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Summary Geometry Related PDB entries

J5V

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C	C1	sing	1.51Å	1.53Å
O	C1	doub	1.21Å	1.24Å
C1	N	sing	1.35Å	1.38Å
N	C2	sing	1.47Å	1.46Å
C2	C3	sing	1.47Å	1.52Å
C3	C4	trip	1.17Å	1.22Å
C4	C5	sing	1.43Å	1.36Å
C6	C5	doub	1.40Å	1.43Å	Aromatic
C6	C7	sing	1.38Å	1.40Å	Aromatic
C5	C10	sing	1.40Å	1.42Å	Aromatic
C7	C8	doub	1.38Å	1.39Å	Aromatic
C10	C9	doub	1.38Å	1.40Å	Aromatic
C8	C9	sing	1.38Å	1.41Å	Aromatic
C6	H1	sing	1.08Å	1.08Å
C7	H2	sing	1.08Å	1.08Å
C8	H3	sing	1.08Å	1.08Å
C10	H4	sing	1.08Å	1.08Å
C	H5	sing	1.09Å	1.10Å
C	H6	sing	1.09Å	1.10Å
C	H7	sing	1.09Å	1.10Å
N	H8	sing	0.97Å	1.00Å
C2	H9	sing	1.09Å	1.10Å
C2	H10	sing	1.09Å	1.10Å
C9	H11	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C	C1	O	119.3°	120.0°
C	C1	N	114.6°	120.0°
C1	C	H5	109.5°	109.5°
C1	C	H6	109.5°	109.5°
C1	C	H7	109.5°	109.4°
O	C1	N	125.9°	120.0°
C1	N	C2	125.3°	120.0°
C1	N	H8	117.3°	120.0°
N	C2	C3	114.6°	109.5°
C2	N	H8	117.3°	119.9°
N	C2	H9	108.2°	109.5°
N	C2	H10	108.2°	109.4°
C2	C3	C4	177.7°	180.0°
C3	C2	H9	108.2°	109.5°
C3	C2	H10	108.2°	109.5°
C3	C4	C5	174.1°	179.9°
C4	C5	C6	121.9°	120.2°
C4	C5	C10	120.4°	120.2°
C5	C6	C7	120.7°	119.9°
C6	C5	C10	117.8°	119.7°
C5	C6	H1	119.7°	120.0°
C6	C7	C8	120.8°	120.2°
C7	C6	H1	119.7°	120.1°
C6	C7	H2	119.6°	119.9°
C5	C10	C9	120.8°	119.9°
C5	C10	H4	119.6°	120.0°
C7	C8	C9	119.6°	120.3°
C8	C7	H2	119.6°	119.9°
C7	C8	H3	120.2°	119.9°
C10	C9	C8	120.3°	120.1°
C9	C10	H4	119.6°	120.1°
C10	C9	H11	119.9°	119.9°
C9	C8	H3	120.2°	119.9°
C8	C9	H11	119.8°	120.0°
H5	C	H6	109.4°	109.5°
H5	C	H7	109.5°	109.5°
H6	C	H7	109.5°	109.5°
H9	C2	H10	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C	C1	O	N	176.1°	179.9°
C	C1	N	C2	178.9°	180.0°
C1	C	H5	H6	120.0°	120.0°
C1	C	H5	H7	120.0°	120.0°
C1	C	H6	H7	120.0°	120.0°
C	C1	N	H8	1.1°	0.0°
O	C1	N	C2	4.8°	0.0°
O	C1	C	H5	0.0°	0.0°
O	C1	C	H6	120.0°	119.9°
O	C1	C	H7	120.0°	120.1°
O	C1	N	H8	175.2°	179.9°
C1	N	C2	H8	180.0°	179.9°
C1	N	C2	C3	106.2°	180.0°
N	C1	C	H5	176.6°	180.0°
N	C1	C	H6	63.4°	60.0°
N	C1	C	H7	56.6°	60.0°
C1	N	C2	H9	14.5°	59.9°
C1	N	C2	H10	133.0°	60.0°
N	C2	C3	H9	120.7°	120.1°
N	C2	C3	H10	120.7°	120.0°
N	C2	C3	C4	126.7°	12.8°
N	C2	H9	H10	117.7°	120.0°
C2	C3	C4	C5	93.8°	132.3°
C3	C2	N	H8	73.8°	0.1°
C3	C2	H9	H10	117.7°	120.0°
C3	C4	C5	C6	71.4°	119.2°
C3	C4	C5	C10	109.3°	60.5°
C4	C3	C2	H9	6.0°	132.9°
C4	C3	C2	H10	112.5°	107.2°
C4	C5	C6	C10	179.3°	179.8°
C4	C5	C6	C7	178.5°	180.0°
C4	C5	C10	C9	179.3°	179.7°
C4	C5	C6	H1	1.5°	0.0°
C4	C5	C10	H4	0.7°	0.0°
C5	C6	C7	H1	180.0°	180.0°
C5	C6	C7	C8	1.9°	0.0°
C6	C5	C10	C9	1.4°	0.6°
C5	C6	C7	H2	178.0°	180.0°
C6	C5	C10	H4	178.6°	179.7°
C7	C6	C5	C10	0.8°	0.3°
C6	C7	C8	H2	180.0°	180.0°
C6	C7	C8	C9	0.8°	0.0°
C6	C7	C8	H3	179.2°	180.0°
C5	C10	C9	H4	180.0°	179.7°
C5	C10	C9	C8	2.5°	0.6°
C10	C5	C6	H1	179.2°	179.7°
C5	C10	C9	H11	177.5°	179.7°
C7	C8	C9	C10	1.4°	0.3°
C7	C8	C9	H3	180.0°	180.0°
C8	C7	C6	H1	178.0°	180.0°
C7	C8	C9	H11	178.6°	180.0°
C10	C9	C8	H11	180.0°	179.7°
C10	C9	C8	H3	178.6°	179.7°
C9	C8	C7	H2	179.1°	180.0°
C8	C9	C10	H4	177.5°	179.7°
H1	C6	C7	H2	2.0°	0.0°
H2	C7	C8	H3	0.9°	0.0°
H3	C8	C9	H11	1.4°	0.0°
H4	C10	C9	H11	2.5°	0.0°
H5	C	H6	H7	120.0°	120.1°
H8	N	C2	H9	165.5°	120.0°
H8	N	C2	H10	47.0°	120.1°

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PDB entries from 2026-01-14

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