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Summary Geometry Related PDB entries

J5J

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O	C1	doub	1.21Å	1.25Å
C	C1	sing	1.51Å	1.51Å
C1	N	sing	1.34Å	1.36Å
N	C2	doub	1.31Å	1.46Å
C2	C3	sing	1.47Å	1.48Å
C3	C9	doub	1.40Å	1.24Å	Aromatic
C3	C4	sing	1.40Å	1.26Å	Aromatic
C9	C7	sing	1.38Å	1.27Å	Aromatic
C4	C5	doub	1.38Å	1.26Å	Aromatic
C7	C8	sing	1.51Å	1.48Å
C7	C6	doub	1.38Å	1.39Å	Aromatic
C5	C6	sing	1.38Å	1.38Å	Aromatic
C	H1	sing	1.09Å	1.10Å
C	H2	sing	1.09Å	1.10Å
C	H3	sing	1.09Å	1.10Å
C2	H4	sing	1.08Å	1.08Å
C4	H5	sing	1.08Å	1.08Å
C5	H6	sing	1.08Å	1.08Å
C6	H7	sing	1.08Å	1.08Å
C9	H8	sing	1.08Å	1.08Å
C8	H9	sing	1.09Å	1.10Å
C8	H10	sing	1.09Å	1.10Å
C8	H11	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O	C1	C	122.6°	120.0°
O	C1	N	121.3°	120.0°
C	C1	N	115.8°	120.0°
C1	C	H1	109.5°	109.4°
C1	C	H2	109.5°	109.5°
C1	C	H3	109.5°	109.4°
C1	N	C2	121.0°	120.0°
N	C2	C3	115.9°	119.9°
N	C2	H4	122.1°	120.0°
C2	C3	C9	131.1°	120.1°
C2	C3	C4	133.3°	120.2°
C3	C2	H4	122.1°	120.0°
C9	C3	C4	95.6°	119.6°
C3	C9	C7	143.7°	119.8°
C3	C9	H8	108.1°	120.1°
C3	C4	C5	143.8°	119.8°
C3	C4	H5	108.1°	120.1°
C9	C7	C8	124.7°	119.9°
C9	C7	C6	110.0°	120.1°
C7	C9	H8	108.2°	120.1°
C4	C5	C6	110.1°	120.2°
C5	C4	H5	108.1°	120.1°
C4	C5	H6	124.9°	119.9°
C8	C7	C6	125.1°	119.9°
C7	C8	H9	109.5°	109.5°
C7	C8	H10	109.5°	109.4°
C7	C8	H11	109.5°	109.4°
C7	C6	C5	116.5°	120.4°
C7	C6	H7	121.8°	119.7°
C6	C5	H6	124.9°	119.9°
C5	C6	H7	121.8°	119.9°
H1	C	H2	109.5°	109.5°
H1	C	H3	109.5°	109.5°
H2	C	H3	109.4°	109.5°
H9	C8	H10	109.4°	109.5°
H9	C8	H11	109.5°	109.5°
H10	C8	H11	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O	C1	C	N	174.0°	180.0°
O	C1	N	C2	5.8°	0.0°
O	C1	C	H1	0.0°	90.0°
O	C1	C	H2	120.0°	150.0°
O	C1	C	H3	120.0°	30.0°
C	C1	N	C2	179.9°	180.0°
C1	C	H1	H2	120.0°	120.0°
C1	C	H1	H3	120.0°	119.9°
C1	C	H2	H3	120.0°	120.0°
C1	N	C2	C3	179.3°	180.0°
N	C1	C	H1	174.0°	90.0°
N	C1	C	H2	54.0°	29.9°
N	C1	C	H3	66.0°	150.0°
C1	N	C2	H4	0.7°	0.1°
N	C2	C3	H4	180.0°	179.9°
N	C2	C3	C9	101.2°	180.0°
N	C2	C3	C4	81.7°	0.3°
C2	C3	C9	C4	177.9°	179.7°
C2	C3	C9	C7	178.5°	179.7°
C2	C3	C4	C5	173.8°	180.0°
C2	C3	C4	H5	6.2°	0.1°
C2	C3	C9	H8	1.4°	0.1°
C3	C9	C7	H8	180.0°	179.7°
C9	C3	C4	C5	4.0°	0.3°
C3	C9	C7	C8	171.3°	179.7°
C3	C9	C7	C6	4.3°	0.6°
C9	C3	C2	H4	78.8°	0.1°
C9	C3	C4	H5	176.0°	179.8°
C4	C3	C9	C7	0.7°	0.6°
C3	C4	C5	H5	180.0°	179.9°
C3	C4	C5	C6	3.1°	0.0°
C4	C3	C2	H4	98.4°	179.7°
C3	C4	C5	H6	176.9°	180.0°
C4	C3	C9	H8	179.3°	179.7°
C9	C7	C8	C6	174.9°	179.7°
C9	C7	C6	C5	4.4°	0.2°
C9	C7	C6	H7	175.6°	179.7°
C9	C7	C8	H9	87.5°	89.7°
C9	C7	C8	H10	152.6°	30.3°
C9	C7	C8	H11	32.6°	150.3°
C4	C5	C6	C7	2.1°	0.0°
C4	C5	C6	H6	180.0°	180.0°
C4	C5	C6	H7	177.9°	180.0°
C8	C7	C6	C5	171.1°	180.0°
C8	C7	C6	H7	8.9°	0.0°
C8	C7	C9	H8	8.8°	0.0°
C7	C8	H9	H10	120.0°	120.0°
C7	C8	H9	H11	120.0°	120.0°
C7	C8	H10	H11	120.0°	120.0°
C7	C6	C5	H7	180.0°	180.0°
C7	C6	C5	H6	177.9°	180.0°
C6	C7	C9	H8	175.7°	179.8°
C6	C7	C8	H9	87.4°	90.0°
C6	C7	C8	H10	32.6°	150.0°
C6	C7	C8	H11	152.6°	30.0°
C6	C5	C4	H5	176.9°	179.9°
H1	C	H2	H3	120.0°	120.1°
H5	C4	C5	H6	3.1°	0.0°
H6	C5	C6	H7	2.1°	0.0°
H9	C8	H10	H11	120.0°	120.1°

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