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Summary Geometry Related PDB entries

S5Y

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C4	O1	sing	1.43Å	1.42Å
C4	C5	sing	1.53Å	1.51Å
C	C1	sing	1.53Å	1.52Å
O1	C3	sing	1.43Å	1.41Å
C5	S	sing	1.81Å	1.81Å
C1	O	sing	1.43Å	1.42Å
O	C2	sing	1.43Å	1.42Å
C3	C2	sing	1.53Å	1.52Å
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C2	H3	sing	1.09Å	1.10Å
C2	H4	sing	1.09Å	1.10Å
C3	H5	sing	1.09Å	1.10Å
C3	H6	sing	1.09Å	1.10Å
C4	H7	sing	1.09Å	1.10Å
C4	H8	sing	1.09Å	1.10Å
C5	H9	sing	1.09Å	1.10Å
C5	H10	sing	1.09Å	1.10Å
S	H11	sing	1.34Å	1.30Å
C	H12	sing	1.09Å	1.10Å
C	H13	sing	1.09Å	1.10Å
C	H14	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C4	C5	111.2°	109.5°
C4	O1	C3	114.9°	113.9°
O1	C4	H7	109.0°	109.5°
O1	C4	H8	109.0°	109.5°
C4	C5	S	107.9°	109.5°
C5	C4	H7	109.0°	109.5°
C5	C4	H8	109.0°	109.5°
C4	C5	H9	109.9°	109.5°
C4	C5	H10	109.9°	109.5°
C	C1	O	105.0°	109.5°
C	C1	H1	110.6°	109.4°
C	C1	H2	110.6°	109.5°
C1	C	H12	109.5°	109.4°
C1	C	H13	109.5°	109.5°
C1	C	H14	109.5°	109.5°
O1	C3	C2	102.6°	109.4°
O1	C3	H5	111.1°	109.5°
O1	C3	H6	111.2°	109.5°
S	C5	H9	109.9°	109.5°
S	C5	H10	109.8°	109.5°
C5	S	H11	102.0°	103.0°
C1	O	C2	115.9°	114.0°
O	C1	H1	110.6°	109.5°
O	C1	H2	110.6°	109.5°
O	C2	C3	103.1°	109.4°
O	C2	H3	111.1°	109.5°
O	C2	H4	111.1°	109.5°
C3	C2	H3	111.0°	109.4°
C3	C2	H4	111.0°	109.4°
C2	C3	H5	111.2°	109.5°
C2	C3	H6	111.2°	109.5°
H1	C1	H2	109.5°	109.5°
H3	C2	H4	109.5°	109.5°
H5	C3	H6	109.5°	109.5°
H7	C4	H8	109.5°	109.5°
H9	C5	H10	109.5°	109.5°
H12	C	H13	109.5°	109.5°
H12	C	H14	109.4°	109.5°
H13	C	H14	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C4	C5	H7	120.3°	120.0°
O1	C4	C5	H8	120.2°	120.0°
O1	C4	C5	S	91.2°	180.0°
C4	O1	C3	C2	168.1°	180.0°
C4	O1	C3	H5	73.0°	60.0°
C4	O1	C3	H6	49.2°	60.0°
O1	C4	H7	H8	119.2°	120.0°
O1	C4	C5	H9	149.1°	60.0°
O1	C4	C5	H10	28.6°	60.0°
C5	C4	O1	C3	68.5°	180.0°
C4	C5	S	H9	119.8°	120.0°
C4	C5	S	H10	119.8°	120.0°
C5	C4	H7	H8	119.2°	120.0°
C4	C5	H9	H10	120.7°	120.0°
C4	C5	S	H11	180.0°	180.0°
C	C1	O	H1	119.3°	120.0°
C	C1	O	H2	119.3°	120.0°
C	C1	O	C2	177.2°	180.0°
C	C1	H1	H2	122.1°	120.0°
C1	C	H12	H13	120.0°	120.0°
C1	C	H12	H14	120.0°	120.0°
C1	C	H13	H14	120.0°	120.0°
O1	C3	C2	O	19.7°	65.0°
O1	C3	C2	H5	118.9°	120.0°
O1	C3	C2	H6	118.9°	120.0°
O1	C3	C2	H3	138.6°	175.0°
O1	C3	C2	H4	99.3°	55.0°
O1	C3	H5	H6	123.2°	120.0°
C3	O1	C4	H7	51.8°	60.0°
C3	O1	C4	H8	171.3°	60.0°
S	C5	C4	H7	29.1°	60.0°
S	C5	C4	H8	148.6°	60.0°
S	C5	H9	H10	120.7°	120.0°
C1	O	C2	C3	159.1°	180.0°
O	C1	H1	H2	122.1°	120.0°
C1	O	C2	H3	81.9°	60.0°
C1	O	C2	H4	40.1°	60.1°
O	C1	C	H12	180.0°	60.0°
O	C1	C	H13	60.0°	60.0°
O	C1	C	H14	60.0°	180.0°
O	C2	C3	H3	119.0°	120.0°
O	C2	C3	H4	119.0°	120.0°
C2	O	C1	H1	63.6°	60.0°
C2	O	C1	H2	57.9°	60.0°
O	C2	H3	H4	123.0°	120.1°
O	C2	C3	H5	138.5°	175.0°
O	C2	C3	H6	99.3°	55.0°
C3	C2	H3	H4	122.9°	120.0°
C2	C3	H5	H6	123.2°	120.0°
H1	C1	C	H12	60.7°	180.0°
H1	C1	C	H13	59.3°	60.0°
H1	C1	C	H14	179.3°	60.0°
H2	C1	C	H12	60.7°	60.0°
H2	C1	C	H13	179.3°	180.0°
H2	C1	C	H14	59.3°	60.0°
H3	C2	C3	H5	102.5°	55.0°
H3	C2	C3	H6	19.7°	65.0°
H4	C2	C3	H5	19.5°	65.0°
H4	C2	C3	H6	141.7°	175.0°
H7	C4	C5	H9	90.7°	60.0°
H7	C4	C5	H10	148.8°	NaN°
H8	C4	C5	H9	28.8°	180.0°
H8	C4	C5	H10	91.7°	60.0°
H9	C5	S	H11	60.2°	60.0°
H10	C5	S	H11	60.2°	60.0°
H12	C	H13	H14	120.0°	120.0°

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PDB entries from 2024-09-04

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