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Summary Geometry Related PDB entries

O8I

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C5	C1	sing	1.53Å	1.50Å
C1	C2	sing	1.51Å	1.51Å
O2	C2	doub	1.21Å	1.19Å
C2	C3	sing	1.47Å	1.50Å
C3	N1	doub	1.30Å	1.29Å
C3	C4	sing	1.48Å	1.51Å
N1	O4	sing	1.42Å	1.38Å
C4	O3	doub	1.21Å	1.18Å
C4	O1	sing	1.35Å	1.38Å
O1	C6	sing	1.45Å	1.41Å
C7	C6	sing	1.53Å	1.53Å
C5	H1	sing	1.09Å	1.10Å
C5	H2	sing	1.09Å	1.10Å
C5	H3	sing	1.09Å	1.10Å
C6	H4	sing	1.09Å	1.10Å
C6	H5	sing	1.09Å	1.10Å
C7	H6	sing	1.09Å	1.10Å
C7	H7	sing	1.09Å	1.10Å
C7	H8	sing	1.09Å	1.10Å
C1	H9	sing	1.09Å	1.10Å
C1	H10	sing	1.09Å	1.10Å
O4	H11	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C5	C1	C2	108.5°	109.4°
C1	C5	H1	109.5°	109.4°
C1	C5	H2	109.5°	109.5°
C1	C5	H3	109.5°	109.5°
C5	C1	H9	109.7°	109.5°
C5	C1	H10	109.7°	109.5°
C1	C2	O2	123.7°	120.0°
C1	C2	C3	118.4°	120.0°
C2	C1	H9	109.7°	109.5°
C2	C1	H10	109.7°	109.5°
O2	C2	C3	117.9°	120.0°
C2	C3	N1	120.6°	120.0°
C2	C3	C4	115.3°	120.0°
N1	C3	C4	124.1°	120.0°
C3	N1	O4	119.9°	120.0°
C3	C4	O3	121.6°	120.0°
C3	C4	O1	116.1°	120.0°
N1	O4	H11	109.5°	114.0°
O3	C4	O1	122.2°	120.0°
C4	O1	C6	115.1°	117.0°
O1	C6	C7	108.5°	109.4°
O1	C6	H4	109.7°	109.5°
O1	C6	H5	109.7°	109.5°
C7	C6	H4	109.7°	109.4°
C7	C6	H5	109.7°	109.4°
C6	C7	H6	109.5°	109.4°
C6	C7	H7	109.5°	109.5°
C6	C7	H8	109.4°	109.5°
H1	C5	H2	109.5°	109.5°
H1	C5	H3	109.5°	109.5°
H2	C5	H3	109.5°	109.5°
H4	C6	H5	109.5°	109.5°
H6	C7	H7	109.4°	109.5°
H6	C7	H8	109.5°	109.5°
H7	C7	H8	109.5°	109.5°
H9	C1	H10	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C5	C1	C2	H9	119.9°	120.0°
C5	C1	C2	H10	119.8°	120.0°
C5	C1	C2	O2	55.9°	0.0°
C5	C1	C2	C3	125.6°	180.0°
C1	C5	H1	H2	120.0°	120.0°
C1	C5	H1	H3	120.0°	120.0°
C1	C5	H2	H3	120.0°	120.0°
C5	C1	H9	H10	120.4°	120.0°
C1	C2	O2	C3	178.5°	180.0°
C1	C2	C3	N1	4.1°	0.0°
C1	C2	C3	C4	173.9°	180.0°
C2	C1	C5	H1	180.0°	180.0°
C2	C1	C5	H2	60.0°	60.0°
C2	C1	C5	H3	60.0°	60.0°
C2	C1	H9	H10	120.5°	120.0°
O2	C2	C3	N1	177.3°	180.0°
O2	C2	C3	C4	4.7°	0.0°
O2	C2	C1	H9	63.9°	120.0°
O2	C2	C1	H10	175.8°	120.0°
C2	C3	N1	C4	177.8°	180.0°
C2	C3	N1	O4	179.5°	180.0°
C2	C3	C4	O3	87.0°	0.0°
C2	C3	C4	O1	90.6°	180.0°
C3	C2	C1	H9	114.6°	60.0°
C3	C2	C1	H10	5.7°	60.0°
N1	C3	C4	O3	95.1°	180.0°
N1	C3	C4	O1	87.3°	0.0°
C3	N1	O4	H11	180.0°	180.0°
C4	C3	N1	O4	1.7°	0.0°
C3	C4	O3	O1	177.5°	180.0°
C3	C4	O1	C6	175.2°	180.0°
O3	C4	O1	C6	7.1°	0.0°
C4	O1	C6	C7	91.8°	180.0°
C4	O1	C6	H4	148.3°	60.0°
C4	O1	C6	H5	28.0°	60.0°
O1	C6	C7	H4	119.8°	120.0°
O1	C6	C7	H5	119.8°	120.0°
O1	C6	H4	H5	120.4°	120.1°
O1	C6	C7	H6	180.0°	180.0°
O1	C6	C7	H7	60.0°	60.0°
O1	C6	C7	H8	60.0°	60.0°
C7	C6	H4	H5	120.5°	119.9°
C6	C7	H6	H7	120.0°	120.0°
C6	C7	H6	H8	120.0°	120.0°
C6	C7	H7	H8	120.0°	120.0°
H1	C5	H2	H3	120.0°	120.0°
H1	C5	C1	H9	60.1°	60.0°
H1	C5	C1	H10	60.2°	60.0°
H2	C5	C1	H9	59.9°	60.0°
H2	C5	C1	H10	179.8°	180.0°
H3	C5	C1	H9	179.8°	180.0°
H3	C5	C1	H10	59.9°	60.0°
H4	C6	C7	H6	60.2°	60.0°
H4	C6	C7	H7	179.8°	60.0°
H4	C6	C7	H8	59.8°	180.0°
H5	C6	C7	H6	60.1°	60.0°
H5	C6	C7	H7	59.8°	180.0°
H5	C6	C7	H8	179.8°	60.0°
H6	C7	H7	H8	120.0°	120.0°

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PDB entries from 2026-01-14

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