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Summary Geometry Related PDB entries

V5R

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C8	C7	sing	1.51Å	1.50Å
O3	C9	doub	1.21Å	1.26Å
N1	C7	sing	1.35Å	1.37Å
N1	C2	sing	1.40Å	1.44Å
C7	O1	doub	1.21Å	1.25Å
C3	C2	doub	1.39Å	1.41Å	Aromatic
C3	C4	sing	1.40Å	1.40Å	Aromatic
C9	O2	sing	1.35Å	1.28Å
C9	C4	sing	1.48Å	1.54Å
C2	C1	sing	1.39Å	1.39Å	Aromatic
C4	C5	doub	1.40Å	1.40Å	Aromatic
C1	C6	doub	1.38Å	1.39Å	Aromatic
C5	C6	sing	1.38Å	1.39Å	Aromatic
C5	CL1	sing	1.74Å	1.75Å
N1	H1	sing	0.97Å	1.00Å
C6	H2	sing	1.08Å	1.08Å
C8	H3	sing	1.09Å	1.10Å
C8	H4	sing	1.09Å	1.10Å
C8	H5	sing	1.09Å	1.10Å
C1	H6	sing	1.08Å	1.08Å
C3	H7	sing	1.08Å	1.08Å
O2	H8	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C8	C7	N1	114.3°	120.0°
C8	C7	O1	119.8°	120.0°
C7	C8	H3	109.5°	109.5°
C7	C8	H4	109.5°	109.5°
C7	C8	H5	109.5°	109.5°
O3	C9	O2	123.8°	120.0°
O3	C9	C4	116.6°	120.1°
C7	N1	C2	131.4°	120.0°
N1	C7	O1	125.8°	120.0°
C7	N1	H1	114.3°	120.0°
N1	C2	C3	116.3°	120.0°
N1	C2	C1	125.2°	120.0°
C2	N1	H1	114.3°	120.0°
C2	C3	C4	121.7°	119.8°
C3	C2	C1	118.5°	120.1°
C2	C3	H7	119.2°	120.1°
C3	C4	C9	118.3°	120.1°
C3	C4	C5	118.1°	119.8°
C4	C3	H7	119.1°	120.1°
O2	C9	C4	119.7°	120.0°
C9	O2	H8	109.5°	117.0°
C9	C4	C5	123.6°	120.1°
C2	C1	C6	120.8°	120.2°
C2	C1	H6	119.6°	119.9°
C4	C5	C6	120.8°	119.9°
C4	C5	CL1	122.0°	120.1°
C1	C6	C5	120.1°	120.2°
C1	C6	H2	120.0°	119.8°
C6	C1	H6	119.6°	119.9°
C6	C5	CL1	117.2°	120.0°
C5	C6	H2	120.0°	119.9°
H3	C8	H4	109.5°	109.5°
H3	C8	H5	109.5°	109.5°
H4	C8	H5	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C8	C7	N1	O1	177.3°	179.9°
C8	C7	N1	C2	168.3°	174.8°
C8	C7	N1	H1	11.7°	5.5°
C7	C8	H3	H4	120.0°	120.0°
C7	C8	H3	H5	120.0°	120.0°
C7	C8	H4	H5	120.0°	120.0°
O3	C9	C4	C3	37.4°	179.8°
O3	C9	O2	C4	179.0°	180.0°
O3	C9	C4	C5	141.2°	0.0°
O3	C9	O2	H8	0.0°	0.0°
C7	N1	C2	H1	180.0°	179.7°
C7	N1	C2	C3	177.3°	33.4°
C7	N1	C2	C1	1.8°	146.6°
N1	C7	C8	H3	177.5°	90.0°
N1	C7	C8	H4	62.5°	150.0°
N1	C7	C8	H5	57.5°	30.1°
C2	N1	C7	O1	14.4°	5.3°
N1	C2	C3	C1	179.2°	180.0°
N1	C2	C3	C4	178.8°	180.0°
N1	C2	C1	C6	179.0°	179.9°
N1	C2	C1	H6	1.1°	0.1°
N1	C2	C3	H7	1.3°	0.1°
O1	C7	N1	H1	165.6°	174.4°
O1	C7	C8	H3	0.0°	90.0°
O1	C7	C8	H4	120.0°	30.1°
O1	C7	C8	H5	120.0°	150.0°
C2	C3	C4	H7	180.0°	179.9°
C2	C3	C4	C9	179.4°	179.7°
C2	C3	C4	C5	0.7°	0.0°
C3	C2	C1	C6	0.2°	0.1°
C3	C2	N1	H1	2.7°	146.9°
C3	C2	C1	H6	179.8°	179.9°
C3	C4	C9	O2	141.6°	0.3°
C3	C4	C9	C5	178.6°	179.7°
C4	C3	C2	C1	0.4°	0.0°
C3	C4	C5	C6	0.7°	0.0°
C3	C4	C5	CL1	179.2°	180.0°
O2	C9	C4	C5	39.8°	180.0°
C9	C4	C5	C6	179.3°	179.7°
C9	C4	C5	CL1	2.2°	0.3°
C9	C4	C3	H7	0.6°	0.3°
C4	C9	O2	H8	179.0°	180.0°
C2	C1	C6	H6	180.0°	179.9°
C2	C1	C6	C5	0.2°	0.1°
C1	C2	N1	H1	178.1°	33.1°
C2	C1	C6	H2	179.8°	179.9°
C1	C2	C3	H7	179.5°	179.9°
C4	C5	C6	C1	0.5°	0.0°
C4	C5	C6	CL1	178.6°	180.0°
C4	C5	C6	H2	179.5°	179.9°
C5	C4	C3	H7	179.3°	180.0°
C1	C6	C5	H2	180.0°	179.9°
C1	C6	C5	CL1	179.0°	179.9°
C5	C6	C1	H6	179.8°	180.0°
CL1	C5	C6	H2	0.9°	0.1°
H2	C6	C1	H6	0.2°	0.2°
H3	C8	H4	H5	120.0°	120.0°

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PDB entries from 2024-09-11

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