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Summary Geometry Related PDB entries

A1D9S

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N1	C3	sing	1.47Å	0.00Å
N1	C4	sing	1.38Å	0.00Å
C3	C2	sing	1.53Å	0.00Å
C4	N2	doub	1.30Å	0.00Å
C4	N3	sing	1.37Å	0.00Å
C2	C1	sing	1.51Å	0.00Å
C1	O2	doub	1.21Å	0.00Å
C1	O1	sing	1.34Å	0.00Å
N1	H1	sing	0.97Å	0.00Å
O1	H2	sing	0.97Å	0.00Å
C2	H3	sing	1.09Å	0.00Å
C2	H4	sing	1.09Å	0.00Å
N2	H5	sing	0.97Å	0.00Å
C3	H6	sing	1.09Å	0.00Å
C3	H7	sing	1.09Å	0.00Å
N3	H8	sing	0.97Å	0.00Å
N3	H9	sing	0.97Å	0.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C3	N1	C4	90.0°	120.0°
N1	C3	C2	90.0°	109.5°
C3	N1	H1	90.0°	120.0°
N1	C3	H6	90.0°	109.5°
N1	C3	H7	90.0°	109.5°
N1	C4	N2	90.0°	120.0°
N1	C4	N3	90.0°	119.9°
C4	N1	H1	90.0°	120.0°
C3	C2	C1	90.0°	109.5°
C3	C2	H3	90.0°	109.5°
C3	C2	H4	90.0°	109.5°
C2	C3	H6	90.0°	109.5°
C2	C3	H7	90.0°	109.5°
N2	C4	N3	90.0°	120.1°
C4	N2	H5	90.0°	120.0°
C4	N3	H8	90.0°	120.0°
C4	N3	H9	90.0°	119.9°
C2	C1	O2	90.0°	119.9°
C2	C1	O1	90.0°	120.0°
C1	C2	H3	90.0°	109.5°
C1	C2	H4	90.0°	109.4°
O2	C1	O1	90.0°	120.0°
C1	O1	H2	90.0°	117.0°
H3	C2	H4	90.0°	109.5°
H6	C3	H7	90.0°	109.5°
H8	N3	H9	90.0°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C3	N1	C4	H1	90.0°	180.0°
N1	C3	C2	H6	90.0°	120.0°
N1	C3	C2	H7	90.0°	120.0°
C3	N1	C4	N2	90.0°	0.0°
C3	N1	C4	N3	90.0°	180.0°
N1	C3	C2	C1	90.0°	180.0°
N1	C3	C2	H3	90.0°	60.0°
N1	C3	C2	H4	90.0°	60.0°
N1	C3	H6	H7	90.0°	120.0°
C4	N1	C3	C2	90.0°	180.0°
N1	C4	N2	N3	90.0°	180.0°
N1	C4	N2	H5	90.0°	180.0°
C4	N1	C3	H6	90.0°	60.0°
C4	N1	C3	H7	90.0°	60.0°
N1	C4	N3	H8	90.0°	0.0°
N1	C4	N3	H9	90.0°	180.0°
C3	C2	C1	H3	90.0°	120.0°
C3	C2	C1	H4	90.0°	120.0°
C3	C2	C1	O2	90.0°	0.0°
C3	C2	C1	O1	90.0°	179.7°
C2	C3	N1	H1	90.0°	0.0°
C3	C2	H3	H4	90.0°	120.0°
C2	C3	H6	H7	90.0°	120.0°
N2	C4	N1	H1	90.0°	179.9°
N2	C4	N3	H8	90.0°	179.9°
N2	C4	N3	H9	90.0°	0.0°
N3	C4	N1	H1	90.0°	0.0°
N3	C4	N2	H5	90.0°	0.0°
C4	N3	H8	H9	90.0°	179.9°
C2	C1	O2	O1	90.0°	179.7°
C2	C1	O1	H2	90.0°	179.7°
C1	C2	H3	H4	90.0°	119.9°
C1	C2	C3	H6	90.0°	60.0°
C1	C2	C3	H7	90.0°	60.0°
O2	C1	O1	H2	90.0°	0.0°
O2	C1	C2	H3	90.0°	120.0°
O2	C1	C2	H4	90.0°	120.0°
O1	C1	C2	H3	90.0°	60.3°
O1	C1	C2	H4	90.0°	59.7°
H1	N1	C3	H6	90.0°	120.0°
H1	N1	C3	H7	90.0°	119.9°
H3	C2	C3	H6	90.0°	60.0°
H3	C2	C3	H7	90.0°	180.0°
H4	C2	C3	H6	90.0°	179.9°
H4	C2	C3	H7	90.0°	60.0°

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PDB entries from 2026-01-21

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