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Summary Geometry Related PDB entries

Y1C

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
BR1	C2	sing	1.89Å	1.87Å
BR12	C11	sing	1.89Å	1.87Å
C2	C11	sing	1.40Å	1.39Å	Aromatic
C2	N3	doub	1.31Å	1.33Å	Aromatic
C11	N10	doub	1.31Å	1.33Å	Aromatic
N3	N4	sing	1.29Å	1.33Å	Aromatic
N10	N4	sing	1.29Å	1.33Å	Aromatic
N4	C5	sing	1.47Å	1.47Å
O8	C7	doub	1.21Å	1.21Å
C5	C6	sing	1.53Å	1.52Å
C7	C6	sing	1.51Å	1.50Å
C7	C9	sing	1.51Å	1.49Å
C5	H1	sing	1.09Å	1.10Å
C5	H2	sing	1.09Å	1.10Å
C6	H3	sing	1.09Å	1.10Å
C6	H4	sing	1.09Å	1.10Å
C9	H5	sing	1.09Å	1.10Å
C9	H6	sing	1.09Å	1.10Å
C9	H7	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
BR1	C2	C11	128.7°	127.1°
BR1	C2	N3	122.0°	127.0°
BR12	C11	C2	128.4°	127.1°
BR12	C11	N10	122.5°	127.0°
C11	C2	N3	109.3°	105.9°
C2	C11	N10	109.1°	105.9°
C2	N3	N4	102.7°	108.7°
C11	N10	N4	102.6°	108.7°
N3	N4	N10	116.2°	110.8°
N3	N4	C5	121.5°	124.6°
N10	N4	C5	122.3°	124.6°
N4	C5	C6	112.1°	109.5°
N4	C5	H1	108.8°	109.5°
N4	C5	H2	108.8°	109.5°
O8	C7	C6	121.7°	120.0°
O8	C7	C9	121.7°	120.0°
C5	C6	C7	115.2°	109.5°
C6	C5	H1	108.8°	109.5°
C6	C5	H2	108.8°	109.5°
C5	C6	H3	108.0°	109.4°
C5	C6	H4	108.0°	109.4°
C6	C7	C9	116.6°	120.0°
C7	C6	H3	108.0°	109.5°
C7	C6	H4	108.0°	109.5°
C7	C9	H5	109.5°	109.5°
C7	C9	H6	109.5°	109.5°
C7	C9	H7	109.5°	109.5°
H1	C5	H2	109.5°	109.5°
H3	C6	H4	109.5°	109.4°
H5	C9	H6	109.5°	109.5°
H5	C9	H7	109.5°	109.5°
H6	C9	H7	109.4°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
BR1	C2	C11	BR12	1.4°	0.0°
BR1	C2	C11	N3	179.2°	180.0°
BR1	C2	C11	N10	179.1°	180.0°
BR1	C2	N3	N4	179.2°	179.9°
BR12	C11	C2	N10	179.4°	180.0°
BR12	C11	C2	N3	179.4°	180.0°
BR12	C11	N10	N4	179.5°	179.9°
C11	C2	N3	N4	0.1°	0.0°
C2	C11	N10	N4	0.0°	0.0°
N3	C2	C11	N10	0.1°	0.0°
C2	N3	N4	N10	0.0°	0.0°
C2	N3	N4	C5	179.7°	180.0°
C11	N10	N4	N3	0.0°	0.0°
C11	N10	N4	C5	179.6°	180.0°
N3	N4	N10	C5	179.6°	180.0°
N3	N4	C5	C6	160.1°	90.0°
N3	N4	C5	H1	79.5°	30.0°
N3	N4	C5	H2	39.7°	150.0°
N10	N4	C5	C6	20.2°	90.0°
N10	N4	C5	H1	100.1°	150.0°
N10	N4	C5	H2	140.6°	30.0°
N4	C5	C6	H1	120.4°	120.0°
N4	C5	C6	H2	120.4°	120.0°
N4	C5	C6	C7	101.2°	180.0°
N4	C5	H1	H2	118.8°	120.0°
N4	C5	C6	H3	19.6°	60.0°
N4	C5	C6	H4	138.0°	60.0°
O8	C7	C6	C5	112.5°	0.0°
O8	C7	C6	C9	179.4°	180.0°
O8	C7	C6	H3	8.4°	120.0°
O8	C7	C6	H4	126.7°	120.0°
O8	C7	C9	H5	0.0°	180.0°
O8	C7	C9	H6	120.0°	60.0°
O8	C7	C9	H7	120.0°	60.0°
C5	C6	C7	H3	120.8°	120.0°
C5	C6	C7	H4	120.8°	120.0°
C5	C6	C7	C9	68.2°	180.0°
C6	C5	H1	H2	118.8°	120.0°
C5	C6	H3	H4	117.4°	119.9°
C7	C6	C5	H1	138.4°	60.0°
C7	C6	C5	H2	19.2°	60.0°
C7	C6	H3	H4	117.4°	120.1°
C6	C7	C9	H5	179.4°	0.0°
C6	C7	C9	H6	59.3°	120.0°
C6	C7	C9	H7	60.6°	120.0°
C9	C7	C6	H3	171.0°	60.0°
C9	C7	C6	H4	52.6°	60.0°
C7	C9	H5	H6	120.0°	120.0°
C7	C9	H5	H7	120.0°	120.0°
C7	C9	H6	H7	120.0°	120.0°
H1	C5	C6	H3	100.7°	60.0°
H1	C5	C6	H4	17.6°	180.0°
H2	C5	C6	H3	140.0°	180.0°
H2	C5	C6	H4	101.6°	60.0°
H5	C9	H6	H7	120.0°	120.0°

250835

PDB entries from 2026-03-18

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