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Summary Geometry Related PDB entries

VJY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C8	C7	sing	1.51Å	1.48Å
C7	O1	doub	1.21Å	1.18Å
C7	N	sing	1.35Å	1.38Å
N	C6	sing	1.47Å	1.46Å
C6	C5	sing	1.51Å	1.51Å
C5	C4	doub	1.34Å	1.34Å	Aromatic
C5	S	sing	1.71Å	1.68Å	Aromatic
C4	C3	sing	1.37Å	1.43Å	Aromatic
S	C2	sing	1.76Å	1.65Å	Aromatic
C3	C2	doub	1.37Å	1.35Å	Aromatic
C2	C1	sing	1.41Å	1.42Å
C1	O	doub	1.21Å	1.19Å
C1	C	sing	1.51Å	1.49Å
C8	H1	sing	1.09Å	1.10Å
C8	H2	sing	1.09Å	1.10Å
C8	H3	sing	1.09Å	1.10Å
C6	H4	sing	1.09Å	1.10Å
C6	H5	sing	1.09Å	1.10Å
C4	H6	sing	1.08Å	1.08Å
C3	H7	sing	1.08Å	1.08Å
N	H8	sing	0.97Å	1.00Å
C	H9	sing	1.09Å	1.10Å
C	H10	sing	1.09Å	1.10Å
C	H11	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C8	C7	O1	121.7°	120.1°
C8	C7	N	116.2°	120.0°
C7	C8	H1	109.5°	109.4°
C7	C8	H2	109.5°	109.5°
C7	C8	H3	109.5°	109.5°
O1	C7	N	122.1°	120.0°
C7	N	C6	122.9°	120.0°
C7	N	H8	118.6°	120.0°
N	C6	C5	111.2°	109.5°
N	C6	H4	109.0°	109.5°
N	C6	H5	109.0°	109.5°
C6	N	H8	118.5°	120.0°
C6	C5	C4	126.4°	124.5°
C6	C5	S	121.6°	124.5°
C5	C6	H4	109.0°	109.5°
C5	C6	H5	109.0°	109.5°
C4	C5	S	112.0°	111.0°
C5	C4	C3	111.8°	115.2°
C5	C4	H6	124.1°	122.4°
C5	S	C2	92.3°	91.6°
C4	C3	C2	110.7°	113.2°
C3	C4	H6	124.1°	122.4°
C4	C3	H7	124.6°	123.3°
S	C2	C3	113.2°	109.1°
S	C2	C1	121.9°	125.5°
C3	C2	C1	124.8°	125.5°
C2	C3	H7	124.7°	123.4°
C2	C1	O	120.9°	120.0°
C2	C1	C	116.2°	120.0°
O	C1	C	122.9°	120.0°
C1	C	H9	109.5°	109.4°
C1	C	H10	109.5°	109.5°
C1	C	H11	109.5°	109.5°
H1	C8	H2	109.5°	109.5°
H1	C8	H3	109.5°	109.4°
H2	C8	H3	109.5°	109.5°
H4	C6	H5	109.5°	109.5°
H9	C	H10	109.5°	109.5°
H9	C	H11	109.4°	109.5°
H10	C	H11	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C8	C7	O1	N	179.0°	179.6°
C8	C7	N	C6	179.3°	179.7°
C7	C8	H1	H2	120.0°	120.0°
C7	C8	H1	H3	120.0°	120.0°
C7	C8	H2	H3	120.0°	120.0°
C8	C7	N	H8	0.7°	0.3°
O1	C7	N	C6	1.6°	0.1°
O1	C7	C8	H1	0.0°	90.0°
O1	C7	C8	H2	120.0°	150.0°
O1	C7	C8	H3	120.0°	29.9°
O1	C7	N	H8	178.4°	180.0°
C7	N	C6	H8	180.0°	179.9°
C7	N	C6	C5	104.6°	180.0°
N	C7	C8	H1	179.1°	90.4°
N	C7	C8	H2	60.9°	29.7°
N	C7	C8	H3	59.1°	149.7°
C7	N	C6	H4	15.7°	60.1°
C7	N	C6	H5	135.2°	59.9°
N	C6	C5	H4	120.2°	120.0°
N	C6	C5	H5	120.2°	120.0°
N	C6	C5	C4	47.8°	90.1°
N	C6	C5	S	133.5°	90.3°
N	C6	H4	H5	119.2°	120.0°
C6	C5	C4	S	178.8°	179.7°
C6	C5	C4	C3	178.7°	179.8°
C6	C5	S	C2	178.4°	179.7°
C5	C6	H4	H5	119.2°	120.0°
C6	C5	C4	H6	1.3°	0.4°
C5	C6	N	H8	75.4°	0.0°
C5	C4	C3	H6	180.0°	179.9°
C4	C5	S	C2	0.5°	0.0°
C5	C4	C3	C2	0.4°	0.0°
C4	C5	C6	H4	168.0°	150.0°
C4	C5	C6	H5	72.5°	30.0°
C5	C4	C3	H7	179.6°	180.0°
S	C5	C4	C3	0.2°	0.1°
C5	S	C2	C3	0.8°	0.0°
C5	S	C2	C1	176.3°	180.0°
S	C5	C6	H4	13.3°	29.7°
S	C5	C6	H5	106.3°	149.7°
S	C5	C4	H6	179.8°	179.9°
C4	C3	C2	S	0.8°	0.0°
C4	C3	C2	H7	180.0°	180.0°
C4	C3	C2	C1	176.1°	180.0°
S	C2	C3	C1	177.0°	180.0°
S	C2	C1	O	159.7°	180.0°
S	C2	C1	C	21.5°	0.0°
S	C2	C3	H7	179.2°	180.0°
C3	C2	C1	O	23.6°	0.1°
C3	C2	C1	C	155.2°	180.0°
C2	C3	C4	H6	179.6°	179.9°
C2	C1	O	C	178.7°	179.9°
C1	C2	C3	H7	3.9°	0.0°
C2	C1	C	H9	178.8°	90.0°
C2	C1	C	H10	61.2°	30.0°
C2	C1	C	H11	58.8°	150.0°
O	C1	C	H9	0.0°	90.1°
O	C1	C	H10	120.0°	150.0°
O	C1	C	H11	120.0°	29.9°
C1	C	H9	H10	120.0°	120.0°
C1	C	H9	H11	120.0°	120.0°
C1	C	H10	H11	120.0°	120.0°
H1	C8	H2	H3	120.0°	120.0°
H4	C6	N	H8	164.3°	120.0°
H5	C6	N	H8	44.9°	120.0°
H6	C4	C3	H7	0.4°	0.1°
H9	C	H10	H11	119.9°	120.0°

248335

PDB entries from 2026-01-28

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