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Summary Geometry Related PDB entries

J5S

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O	C1	doub	1.21Å	1.24Å
C	C1	sing	1.51Å	1.50Å
C1	N	sing	1.34Å	1.35Å
N	C2	doub	1.31Å	1.45Å
C2	C3	sing	1.47Å	1.51Å
C4	C3	doub	1.40Å	1.40Å	Aromatic
C4	C5	sing	1.38Å	1.41Å	Aromatic
C3	C9	sing	1.40Å	1.40Å	Aromatic
C5	C6	doub	1.38Å	1.41Å	Aromatic
C9	C8	doub	1.38Å	1.40Å	Aromatic
C6	C8	sing	1.38Å	1.41Å	Aromatic
C6	C7	sing	1.51Å	1.50Å
C4	H1	sing	1.08Å	1.08Å
C5	H2	sing	1.08Å	1.08Å
C7	H3	sing	1.09Å	1.10Å
C7	H4	sing	1.09Å	1.10Å
C7	H5	sing	1.09Å	1.10Å
C8	H6	sing	1.08Å	1.08Å
C	H7	sing	1.09Å	1.10Å
C	H8	sing	1.09Å	1.10Å
C	H9	sing	1.09Å	1.10Å
C2	H10	sing	1.08Å	1.08Å
C9	H11	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O	C1	C	123.6°	120.0°
O	C1	N	122.5°	120.0°
C	C1	N	114.0°	120.0°
C1	C	H7	109.5°	109.4°
C1	C	H8	109.5°	109.5°
C1	C	H9	109.5°	109.5°
C1	N	C2	120.8°	120.0°
N	C2	C3	115.0°	120.0°
N	C2	H10	122.5°	120.0°
C2	C3	C4	119.3°	120.1°
C2	C3	C9	119.3°	120.2°
C3	C2	H10	122.5°	120.0°
C3	C4	C5	120.6°	119.8°
C4	C3	C9	121.3°	119.7°
C3	C4	H1	119.7°	120.1°
C4	C5	C6	118.0°	120.2°
C5	C4	H1	119.7°	120.1°
C4	C5	H2	121.0°	119.9°
C3	C9	C8	118.3°	119.8°
C3	C9	H11	120.9°	120.1°
C5	C6	C8	121.2°	120.4°
C5	C6	C7	119.5°	119.8°
C6	C5	H2	121.0°	119.9°
C9	C8	C6	120.6°	120.2°
C9	C8	H6	119.7°	119.9°
C8	C9	H11	120.8°	120.1°
C8	C6	C7	119.4°	119.8°
C6	C8	H6	119.7°	120.0°
C6	C7	H3	109.5°	109.4°
C6	C7	H4	109.5°	109.5°
C6	C7	H5	109.5°	109.4°
H3	C7	H4	109.5°	109.5°
H3	C7	H5	109.5°	109.5°
H4	C7	H5	109.5°	109.5°
H7	C	H8	109.4°	109.5°
H7	C	H9	109.5°	109.5°
H8	C	H9	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O	C1	C	N	179.9°	180.0°
O	C1	N	C2	4.8°	0.0°
O	C1	C	H7	0.0°	0.0°
O	C1	C	H8	120.0°	120.0°
O	C1	C	H9	120.0°	120.0°
C	C1	N	C2	175.3°	180.0°
C1	C	H7	H8	120.0°	120.0°
C1	C	H7	H9	120.0°	120.0°
C1	C	H8	H9	120.0°	120.1°
C1	N	C2	C3	167.7°	180.0°
N	C1	C	H7	179.8°	180.0°
N	C1	C	H8	59.9°	60.0°
N	C1	C	H9	60.1°	60.0°
C1	N	C2	H10	12.3°	0.0°
N	C2	C3	H10	180.0°	180.0°
N	C2	C3	C4	85.8°	180.0°
N	C2	C3	C9	97.4°	0.0°
C2	C3	C4	C9	176.8°	180.0°
C2	C3	C4	C5	178.6°	180.0°
C2	C3	C9	C8	179.4°	180.0°
C2	C3	C4	H1	1.3°	0.2°
C2	C3	C9	H11	0.6°	0.0°
C3	C4	C5	H1	180.0°	179.8°
C3	C4	C5	C6	0.7°	0.0°
C4	C3	C9	C8	2.6°	0.0°
C3	C4	C5	H2	179.2°	180.0°
C4	C3	C2	H10	94.2°	0.0°
C4	C3	C9	H11	177.4°	180.0°
C5	C4	C3	C9	1.9°	0.0°
C4	C5	C6	H2	180.0°	180.0°
C4	C5	C6	C8	0.5°	0.0°
C4	C5	C6	C7	179.9°	180.0°
C3	C9	C8	H11	180.0°	180.0°
C3	C9	C8	C6	2.3°	0.0°
C9	C3	C4	H1	178.1°	179.8°
C3	C9	C8	H6	177.7°	179.9°
C9	C3	C2	H10	82.6°	180.0°
C5	C6	C8	C9	1.3°	0.0°
C5	C6	C8	C7	179.4°	180.0°
C6	C5	C4	H1	179.2°	179.8°
C5	C6	C7	H3	89.7°	90.0°
C5	C6	C7	H4	150.3°	150.0°
C5	C6	C7	H5	30.3°	30.0°
C5	C6	C8	H6	178.7°	179.9°
C9	C8	C6	H6	180.0°	179.9°
C9	C8	C6	C7	179.3°	180.0°
C8	C6	C5	H2	179.5°	180.0°
C8	C6	C7	H3	89.7°	90.0°
C8	C6	C7	H4	30.3°	30.0°
C8	C6	C7	H5	150.3°	150.0°
C6	C8	C9	H11	177.7°	180.0°
C7	C6	C5	H2	0.1°	0.0°
C6	C7	H3	H4	120.0°	120.0°
C6	C7	H3	H5	120.0°	119.9°
C6	C7	H4	H5	120.0°	120.0°
C7	C6	C8	H6	0.7°	0.1°
H1	C4	C5	H2	0.8°	0.2°
H3	C7	H4	H5	120.0°	120.0°
H6	C8	C9	H11	2.3°	0.1°
H7	C	H8	H9	120.0°	120.0°

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