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Summary Geometry Related PDB entries

3EE

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C2	doub	1.21Å	1.23Å
C2	C1	sing	1.47Å	1.49Å
C2	C3	sing	1.51Å	1.52Å
C1	C5	doub	1.40Å	1.40Å	Aromatic
C1	C4	sing	1.41Å	1.49Å	Aromatic
C5	C7	sing	1.38Å	1.37Å	Aromatic
C7	C8	doub	1.39Å	1.37Å	Aromatic
C4	N	sing	1.39Å	1.38Å
C4	C6	doub	1.39Å	1.39Å	Aromatic
C3	C9	sing	1.51Å	1.52Å
C8	C6	sing	1.38Å	1.39Å	Aromatic
O4	C10	doub	1.21Å	1.18Å
C9	C10	sing	1.49Å	1.45Å
C9	O2	doub	1.21Å	1.20Å
C10	O3	sing	1.35Å	1.32Å
C3	H1	sing	1.09Å	1.10Å
C3	H2	sing	1.09Å	1.10Å
O3	H3	sing	0.97Å	0.95Å
N	H4	sing	0.97Å	1.00Å
N	H5	sing	0.97Å	1.00Å
C6	H6	sing	1.08Å	1.08Å
C8	H7	sing	1.08Å	1.08Å
C7	H8	sing	1.08Å	1.08Å
C5	H9	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C2	C1	121.9°	120.0°
O1	C2	C3	122.9°	120.0°
C1	C2	C3	115.2°	120.0°
C2	C1	C5	119.6°	120.2°
C2	C1	C4	119.6°	120.2°
C2	C3	C9	118.6°	109.5°
C2	C3	H1	107.1°	109.4°
C2	C3	H2	107.1°	109.5°
C5	C1	C4	120.8°	119.6°
C1	C5	C7	122.3°	119.9°
C1	C5	H9	118.9°	120.1°
C1	C4	N	125.1°	120.2°
C1	C4	C6	114.1°	119.6°
C5	C7	C8	116.9°	120.4°
C5	C7	H8	121.5°	119.8°
C7	C5	H9	118.9°	120.0°
C7	C8	C6	123.9°	120.5°
C7	C8	H7	118.1°	119.7°
C8	C7	H8	121.5°	119.9°
N	C4	C6	120.8°	120.2°
C4	N	H4	109.5°	120.0°
C4	N	H5	109.5°	120.0°
C4	C6	C8	122.1°	120.1°
C4	C6	H6	119.0°	119.9°
C3	C9	C10	121.0°	120.0°
C3	C9	O2	120.6°	120.0°
C9	C3	H1	107.2°	109.5°
C9	C3	H2	107.1°	109.5°
C8	C6	H6	119.0°	120.0°
C6	C8	H7	118.0°	119.7°
O4	C10	C9	118.2°	120.0°
O4	C10	O3	117.5°	120.0°
C10	C9	O2	118.5°	120.0°
C9	C10	O3	124.3°	120.0°
C10	O3	H3	109.5°	117.0°
H1	C3	H2	109.5°	109.5°
H4	N	H5	109.5°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C2	C1	C3	179.5°	179.7°
O1	C2	C1	C5	100.0°	174.2°
O1	C2	C1	C4	82.3°	5.4°
O1	C2	C3	C9	171.1°	0.0°
O1	C2	C3	H1	67.5°	120.0°
O1	C2	C3	H2	49.8°	120.0°
C2	C1	C5	C4	177.6°	179.6°
C2	C1	C5	C7	179.6°	179.7°
C2	C1	C4	N	2.1°	0.1°
C2	C1	C4	C6	179.1°	180.0°
C1	C2	C3	C9	8.4°	179.7°
C1	C2	C3	H1	113.0°	59.7°
C1	C2	C3	H2	129.7°	60.3°
C2	C1	C5	H9	0.4°	0.1°
C3	C2	C1	C5	80.5°	6.1°
C3	C2	C1	C4	97.2°	174.3°
C2	C3	C9	H1	121.3°	120.0°
C2	C3	C9	H2	121.3°	120.0°
C2	C3	C9	C10	78.2°	180.0°
C2	C3	C9	O2	103.6°	0.0°
C2	C3	H1	H2	115.8°	120.0°
C1	C5	C7	H9	180.0°	179.7°
C1	C5	C7	C8	1.2°	0.6°
C5	C1	C4	N	179.8°	179.7°
C5	C1	C4	C6	1.5°	0.3°
C1	C5	C7	H8	178.8°	179.7°
C4	C1	C5	C7	2.0°	0.6°
C1	C4	N	C6	178.7°	179.9°
C1	C4	C6	C8	0.4°	0.1°
C1	C4	N	H4	180.0°	5.6°
C1	C4	N	H5	60.0°	174.4°
C1	C4	C6	H6	179.6°	179.9°
C4	C1	C5	H9	178.1°	179.7°
C5	C7	C8	H8	180.0°	179.7°
C5	C7	C8	C6	0.1°	0.4°
C5	C7	C8	H7	179.9°	179.7°
C7	C8	C6	C4	0.3°	0.1°
C7	C8	C6	H7	180.0°	179.9°
C7	C8	C6	H6	179.7°	179.9°
C8	C7	C5	H9	178.8°	179.7°
N	C4	C6	C8	179.2°	180.0°
C4	N	H4	H5	120.0°	180.0°
N	C4	C6	H6	0.8°	0.0°
C4	C6	C8	H6	180.0°	180.0°
C6	C4	N	H4	1.3°	174.5°
C6	C4	N	H5	121.3°	5.5°
C4	C6	C8	H7	179.7°	180.0°
C3	C9	C10	O4	5.3°	0.0°
C3	C9	C10	O2	178.2°	180.0°
C3	C9	C10	O3	173.5°	180.0°
C9	C3	H1	H2	115.8°	120.0°
C6	C8	C7	H8	179.9°	180.0°
O4	C10	C9	O3	178.8°	180.0°
O4	C10	C9	O2	176.5°	180.0°
O4	C10	O3	H3	0.0°	0.0°
C10	C9	C3	H1	43.1°	60.0°
C10	C9	C3	H2	160.5°	60.0°
C9	C10	O3	H3	178.8°	180.0°
O2	C9	C10	O3	4.7°	0.0°
O2	C9	C3	H1	135.1°	120.0°
O2	C9	C3	H2	17.7°	120.0°
H6	C6	C8	H7	0.3°	0.0°
H7	C8	C7	H8	0.1°	0.0°
H8	C7	C5	H9	1.2°	0.0°

219140

PDB entries from 2024-05-01

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