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Summary Geometry Related PDB entries

PJY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	S2	sing	1.81Å	1.82Å
S2	C3	sing	1.76Å	1.77Å
C12	N11	sing	1.47Å	1.46Å
N4	C3	doub	1.32Å	1.35Å	Aromatic
N4	C5	sing	1.32Å	1.35Å	Aromatic
C3	C8	sing	1.41Å	1.40Å	Aromatic
C5	C6	doub	1.38Å	1.39Å	Aromatic
N11	C13	sing	1.47Å	1.46Å
N11	C9	sing	1.35Å	1.36Å
C8	C9	sing	1.47Å	1.51Å
C8	C7	doub	1.40Å	1.40Å	Aromatic
C9	O10	doub	1.22Å	1.22Å
C6	C7	sing	1.38Å	1.39Å	Aromatic
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C1	H3	sing	1.09Å	1.10Å
C12	H4	sing	1.09Å	1.10Å
C12	H5	sing	1.09Å	1.10Å
C12	H6	sing	1.09Å	1.10Å
C13	H7	sing	1.09Å	1.10Å
C13	H8	sing	1.09Å	1.10Å
C13	H9	sing	1.09Å	1.10Å
C5	H10	sing	1.08Å	1.08Å
C6	H11	sing	1.08Å	1.08Å
C7	H12	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	S2	C3	97.7°	100.0°
S2	C1	H1	109.5°	109.5°
S2	C1	H2	109.5°	109.5°
S2	C1	H3	109.5°	109.5°
S2	C3	N4	118.4°	119.9°
S2	C3	C8	121.2°	119.8°
C12	N11	C13	121.8°	120.0°
C12	N11	C9	117.9°	120.0°
N11	C12	H4	109.5°	109.5°
N11	C12	H5	109.5°	109.5°
N11	C12	H6	109.5°	109.5°
C3	N4	C5	121.6°	121.8°
N4	C3	C8	120.4°	120.3°
N4	C5	C6	120.6°	121.3°
N4	C5	H10	119.7°	119.3°
C3	C8	C9	121.8°	120.6°
C3	C8	C7	118.7°	118.8°
C5	C6	C7	118.7°	119.5°
C6	C5	H10	119.7°	119.4°
C5	C6	H11	120.6°	120.3°
C13	N11	C9	120.2°	120.0°
N11	C13	H7	109.5°	109.5°
N11	C13	H8	109.5°	109.4°
N11	C13	H9	109.4°	109.5°
N11	C9	C8	121.8°	120.0°
N11	C9	O10	121.9°	119.9°
C9	C8	C7	119.5°	120.6°
C8	C9	O10	116.3°	120.0°
C8	C7	C6	120.0°	118.3°
C8	C7	H12	120.0°	120.8°
C7	C6	H11	120.6°	120.2°
C6	C7	H12	120.0°	120.8°
H1	C1	H2	109.5°	109.5°
H1	C1	H3	109.5°	109.5°
H2	C1	H3	109.5°	109.5°
H4	C12	H5	109.4°	109.5°
H4	C12	H6	109.5°	109.5°
H5	C12	H6	109.4°	109.4°
H7	C13	H8	109.5°	109.4°
H7	C13	H9	109.5°	109.5°
H8	C13	H9	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	S2	C3	N4	21.4°	0.3°
C1	S2	C3	C8	158.4°	180.0°
S2	C1	H1	H2	120.0°	120.0°
S2	C1	H1	H3	120.0°	120.1°
S2	C1	H2	H3	120.0°	120.0°
S2	C3	N4	C8	179.8°	179.7°
S2	C3	N4	C5	179.9°	179.7°
S2	C3	C8	C9	0.1°	0.3°
S2	C3	C8	C7	180.0°	179.7°
C3	S2	C1	H1	180.0°	60.0°
C3	S2	C1	H2	60.0°	180.0°
C3	S2	C1	H3	60.0°	60.0°
C12	N11	C13	C9	178.0°	179.9°
C12	N11	C9	C8	2.6°	175.8°
C12	N11	C9	O10	179.9°	4.2°
N11	C12	H4	H5	120.0°	120.0°
N11	C12	H4	H6	120.0°	120.1°
N11	C12	H5	H6	120.0°	120.0°
C12	N11	C13	H7	180.0°	3.8°
C12	N11	C13	H8	60.0°	116.1°
C12	N11	C13	H9	60.0°	123.9°
C3	N4	C5	C6	0.1°	0.0°
N4	C3	C8	C9	180.0°	180.0°
N4	C3	C8	C7	0.2°	0.0°
C3	N4	C5	H10	179.9°	179.9°
C5	N4	C3	C8	0.1°	0.0°
N4	C5	C6	H10	180.0°	179.9°
N4	C5	C6	C7	0.2°	0.0°
N4	C5	C6	H11	179.9°	179.9°
C3	C8	C9	N11	96.9°	125.1°
C3	C8	C9	C7	179.8°	180.0°
C3	C8	C9	O10	85.7°	54.9°
C3	C8	C7	C6	0.3°	0.0°
C3	C8	C7	H12	179.8°	179.9°
C5	C6	C7	C8	0.2°	0.0°
C5	C6	C7	H11	180.0°	180.0°
C5	C6	C7	H12	179.8°	179.9°
C13	N11	C9	C8	179.4°	4.3°
C13	N11	C9	O10	2.1°	175.7°
C13	N11	C12	H4	180.0°	90.0°
C13	N11	C12	H5	60.0°	150.0°
C13	N11	C12	H6	60.0°	30.1°
N11	C13	H7	H8	120.0°	119.9°
N11	C13	H7	H9	120.0°	120.1°
N11	C13	H8	H9	119.9°	120.0°
N11	C9	C8	O10	177.4°	180.0°
N11	C9	C8	C7	83.3°	54.9°
C9	N11	C12	H4	2.0°	89.9°
C9	N11	C12	H5	118.0°	30.0°
C9	N11	C12	H6	122.0°	150.0°
C9	N11	C13	H7	2.0°	176.1°
C9	N11	C13	H8	122.1°	64.0°
C9	N11	C13	H9	118.0°	56.0°
C9	C8	C7	C6	179.9°	180.0°
C9	C8	C7	H12	0.1°	0.1°
C7	C8	C9	O10	94.1°	125.1°
C8	C7	C6	H12	180.0°	179.9°
C8	C7	C6	H11	179.8°	179.9°
C7	C6	C5	H10	179.8°	179.9°
H1	C1	H2	H3	120.0°	120.0°
H4	C12	H5	H6	120.0°	120.0°
H7	C13	H8	H9	120.0°	120.0°
H10	C5	C6	H11	0.2°	0.1°
H11	C6	C7	H12	0.2°	0.0°

249697

PDB entries from 2026-02-25

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