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Summary Geometry Related PDB entries

W1D

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C6	C7	sing	1.51Å	1.51Å
C6	O1	sing	1.43Å	1.43Å
O2	C7	doub	1.21Å	1.21Å
C7	O3	sing	1.34Å	1.31Å
O1	C5	sing	1.36Å	1.38Å
C5	C8	doub	1.39Å	1.39Å	Aromatic
C5	C4	sing	1.39Å	1.39Å	Aromatic
C8	C9	sing	1.37Å	1.38Å	Aromatic
C4	C3	doub	1.37Å	1.38Å	Aromatic
C9	C2	doub	1.40Å	1.40Å	Aromatic
C3	C2	sing	1.40Å	1.40Å	Aromatic
C2	C1	sing	1.47Å	1.49Å
C1	C	sing	1.51Å	1.49Å
C1	O	doub	1.21Å	1.22Å
C4	H1	sing	1.08Å	1.08Å
C6	H2	sing	1.09Å	1.10Å
C6	H3	sing	1.09Å	1.10Å
C8	H4	sing	1.08Å	1.08Å
O3	H5	sing	0.97Å	0.95Å
C3	H6	sing	1.08Å	1.08Å
C9	H7	sing	1.08Å	1.08Å
C	H8	sing	1.09Å	1.10Å
C	H9	sing	1.09Å	1.10Å
C	H10	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C7	C6	O1	113.5°	109.5°
C6	C7	O2	122.7°	120.0°
C6	C7	O3	114.4°	120.0°
C7	C6	H2	108.5°	109.5°
C7	C6	H3	108.5°	109.5°
C6	O1	C5	120.4°	117.0°
O1	C6	H2	108.5°	109.5°
O1	C6	H3	108.4°	109.5°
O2	C7	O3	122.9°	120.0°
C7	O3	H5	109.5°	117.0°
O1	C5	C8	118.2°	119.9°
O1	C5	C4	121.6°	119.9°
C8	C5	C4	120.2°	120.3°
C5	C8	C9	119.8°	120.1°
C5	C8	H4	120.1°	120.0°
C5	C4	C3	119.8°	120.1°
C5	C4	H1	120.1°	120.0°
C8	C9	C2	120.6°	119.9°
C9	C8	H4	120.1°	120.0°
C8	C9	H7	119.7°	120.0°
C4	C3	C2	120.8°	119.9°
C3	C4	H1	120.1°	119.9°
C4	C3	H6	119.6°	120.0°
C9	C2	C3	118.9°	119.7°
C9	C2	C1	121.8°	120.1°
C2	C9	H7	119.7°	120.1°
C3	C2	C1	119.3°	120.2°
C2	C3	H6	119.6°	120.0°
C2	C1	C	119.4°	120.0°
C2	C1	O	120.1°	120.0°
C	C1	O	120.5°	120.0°
C1	C	H8	109.5°	109.4°
C1	C	H9	109.5°	109.5°
C1	C	H10	109.4°	109.5°
H2	C6	H3	109.5°	109.4°
H8	C	H9	109.5°	109.4°
H8	C	H10	109.4°	109.5°
H9	C	H10	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C7	C6	O1	H2	120.6°	120.0°
C7	C6	O1	H3	120.6°	120.0°
C6	C7	O2	O3	179.0°	179.9°
C7	C6	O1	C5	78.4°	180.0°
C7	C6	H2	H3	118.2°	120.0°
C6	C7	O3	H5	179.1°	180.0°
O1	C6	C7	O2	173.1°	0.0°
O1	C6	C7	O3	7.8°	179.9°
C6	O1	C5	C8	177.7°	180.0°
C6	O1	C5	C4	0.2°	0.0°
O1	C6	H2	H3	118.2°	120.0°
O2	C7	C6	H2	66.3°	120.1°
O2	C7	C6	H3	52.5°	120.0°
O2	C7	O3	H5	0.0°	0.1°
O3	C7	C6	H2	112.8°	60.0°
O3	C7	C6	H3	128.4°	59.9°
O1	C5	C8	C4	177.9°	180.0°
O1	C5	C8	C9	176.8°	179.9°
O1	C5	C4	C3	176.7°	180.0°
O1	C5	C4	H1	3.3°	0.2°
C5	O1	C6	H2	161.1°	60.0°
C5	O1	C6	H3	42.2°	60.0°
O1	C5	C8	H4	3.2°	0.0°
C5	C8	C9	H4	180.0°	180.0°
C8	C5	C4	C3	1.2°	0.0°
C5	C8	C9	C2	0.2°	0.2°
C8	C5	C4	H1	178.8°	179.8°
C5	C8	C9	H7	179.8°	180.0°
C4	C5	C8	C9	1.1°	0.1°
C5	C4	C3	H1	180.0°	179.8°
C5	C4	C3	C2	0.3°	0.2°
C4	C5	C8	H4	178.9°	180.0°
C5	C4	C3	H6	179.7°	179.7°
C8	C9	C2	H7	180.0°	179.8°
C8	C9	C2	C3	0.7°	0.5°
C8	C9	C2	C1	178.1°	179.9°
C4	C3	C2	C9	0.6°	0.5°
C4	C3	C2	H6	180.0°	180.0°
C4	C3	C2	C1	178.1°	180.0°
C9	C2	C3	C1	178.8°	179.4°
C9	C2	C1	C	0.8°	6.1°
C9	C2	C1	O	178.5°	173.9°
C2	C9	C8	H4	179.8°	179.8°
C9	C2	C3	H6	179.3°	179.4°
C3	C2	C1	C	179.6°	174.4°
C3	C2	C1	O	0.2°	5.5°
C2	C3	C4	H1	179.7°	180.0°
C3	C2	C9	H7	179.3°	179.7°
C2	C1	C	O	179.3°	179.9°
C1	C2	C3	H6	1.9°	0.0°
C1	C2	C9	H7	1.9°	0.3°
C2	C1	C	H8	179.3°	5.1°
C2	C1	C	H9	59.3°	125.1°
C2	C1	C	H10	60.7°	114.9°
C1	C	H8	H9	120.0°	120.0°
C1	C	H8	H10	120.0°	120.0°
C1	C	H9	H10	120.0°	120.1°
O	C1	C	H8	0.0°	175.0°
O	C1	C	H9	120.0°	55.0°
O	C1	C	H10	120.0°	65.0°
H1	C4	C3	H6	0.2°	0.1°
H4	C8	C9	H7	0.2°	0.0°
H8	C	H9	H10	120.0°	120.0°

249697

PDB entries from 2026-02-25

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