4	H7	26.5°	46.5°

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PDB entries from 2024-07-10

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