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Summary Geometry Related PDB entries

Q5H

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C	C1	sing	1.51Å	1.50Å
O	C1	doub	1.21Å	1.24Å
C1	N	sing	1.35Å	1.40Å
N	C2	sing	1.40Å	1.43Å
C2	C3	sing	1.39Å	1.39Å	Aromatic
C3	C4	doub	1.38Å	1.39Å	Aromatic
C4	C5	sing	1.38Å	1.39Å	Aromatic
C5	C6	doub	1.40Å	1.40Å	Aromatic
C6	C7	sing	1.48Å	1.47Å
C7	O1	doub	1.22Å	1.24Å
O2	C7	sing	1.35Å	1.35Å
C8	C6	sing	1.40Å	1.37Å	Aromatic
C2	C8	doub	1.39Å	1.44Å	Aromatic
C9	C8	sing	1.51Å	1.49Å
C4	H5	sing	1.08Å	1.08Å
C5	H6	sing	1.08Å	1.08Å
N	H3	sing	0.97Å	1.00Å
C	H2	sing	1.09Å	1.10Å
C	H	sing	1.09Å	1.10Å
C	H1	sing	1.09Å	1.10Å
C3	H4	sing	1.08Å	1.08Å
C9	H10	sing	1.09Å	1.10Å
C9	H9	sing	1.09Å	1.10Å
C9	H8	sing	1.09Å	1.10Å
O2	H7	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C	C1	O	121.9°	120.0°
C	C1	N	115.8°	120.0°
C1	C	H2	109.5°	109.5°
C1	C	H	109.5°	109.4°
C1	C	H1	109.5°	109.5°
O	C1	N	122.2°	120.0°
C1	N	C2	123.2°	120.0°
C1	N	H3	118.4°	120.0°
N	C2	C3	117.5°	120.0°
N	C2	C8	122.7°	120.0°
C2	N	H3	118.4°	120.0°
C2	C3	C4	120.1°	120.3°
C3	C2	C8	119.8°	120.0°
C2	C3	H4	120.0°	119.9°
C3	C4	C5	121.0°	120.2°
C3	C4	H5	119.5°	119.9°
C4	C3	H4	120.0°	119.8°
C4	C5	C6	118.8°	120.0°
C5	C4	H5	119.5°	119.9°
C4	C5	H6	120.6°	120.0°
C5	C6	C7	117.6°	120.1°
C5	C6	C8	122.3°	119.8°
C6	C5	H6	120.6°	120.0°
C6	C7	O1	127.6°	120.0°
C6	C7	O2	111.1°	120.1°
C7	C6	C8	120.0°	120.1°
O1	C7	O2	121.3°	119.9°
C7	O2	H7	109.5°	117.0°
C6	C8	C2	118.1°	119.8°
C6	C8	C9	118.9°	120.1°
C2	C8	C9	123.0°	120.1°
C8	C9	H10	109.5°	109.5°
C8	C9	H9	109.5°	109.5°
C8	C9	H8	109.5°	109.4°
H2	C	H	109.5°	109.5°
H2	C	H1	109.4°	109.5°
H	C	H1	109.5°	109.5°
H10	C9	H9	109.5°	109.5°
H10	C9	H8	109.4°	109.5°
H9	C9	H8	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C	C1	O	N	178.3°	180.0°
C	C1	N	C2	179.7°	175.3°
C	C1	N	H3	0.3°	4.7°
C1	C	H2	H	120.0°	120.0°
C1	C	H2	H1	120.0°	120.0°
C1	C	H	H1	120.0°	120.0°
O	C1	N	C2	2.0°	4.7°
O	C1	N	H3	178.0°	175.3°
O	C1	C	H2	0.0°	0.0°
O	C1	C	H	120.0°	120.0°
O	C1	C	H1	120.0°	120.0°
C1	N	C2	H3	180.0°	180.0°
C1	N	C2	C3	120.6°	33.2°
C1	N	C2	C8	60.2°	147.4°
N	C1	C	H2	178.4°	180.0°
N	C1	C	H	58.4°	60.0°
N	C1	C	H1	61.6°	59.9°
N	C2	C3	C8	179.2°	179.4°
N	C2	C3	C4	179.6°	180.0°
N	C2	C8	C6	179.5°	179.7°
N	C2	C8	C9	3.6°	0.3°
N	C2	C3	H4	0.4°	0.0°
C2	C3	C4	H4	180.0°	180.0°
C2	C3	C4	C5	0.3°	0.5°
C3	C2	C8	C6	1.3°	0.3°
C3	C2	C8	C9	175.6°	179.8°
C2	C3	C4	H5	179.7°	179.8°
C3	C2	N	H3	59.4°	146.9°
C3	C4	C5	H5	180.0°	179.7°
C3	C4	C5	C6	1.6°	0.3°
C4	C3	C2	C8	1.1°	0.6°
C3	C4	C5	H6	178.5°	179.8°
C4	C5	C6	H6	180.0°	179.9°
C4	C5	C6	C7	175.4°	180.0°
C4	C5	C6	C8	1.4°	0.0°
C5	C4	C3	H4	179.7°	179.4°
C5	C6	C7	C8	176.9°	179.9°
C5	C6	C7	O1	114.2°	173.5°
C5	C6	C7	O2	65.7°	6.5°
C5	C6	C8	C2	0.0°	0.1°
C5	C6	C8	C9	177.1°	180.0°
C6	C5	C4	H5	178.4°	179.9°
C6	C7	O1	O2	179.9°	180.0°
C7	C6	C8	C2	176.7°	180.0°
C7	C6	C8	C9	0.3°	0.1°
C7	C6	C5	H6	4.6°	0.1°
C6	C7	O2	H7	179.9°	180.0°
O1	C7	C6	C8	62.7°	6.4°
O1	C7	O2	H7	0.0°	0.0°
O2	C7	C6	C8	117.4°	173.6°
C6	C8	C2	C9	176.9°	179.9°
C8	C6	C5	H6	178.6°	180.0°
C6	C8	C9	H10	88.6°	83.1°
C6	C8	C9	H9	151.4°	156.8°
C6	C8	C9	H8	31.4°	36.9°
C8	C2	N	H3	119.8°	32.6°
C8	C2	C3	H4	178.9°	179.4°
C2	C8	C9	H10	88.3°	97.0°
C2	C8	C9	H9	31.7°	23.1°
C2	C8	C9	H8	151.7°	143.1°
C8	C9	H10	H9	120.0°	120.1°
C8	C9	H10	H8	120.0°	120.0°
C8	C9	H9	H8	120.0°	120.0°
H5	C4	C5	H6	1.5°	0.1°
H5	C4	C3	H4	0.3°	0.2°
H2	C	H	H1	120.0°	120.0°
H10	C9	H9	H8	119.9°	120.0°

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PDB entries from 2024-07-10

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