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Summary Geometry Related PDB entries

D3H

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N2	C8	sing	1.47Å	1.47Å
O1	C7	doub	1.21Å	1.23Å
C8	C7	sing	1.51Å	1.53Å
C7	N1	sing	1.35Å	1.35Å
N1	C4	sing	1.40Å	1.34Å
C4	C5	doub	1.39Å	1.40Å	Aromatic
C4	C3	sing	1.39Å	1.39Å	Aromatic
C5	C6	sing	1.38Å	1.39Å	Aromatic
C3	C2	doub	1.38Å	1.39Å	Aromatic
C6	C1	doub	1.39Å	1.39Å	Aromatic
C2	C1	sing	1.39Å	1.39Å	Aromatic
C1	N3	sing	1.40Å	1.33Å
C5	H1	sing	1.08Å	1.08Å
C6	H2	sing	1.08Å	1.08Å
C8	H3	sing	1.09Å	1.10Å
C8	H4	sing	1.09Å	1.10Å
N1	H5	sing	0.97Å	1.00Å
N2	H6	sing	1.01Å	1.00Å
N2	H7	sing	1.01Å	1.00Å
C3	H9	sing	1.08Å	1.08Å
N3	H10	sing	0.97Å	1.00Å
N3	H11	sing	0.97Å	1.00Å
C2	H12	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N2	C8	C7	110.3°	109.4°
N2	C8	H3	109.3°	109.5°
N2	C8	H4	109.3°	109.5°
C8	N2	H6	109.5°	110.9°
C8	N2	H7	109.5°	111.0°
O1	C7	C8	120.7°	120.0°
O1	C7	N1	124.6°	120.0°
C8	C7	N1	114.6°	120.0°
C7	C8	H3	109.3°	109.5°
C7	C8	H4	109.2°	109.5°
C7	N1	C4	118.3°	120.0°
C7	N1	H5	120.9°	120.0°
N1	C4	C5	120.9°	120.0°
N1	C4	C3	119.5°	120.0°
C4	N1	H5	120.9°	120.0°
C5	C4	C3	119.6°	120.0°
C4	C5	C6	120.2°	120.0°
C4	C5	H1	119.9°	120.0°
C4	C3	C2	120.3°	120.0°
C4	C3	H9	119.8°	120.0°
C5	C6	C1	120.2°	120.0°
C6	C5	H1	119.9°	120.0°
C5	C6	H2	119.9°	120.0°
C3	C2	C1	120.1°	120.0°
C2	C3	H9	119.9°	120.0°
C3	C2	H12	119.9°	120.0°
C6	C1	C2	119.7°	120.0°
C6	C1	N3	120.1°	120.0°
C1	C6	H2	119.9°	120.0°
C2	C1	N3	120.2°	120.0°
C1	C2	H12	119.9°	120.0°
C1	N3	H10	109.5°	120.1°
C1	N3	H11	109.5°	120.0°
H3	C8	H4	109.5°	109.5°
H6	N2	H7	109.5°	111.0°
H10	N3	H11	109.4°	119.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N2	C8	C7	O1	19.6°	0.1°
N2	C8	C7	H3	120.1°	119.9°
N2	C8	C7	H4	120.1°	120.0°
N2	C8	C7	N1	161.7°	180.0°
N2	C8	H3	H4	119.6°	120.0°
C8	N2	H6	H7	120.0°	123.9°
O1	C7	C8	N1	178.7°	179.9°
O1	C7	N1	C4	1.9°	5.2°
O1	C7	C8	H3	139.7°	120.0°
O1	C7	C8	H4	100.5°	119.9°
O1	C7	N1	H5	178.1°	174.8°
C8	C7	N1	C4	179.5°	174.7°
C7	C8	H3	H4	119.6°	120.0°
C8	C7	N1	H5	0.5°	5.3°
C7	C8	N2	H6	180.0°	180.0°
C7	C8	N2	H7	60.0°	56.1°
C7	N1	C4	H5	180.0°	180.0°
C7	N1	C4	C5	63.2°	146.8°
C7	N1	C4	C3	118.9°	33.5°
N1	C7	C8	H3	41.5°	60.0°
N1	C7	C8	H4	78.2°	60.0°
N1	C4	C5	C3	177.9°	179.7°
N1	C4	C5	C6	179.2°	179.7°
N1	C4	C3	C2	179.1°	179.7°
N1	C4	C5	H1	0.8°	0.2°
N1	C4	C3	H9	0.9°	0.3°
C4	C5	C6	H1	180.0°	179.9°
C5	C4	C3	C2	1.2°	0.0°
C4	C5	C6	C1	0.8°	0.1°
C4	C5	C6	H2	179.1°	180.0°
C5	C4	N1	H5	116.7°	33.3°
C5	C4	C3	H9	178.8°	180.0°
C3	C4	C5	C6	1.3°	0.0°
C4	C3	C2	H9	180.0°	180.0°
C4	C3	C2	C1	0.6°	0.0°
C3	C4	C5	H1	178.7°	179.9°
C3	C4	N1	H5	61.1°	146.4°
C4	C3	C2	H12	179.4°	179.9°
C5	C6	C1	H2	180.0°	179.9°
C5	C6	C1	C2	0.2°	0.1°
C5	C6	C1	N3	179.8°	180.0°
C3	C2	C1	C6	0.1°	0.0°
C3	C2	C1	H12	180.0°	179.9°
C3	C2	C1	N3	179.9°	180.0°
C6	C1	C2	N3	180.0°	179.9°
C1	C6	C5	H1	179.2°	180.0°
C6	C1	N3	H10	180.0°	0.1°
C6	C1	N3	H11	60.0°	180.0°
C6	C1	C2	H12	179.9°	180.0°
C2	C1	C6	H2	179.7°	180.0°
C1	C2	C3	H9	179.4°	180.0°
C2	C1	N3	H10	0.0°	179.9°
C2	C1	N3	H11	120.0°	0.0°
N3	C1	C6	H2	0.2°	0.1°
C1	N3	H10	H11	120.0°	179.9°
N3	C1	C2	H12	0.1°	0.1°
H1	C5	C6	H2	0.8°	0.1°
H3	C8	N2	H6	59.9°	60.0°
H3	C8	N2	H7	60.1°	176.1°
H4	C8	N2	H6	59.9°	60.0°
H4	C8	N2	H7	179.9°	63.9°
H9	C3	C2	H12	0.6°	0.1°

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PDB entries from 2024-10-09

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