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Summary Geometry Related PDB entries

X1M

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C5	C1	doub	1.39Å	1.38Å	Aromatic
C5	C4	sing	1.38Å	1.38Å	Aromatic
C1	C2	sing	1.38Å	1.36Å	Aromatic
C6	C4	sing	1.51Å	1.51Å
C6	N2	sing	1.47Å	1.45Å
C4	N1	doub	1.32Å	1.34Å	Aromatic
C2	C3	doub	1.39Å	1.39Å	Aromatic
C7	N2	sing	1.47Å	1.46Å
N1	C3	sing	1.32Å	1.32Å	Aromatic
C3	O1	sing	1.36Å	1.36Å
O1	C8	sing	1.43Å	1.43Å
C5	H3	sing	1.08Å	1.08Å
C6	H4	sing	1.09Å	1.10Å
C6	H5	sing	1.09Å	1.10Å
C7	H7	sing	1.09Å	1.10Å
C7	H8	sing	1.09Å	1.10Å
C7	H9	sing	1.09Å	1.10Å
C8	H12	sing	1.09Å	1.10Å
C8	H10	sing	1.09Å	1.10Å
C8	H11	sing	1.09Å	1.10Å
N2	H6	sing	1.01Å	1.00Å
C1	H1	sing	1.08Å	1.08Å
C2	H2	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	C5	C4	118.8°	119.3°
C5	C1	C2	120.0°	118.5°
C1	C5	H3	120.6°	120.4°
C5	C1	H1	120.0°	120.7°
C5	C4	C6	122.3°	119.6°
C5	C4	N1	121.6°	120.8°
C4	C5	H3	120.6°	120.3°
C1	C2	C3	117.5°	119.1°
C2	C1	H1	120.0°	120.8°
C1	C2	H2	121.2°	120.4°
C4	C6	N2	113.3°	109.4°
C6	C4	N1	116.1°	119.6°
C4	C6	H4	108.5°	109.5°
C4	C6	H5	108.5°	109.5°
C6	N2	C7	112.8°	111.0°
N2	C6	H4	108.5°	109.4°
N2	C6	H5	108.5°	109.5°
C6	N2	H6	108.6°	111.0°
C4	N1	C3	118.3°	121.7°
C2	C3	N1	123.7°	120.7°
C2	C3	O1	117.0°	119.6°
C3	C2	H2	121.3°	120.5°
N2	C7	H7	109.5°	109.5°
N2	C7	H8	109.5°	109.5°
N2	C7	H9	109.5°	109.5°
C7	N2	H6	108.6°	111.0°
N1	C3	O1	119.2°	119.7°
C3	O1	C8	117.5°	117.0°
O1	C8	H12	109.5°	109.4°
O1	C8	H10	109.4°	109.5°
O1	C8	H11	109.4°	109.5°
H4	C6	H5	109.5°	109.5°
H7	C7	H8	109.4°	109.5°
H7	C7	H9	109.5°	109.5°
H8	C7	H9	109.5°	109.5°
H12	C8	H10	109.5°	109.4°
H12	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)
C1	C5	C4	H3	180.0°	179.9°
C5	C1	C2	H1	180.0°	179.9°
C1	C5	C4	C6	179.7°	179.7°
C1	C5	C4	N1	0.7°	0.1°
C5	C1	C2	C3	0.4°	0.1°
C5	C1	C2	H2	179.6°	180.0°
C4	C5	C1	C2	0.5°	0.1°
C5	C4	C6	N1	179.0°	179.8°
C5	C4	C6	N2	141.5°	94.8°
C5	C4	N1	C3	0.8°	0.1°
C5	C4	C6	H4	20.9°	145.2°
C5	C4	C6	H5	98.0°	25.2°
C4	C5	C1	H1	179.5°	180.0°
C1	C2	C3	H2	180.0°	180.0°
C1	C2	C3	N1	0.5°	0.0°
C1	C2	C3	O1	179.7°	180.0°
C2	C1	C5	H3	179.5°	180.0°
C4	C6	N2	H4	120.6°	120.0°
C4	C6	N2	H5	120.6°	120.0°
C4	C6	N2	C7	177.6°	180.0°
C6	C4	N1	C3	179.8°	179.7°
C6	C4	C5	H3	0.3°	0.2°
C4	C6	H4	H5	118.3°	120.0°
C4	C6	N2	H6	57.1°	56.1°
N2	C6	C4	N1	37.6°	85.0°
C6	N2	C7	H6	120.5°	123.9°
N2	C6	H4	H5	118.3°	120.0°
C6	N2	C7	H7	180.0°	60.0°
C6	N2	C7	H8	60.0°	60.0°
C6	N2	C7	H9	60.0°	180.0°
C4	N1	C3	C2	0.7°	0.0°
C4	N1	C3	O1	179.5°	180.0°
N1	C4	C5	H3	179.3°	180.0°
N1	C4	C6	H4	158.1°	34.9°
N1	C4	C6	H5	83.0°	155.0°
C2	C3	N1	O1	179.8°	180.0°
C2	C3	O1	C8	174.4°	180.0°
C3	C2	C1	H1	179.6°	180.0°
C7	N2	C6	H4	61.9°	60.0°
C7	N2	C6	H5	57.0°	60.0°
N2	C7	H7	H8	120.0°	120.0°
N2	C7	H7	H9	120.0°	120.0°
N2	C7	H8	H9	120.0°	120.0°
N1	C3	O1	C8	5.8°	0.0°
N1	C3	C2	H2	179.5°	180.0°
C3	O1	C8	H12	180.0°	180.0°
C3	O1	C8	H10	60.0°	60.1°
C3	O1	C8	H11	60.0°	60.0°
O1	C3	C2	H2	0.3°	0.0°
O1	C8	H12	H10	120.0°	120.0°
O1	C8	H12	H11	120.0°	120.0°
O1	C8	H10	H11	120.0°	120.0°
H3	C5	C1	H1	0.5°	0.1°
H4	C6	N2	H6	177.6°	176.1°
H5	C6	N2	H6	63.5°	63.9°
H7	C7	H8	H9	120.0°	120.0°
H7	C7	N2	H6	59.5°	176.1°
H8	C7	N2	H6	179.5°	63.9°
H9	C7	N2	H6	60.5°	56.1°
H12	C8	H10	H11	120.0°	120.0°
H1	C1	C2	H2	0.4°	0.0°

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PDB entries from 2026-01-14

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