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Summary Geometry Related PDB entries

Z5I

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O	C	sing	1.35Å	1.25Å
O2	C	doub	1.22Å	1.25Å
C	C2	sing	1.41Å	1.39Å
C2	C3	doub	1.36Å	1.38Å
C3	C4	sing	1.46Å	1.39Å
C4	C5	doub	1.37Å	1.33Å	Aromatic
C4	C11	sing	1.48Å	1.39Å	Aromatic
C5	N	sing	1.36Å	1.33Å	Aromatic
C11	C10	doub	1.39Å	1.39Å	Aromatic
C11	C6	sing	1.40Å	1.39Å	Aromatic
C10	C9	sing	1.38Å	1.39Å	Aromatic
N	C6	sing	1.38Å	1.34Å	Aromatic
C6	C7	doub	1.39Å	1.39Å	Aromatic
C9	C8	doub	1.39Å	1.39Å	Aromatic
C7	C8	sing	1.38Å	1.39Å	Aromatic
C5	H5	sing	1.08Å	1.08Å
C7	H1	sing	1.08Å	1.08Å
C8	H2	sing	1.08Å	1.08Å
C10	H4	sing	1.08Å	1.08Å
O	H	sing	0.97Å	0.95Å
C2	H7	sing	1.08Å	1.08Å
C3	H6	sing	1.08Å	1.08Å
N	H55	sing	0.97Å	1.00Å
C9	H3	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O	C	O2	123.7°	119.9°
O	C	C2	118.1°	120.0°
C	O	H	109.5°	114.0°
O2	C	C2	118.3°	120.0°
C	C2	C3	120.0°	120.0°
C	C2	H7	120.0°	120.0°
C2	C3	C4	120.2°	120.0°
C3	C2	H7	120.0°	120.0°
C2	C3	H6	119.9°	120.0°
C3	C4	C5	125.2°	126.8°
C3	C4	C11	125.7°	126.8°
C4	C3	H6	119.9°	120.0°
C5	C4	C11	109.1°	106.4°
C4	C5	N	108.1°	109.7°
C4	C5	H5	126.0°	125.1°
C4	C11	C10	134.1°	134.0°
C4	C11	C6	105.1°	105.9°
C5	N	C6	109.8°	110.5°
N	C5	H5	125.9°	125.2°
C5	N	H55	125.1°	124.8°
C10	C11	C6	120.8°	120.1°
C11	C10	C9	119.4°	119.7°
C11	C10	H4	120.3°	120.1°
C11	C6	N	107.8°	107.5°
C11	C6	C7	119.7°	119.4°
C10	C9	C8	120.1°	120.3°
C9	C10	H4	120.3°	120.2°
C10	C9	H3	120.0°	119.8°
N	C6	C7	132.4°	133.1°
C6	N	H55	125.1°	124.7°
C6	C7	C8	119.8°	119.9°
C6	C7	H1	120.1°	120.1°
C9	C8	C7	120.2°	120.6°
C9	C8	H2	119.9°	119.7°
C8	C9	H3	120.0°	119.8°
C8	C7	H1	120.1°	120.1°
C7	C8	H2	119.9°	119.7°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O	C	O2	C2	179.5°	180.0°
O	C	C2	C3	179.4°	180.0°
O	C	C2	H7	0.6°	0.0°
O2	C	C2	C3	0.1°	0.1°
O2	C	O	H	0.0°	0.0°
O2	C	C2	H7	179.9°	180.0°
C	C2	C3	H7	180.0°	179.9°
C	C2	C3	C4	179.9°	180.0°
C2	C	O	H	179.5°	180.0°
C	C2	C3	H6	0.2°	0.1°
C2	C3	C4	H6	180.0°	179.9°
C2	C3	C4	C5	0.5°	0.0°
C2	C3	C4	C11	180.0°	179.7°
C3	C4	C5	C11	179.6°	179.8°
C3	C4	C5	N	179.5°	179.8°
C3	C4	C11	C10	0.5°	0.2°
C3	C4	C11	C6	179.5°	179.7°
C3	C4	C5	H5	0.5°	0.2°
C4	C3	C2	H7	0.1°	0.1°
C4	C5	N	H5	180.0°	180.0°
C5	C4	C11	C10	179.9°	180.0°
C5	C4	C11	C6	0.1°	0.0°
C4	C5	N	C6	0.1°	0.0°
C5	C4	C3	H6	179.6°	179.9°
C4	C5	N	H55	179.9°	180.0°
C11	C4	C5	N	0.1°	0.0°
C4	C11	C10	C6	179.9°	179.9°
C4	C11	C10	C9	179.9°	179.9°
C4	C11	C6	N	0.0°	0.1°
C4	C11	C6	C7	179.9°	180.0°
C11	C4	C5	H5	179.9°	180.0°
C4	C11	C10	H4	0.2°	0.0°
C11	C4	C3	H6	0.0°	0.2°
C5	N	C6	C11	0.0°	0.1°
C5	N	C6	H55	180.0°	179.9°
C5	N	C6	C7	180.0°	180.0°
C11	C10	C9	H4	180.0°	179.9°
C10	C11	C6	N	179.9°	180.0°
C10	C11	C6	C7	0.1°	0.0°
C11	C10	C9	C8	0.2°	0.0°
C11	C10	C9	H3	179.8°	179.9°
C6	C11	C10	C9	0.2°	0.0°
C11	C6	N	C7	180.0°	179.9°
C11	C6	C7	C8	0.0°	0.0°
C11	C6	C7	H1	180.0°	180.0°
C6	C11	C10	H4	179.8°	179.9°
C11	C6	N	H55	180.0°	180.0°
C10	C9	C8	H3	180.0°	180.0°
C10	C9	C8	C7	0.0°	0.0°
C10	C9	C8	H2	179.9°	180.0°
N	C6	C7	C8	180.0°	180.0°
C6	N	C5	H5	179.9°	180.0°
N	C6	C7	H1	0.0°	0.1°
C6	C7	C8	C9	0.1°	0.0°
C6	C7	C8	H1	180.0°	180.0°
C6	C7	C8	H2	180.0°	180.0°
C7	C6	N	H55	0.0°	0.0°
C9	C8	C7	H2	180.0°	180.0°
C9	C8	C7	H1	180.0°	180.0°
C8	C9	C10	H4	179.8°	179.9°
C7	C8	C9	H3	179.9°	179.9°
H5	C5	N	H55	0.1°	0.0°
H1	C7	C8	H2	0.0°	0.0°
H2	C8	C9	H3	0.1°	0.0°
H4	C10	C9	H3	0.2°	0.1°
H7	C2	C3	H6	179.8°	180.0°

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PDB entries from 2026-01-14

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