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Summary Geometry Related PDB entries

Q5L

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C	C1	sing	1.53Å	1.55Å
C2	C1	sing	1.53Å	1.54Å
C1	N	sing	1.46Å	1.49Å
N	C3	sing	1.35Å	1.40Å
C3	O	doub	1.22Å	1.21Å
C4	C3	sing	1.48Å	1.47Å
C4	C5	sing	1.42Å	1.41Å	Aromatic
C5	C6	doub	1.35Å	1.39Å	Aromatic
C6	N1	sing	1.35Å	1.40Å	Aromatic
N1	N2	sing	1.28Å	1.35Å	Aromatic
N2	C4	doub	1.32Å	1.38Å	Aromatic
N1	H10	sing	0.97Å	1.00Å
C5	H8	sing	1.08Å	1.08Å
C6	H9	sing	1.08Å	1.08Å
N	H7	sing	0.97Å	1.00Å
C	H2	sing	1.09Å	1.10Å
C	H1	sing	1.09Å	1.10Å
C	H	sing	1.09Å	1.10Å
C1	H3	sing	1.09Å	1.10Å
C2	H4	sing	1.09Å	1.10Å
C2	H6	sing	1.09Å	1.10Å
C2	H5	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C	C1	C2	110.7°	109.4°
C	C1	N	109.1°	109.5°
C1	C	H2	109.5°	109.5°
C1	C	H1	109.5°	109.5°
C1	C	H	109.5°	109.4°
C	C1	H3	108.3°	109.5°
C2	C1	N	111.1°	109.5°
C2	C1	H3	108.4°	109.4°
C1	C2	H4	109.5°	109.5°
C1	C2	H6	109.5°	109.5°
C1	C2	H5	109.5°	109.5°
C1	N	C3	121.9°	120.0°
C1	N	H7	119.1°	120.0°
N	C1	H3	109.1°	109.5°
N	C3	O	123.8°	120.0°
N	C3	C4	115.2°	120.0°
C3	N	H7	119.1°	120.0°
O	C3	C4	121.0°	120.1°
C3	C4	C5	125.1°	126.5°
C3	C4	N2	123.3°	126.6°
C4	C5	C6	105.0°	105.5°
C5	C4	N2	111.6°	106.9°
C4	C5	H8	127.5°	127.2°
C5	C6	N1	106.4°	107.2°
C6	C5	H8	127.5°	127.2°
C5	C6	H9	126.8°	126.4°
C6	N1	N2	112.5°	110.2°
C6	N1	H10	123.7°	124.9°
N1	C6	H9	126.8°	126.3°
N1	N2	C4	104.6°	110.2°
N2	N1	H10	123.8°	124.9°
H2	C	H1	109.5°	109.4°
H2	C	H	109.4°	109.5°
H1	C	H	109.4°	109.4°
H4	C2	H6	109.4°	109.4°
H4	C2	H5	109.5°	109.4°
H6	C2	H5	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C	C1	C2	N	121.5°	120.0°
C	C1	C2	H3	118.7°	120.0°
C	C1	N	H3	118.2°	120.1°
C	C1	N	C3	70.1°	85.1°
C	C1	N	H7	109.9°	95.0°
C1	C	H2	H1	120.0°	120.0°
C1	C	H2	H	120.0°	120.0°
C1	C	H1	H	120.0°	120.0°
C	C1	C2	H4	180.0°	60.0°
C	C1	C2	H6	60.0°	180.0°
C	C1	C2	H5	60.0°	60.0°
C2	C1	N	H3	119.4°	120.0°
C2	C1	N	C3	167.5°	155.0°
C2	C1	N	H7	12.5°	24.9°
C2	C1	C	H2	180.0°	60.0°
C2	C1	C	H1	60.0°	60.0°
C2	C1	C	H	60.0°	180.0°
C1	C2	H4	H6	120.0°	120.0°
C1	C2	H4	H5	120.0°	120.1°
C1	C2	H6	H5	120.0°	120.0°
C1	N	C3	H7	180.0°	179.9°
C1	N	C3	O	0.1°	0.1°
C1	N	C3	C4	179.9°	180.0°
N	C1	C	H2	57.4°	60.0°
N	C1	C	H1	62.7°	180.0°
N	C1	C	H	177.4°	60.1°
N	C1	C2	H4	58.5°	60.0°
N	C1	C2	H6	178.5°	60.0°
N	C1	C2	H5	61.5°	180.0°
N	C3	O	C4	180.0°	179.9°
N	C3	C4	C5	177.3°	180.0°
N	C3	C4	N2	1.7°	0.5°
C3	N	C1	H3	48.0°	35.0°
O	C3	C4	C5	2.8°	0.1°
O	C3	C4	N2	178.3°	179.4°
O	C3	N	H7	179.9°	180.0°
C3	C4	C5	N2	179.0°	179.6°
C3	C4	C5	C6	178.5°	180.0°
C3	C4	N2	N1	178.6°	180.0°
C3	C4	C5	H8	1.5°	0.0°
C4	C3	N	H7	0.1°	0.1°
C4	C5	C6	H8	180.0°	179.9°
C4	C5	C6	N1	0.3°	0.2°
C5	C4	N2	N1	0.5°	0.4°
C4	C5	C6	H9	179.7°	179.8°
C5	C6	N1	H9	180.0°	180.0°
C5	C6	N1	N2	0.0°	0.0°
C6	C5	C4	N2	0.5°	0.4°
C5	C6	N1	H10	180.0°	179.8°
C6	N1	N2	H10	180.0°	179.8°
C6	N1	N2	C4	0.3°	0.3°
N1	C6	C5	H8	179.7°	179.7°
N2	N1	C6	H9	180.0°	180.0°
C4	N2	N1	H10	179.7°	180.0°
N2	C4	C5	H8	179.5°	179.5°
H10	N1	C6	H9	0.0°	0.2°
H8	C5	C6	H9	0.3°	0.3°
H7	N	C1	H3	131.9°	144.9°
H2	C	H1	H	120.0°	120.0°
H2	C	C1	H3	61.2°	179.9°
H1	C	C1	H3	178.7°	59.9°
H	C	C1	H3	58.7°	60.0°
H3	C1	C2	H4	61.3°	180.0°
H3	C1	C2	H6	58.7°	60.0°
H3	C1	C2	H5	178.7°	60.0°
H4	C2	H6	H5	120.0°	119.9°

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PDB entries from 2024-07-10

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