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Summary Geometry Related PDB entries

BJK

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C6	C4	sing	1.51Å	1.50Å
C6	N	sing	1.47Å	1.49Å
C3	C4	doub	1.38Å	1.39Å	Aromatic
C3	C2	sing	1.39Å	1.38Å	Aromatic
C4	C5	sing	1.38Å	1.39Å	Aromatic
O	C2	sing	1.36Å	1.36Å
C2	C1	doub	1.39Å	1.40Å	Aromatic
C5	C	doub	1.38Å	1.38Å	Aromatic
C1	C	sing	1.39Å	1.38Å	Aromatic
C1	O1	sing	1.36Å	1.37Å
O1	C7	sing	1.43Å	1.43Å
C5	H1	sing	1.08Å	1.08Å
C6	H3	sing	1.09Å	1.10Å
C6	H2	sing	1.09Å	1.10Å
C7	H6	sing	1.09Å	1.10Å
C7	H4	sing	1.09Å	1.10Å
C7	H5	sing	1.09Å	1.10Å
O	H7	sing	0.97Å	0.95Å
C3	H8	sing	1.08Å	1.08Å
C	H9	sing	1.08Å	1.08Å
N	H10	sing	1.01Å	1.00Å
N	H11	sing	1.01Å	1.00Å
N	H12	sing	1.01Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C4	C6	N	112.2°	109.5°
C6	C4	C3	120.4°	119.9°
C6	C4	C5	120.9°	119.9°
C4	C6	H3	108.8°	109.5°
C4	C6	H2	108.8°	109.5°
N	C6	H3	108.8°	109.5°
N	C6	H2	108.8°	109.5°
C6	N	H10	109.5°	109.5°
C6	N	H11	109.5°	109.5°
C6	N	H12	109.5°	109.4°
C4	C3	C2	121.0°	120.0°
C3	C4	C5	118.7°	120.2°
C4	C3	H8	119.5°	120.0°
C3	C2	O	119.7°	120.0°
C3	C2	C1	119.5°	119.8°
C2	C3	H8	119.5°	120.0°
C4	C5	C	121.2°	120.2°
C4	C5	H1	119.4°	119.9°
O	C2	C1	120.8°	120.1°
C2	O	H7	109.5°	114.0°
C2	C1	C	119.9°	119.9°
C2	C1	O1	114.8°	120.0°
C5	C	C1	119.6°	120.0°
C	C5	H1	119.4°	119.9°
C5	C	H9	120.2°	120.0°
C	C1	O1	125.0°	120.1°
C1	C	H9	120.2°	120.0°
C1	O1	C7	117.6°	117.0°
O1	C7	H6	109.5°	109.5°
O1	C7	H4	109.5°	109.5°
O1	C7	H5	109.4°	109.5°
H3	C6	H2	109.5°	109.4°
H6	C7	H4	109.5°	109.4°
H6	C7	H5	109.5°	109.5°
H4	C7	H5	109.5°	109.4°
H10	N	H11	109.5°	109.5°
H10	N	H12	109.4°	109.5°
H11	N	H12	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C4	C6	N	H3	120.4°	120.0°
C4	C6	N	H2	120.4°	120.0°
C6	C4	C3	C5	177.0°	179.7°
C6	C4	C3	C2	175.6°	179.7°
C6	C4	C5	C	175.1°	179.9°
C6	C4	C5	H1	4.9°	0.0°
C4	C6	H3	H2	118.8°	120.0°
C6	C4	C3	H8	4.4°	0.3°
C4	C6	N	H10	180.0°	180.0°
C4	C6	N	H11	60.0°	60.0°
C4	C6	N	H12	60.0°	60.0°
N	C6	C4	C3	79.2°	89.7°
N	C6	C4	C5	97.8°	90.0°
N	C6	H3	H2	118.7°	120.0°
C6	N	H10	H11	120.0°	120.0°
C6	N	H10	H12	120.0°	120.0°
C6	N	H11	H12	120.0°	119.9°
C4	C3	C2	H8	180.0°	180.0°
C4	C3	C2	O	178.5°	179.8°
C4	C3	C2	C1	1.0°	0.5°
C3	C4	C5	C	2.0°	0.2°
C3	C4	C5	H1	178.1°	179.7°
C3	C4	C6	H3	41.2°	30.3°
C3	C4	C6	H2	160.5°	150.2°
C2	C3	C4	C5	1.4°	0.0°
C3	C2	O	C1	179.4°	179.3°
C3	C2	C1	C	2.8°	0.8°
C3	C2	C1	O1	171.8°	179.3°
C3	C2	O	H7	180.0°	89.3°
C4	C5	C	H1	180.0°	180.0°
C4	C5	C	C1	0.1°	0.1°
C5	C4	C6	H3	141.8°	150.0°
C5	C4	C6	H2	22.6°	30.0°
C5	C4	C3	H8	178.6°	180.0°
C4	C5	C	H9	179.9°	180.0°
O	C2	C1	C	176.6°	180.0°
O	C2	C1	O1	8.7°	0.0°
O	C2	C3	H8	1.6°	0.2°
C2	C1	C	C5	2.3°	0.6°
C2	C1	C	O1	174.1°	179.9°
C2	C1	O1	C7	164.4°	179.9°
C1	C2	O	H7	0.6°	90.0°
C1	C2	C3	H8	179.0°	179.5°
C2	C1	C	H9	177.7°	179.5°
C5	C	C1	H9	180.0°	179.9°
C5	C	C1	O1	171.8°	179.5°
C	C1	O1	C7	10.0°	0.0°
C1	C	C5	H1	179.9°	180.0°
C1	O1	C7	H6	180.0°	59.9°
C1	O1	C7	H4	60.0°	60.1°
C1	O1	C7	H5	60.0°	180.0°
O1	C1	C	H9	8.2°	0.4°
O1	C7	H6	H4	120.0°	120.0°
O1	C7	H6	H5	120.0°	120.1°
O1	C7	H4	H5	120.0°	120.0°
H1	C5	C	H9	0.1°	0.0°
H3	C6	N	H10	59.6°	60.0°
H3	C6	N	H11	179.6°	180.0°
H3	C6	N	H12	60.4°	60.1°
H2	C6	N	H10	59.6°	60.0°
H2	C6	N	H11	60.4°	60.1°
H2	C6	N	H12	179.6°	180.0°
H6	C7	H4	H5	120.0°	120.0°
H10	N	H11	H12	120.0°	120.0°

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PDB entries from 2026-03-18

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