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Summary Geometry Related PDB entries

PIY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C2	N1	sing	1.36Å	1.35Å	Aromatic
N1	C4	sing	1.37Å	1.34Å	Aromatic
C6	C2	sing	1.48Å	1.49Å	Aromatic
C2	N3	doub	1.31Å	1.35Å	Aromatic
N3	C5	sing	1.34Å	1.35Å	Aromatic
C4	C5	doub	1.35Å	1.38Å	Aromatic
C4	H4	sing	1.08Å	1.08Å
C5	H5	sing	1.08Å	1.08Å
C7	C6	doub	1.40Å	1.40Å	Aromatic
C11	C6	sing	1.40Å	1.40Å	Aromatic
C8	C7	sing	1.38Å	1.40Å	Aromatic
C7	H7	sing	1.08Å	1.08Å
C9	C8	doub	1.38Å	1.40Å	Aromatic
C8	H8	sing	1.08Å	1.08Å
C9	C10	sing	1.38Å	1.39Å	Aromatic
C9	H9	sing	1.08Å	1.08Å
C10	C11	doub	1.38Å	1.40Å	Aromatic
C10	H10	sing	1.08Å	1.08Å
C11	H11	sing	1.08Å	1.08Å
N1	HN1	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	N1	C4	107.8°	107.0°
N1	C2	C6	125.6°	125.8°
N1	C2	N3	109.2°	108.3°
C2	N1	HN1	126.1°	126.6°
N1	C4	C5	107.4°	107.0°
N1	C4	H4	126.3°	126.5°
C4	N1	HN1	126.1°	126.4°
C6	C2	N3	125.3°	125.8°
C2	C6	C7	119.9°	120.1°
C2	C6	C11	120.0°	120.1°
C2	N3	C5	107.4°	109.2°
N3	C5	C4	108.2°	108.4°
N3	C5	H5	125.9°	125.8°
C5	C4	H4	126.3°	126.5°
C4	C5	H5	125.9°	125.8°
C7	C6	C11	120.1°	119.7°
C6	C7	C8	119.5°	119.8°
C6	C7	H7	120.2°	120.1°
C6	C11	C10	120.3°	119.8°
C6	C11	H11	119.8°	120.1°
C8	C7	H7	120.2°	120.1°
C7	C8	C9	120.2°	120.2°
C7	C8	H8	119.9°	119.9°
C9	C8	H8	119.9°	119.9°
C8	C9	C10	120.3°	120.3°
C8	C9	H9	119.8°	119.9°
C10	C9	H9	119.8°	119.8°
C9	C10	C11	119.5°	120.2°
C9	C10	H10	120.2°	119.9°
C11	C10	H10	120.2°	119.9°
C10	C11	H11	119.8°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	N1	C4	HN1	180.0°	179.8°
N1	C2	C6	N3	179.9°	179.9°
N1	C2	N3	C5	0.0°	0.0°
C2	N1	C4	C5	0.2°	0.0°
C2	N1	C4	H4	179.8°	179.7°
N1	C2	C6	C7	19.3°	180.0°
N1	C2	C6	C11	160.9°	0.2°
C4	N1	C2	C6	179.9°	180.0°
C4	N1	C2	N3	0.1°	0.0°
N1	C4	C5	N3	0.2°	0.0°
N1	C4	C5	H4	180.0°	179.7°
N1	C4	C5	H5	179.8°	180.0°
C6	C2	N3	C5	179.9°	179.9°
C2	C6	C7	C11	179.8°	179.7°
C2	C6	C7	C8	179.8°	180.0°
C2	C6	C7	H7	0.2°	0.1°
C2	C6	C11	C10	179.9°	179.7°
C2	C6	C11	H11	0.1°	0.2°
C6	C2	N1	HN1	0.1°	0.3°
C2	N3	C5	C4	0.1°	0.0°
C2	N3	C5	H5	179.9°	180.0°
N3	C2	C6	C7	160.6°	0.0°
N3	C2	C6	C11	19.2°	179.7°
N3	C2	N1	HN1	179.9°	179.8°
N3	C5	C4	H5	180.0°	180.0°
N3	C5	C4	H4	179.8°	179.7°
C5	C4	N1	HN1	179.8°	179.8°
H4	C4	C5	H5	0.2°	0.3°
H4	C4	N1	HN1	0.2°	0.0°
C6	C7	C8	H7	180.0°	179.9°
C6	C7	C8	C9	0.1°	0.0°
C6	C7	C8	H8	179.9°	180.0°
C7	C6	C11	C10	0.1°	0.6°
C7	C6	C11	H11	179.9°	180.0°
C11	C6	C7	C8	0.0°	0.3°
C11	C6	C7	H7	180.0°	179.8°
C6	C11	C10	C9	0.1°	0.6°
C6	C11	C10	H11	180.0°	179.5°
C6	C11	C10	H10	179.9°	179.7°
C7	C8	C9	H8	180.0°	180.0°
C7	C8	C9	C10	0.1°	0.0°
C7	C8	C9	H9	179.9°	180.0°
H7	C7	C8	C9	179.9°	179.9°
H7	C7	C8	H8	0.1°	0.1°
C8	C9	C10	H9	180.0°	180.0°
C8	C9	C10	C11	0.0°	0.3°
C8	C9	C10	H10	180.0°	180.0°
H8	C8	C9	C10	179.9°	180.0°
H8	C8	C9	H9	0.1°	0.0°
C9	C10	C11	H10	180.0°	179.7°
C9	C10	C11	H11	179.9°	180.0°
H9	C9	C10	C11	180.0°	179.7°
H9	C9	C10	H10	0.0°	0.0°
H10	C10	C11	H11	0.1°	0.2°

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PDB entries from 2026-02-04

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