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Summary Geometry Related PDB entries

PBY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C11	N14	doub	1.32Å	1.35Å	Aromatic
C11	N7	sing	1.32Å	1.35Å	Aromatic
N14	C10	sing	1.33Å	1.35Å	Aromatic
N7	C3	doub	1.33Å	1.35Å	Aromatic
C10	N15	sing	1.39Å	1.35Å
C10	C6	doub	1.39Å	1.40Å	Aromatic
C3	C6	sing	1.39Å	1.40Å	Aromatic
C3	N1	sing	1.39Å	1.36Å
C5	C9	doub	1.38Å	1.40Å	Aromatic
C5	C2	sing	1.39Å	1.40Å	Aromatic
N1	C2	sing	1.40Å	1.36Å
C9	C12	sing	1.38Å	1.40Å	Aromatic
C2	C4	doub	1.39Å	1.40Å	Aromatic
C12	C8	doub	1.38Å	1.40Å	Aromatic
C4	C8	sing	1.38Å	1.40Å	Aromatic
C8	CL13	sing	1.74Å	1.75Å
C11	H1	sing	1.08Å	1.08Å
C12	H2	sing	1.08Å	1.08Å
C4	H3	sing	1.08Å	1.08Å
C5	H4	sing	1.08Å	1.08Å
C6	H5	sing	1.08Å	1.08Å
C9	H6	sing	1.08Å	1.08Å
N1	H7	sing	0.97Å	1.00Å
N15	H8	sing	0.97Å	1.00Å
N15	H9	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N14	C11	N7	120.6°	121.9°
C11	N14	C10	120.8°	120.8°
N14	C11	H1	119.7°	119.0°
C11	N7	C3	121.6°	120.9°
N7	C11	H1	119.7°	119.0°
N14	C10	N15	119.3°	120.5°
N14	C10	C6	119.3°	119.1°
N7	C3	C6	118.4°	119.0°
N7	C3	N1	121.7°	120.5°
N15	C10	C6	121.4°	120.4°
C10	N15	H8	109.5°	120.0°
C10	N15	H9	109.5°	120.0°
C10	C6	C3	119.2°	118.2°
C10	C6	H5	120.4°	120.9°
C6	C3	N1	119.9°	120.4°
C3	C6	H5	120.4°	120.8°
C3	N1	C2	124.9°	120.0°
C3	N1	H7	117.6°	120.1°
C9	C5	C2	120.8°	120.0°
C5	C9	C12	120.0°	120.1°
C9	C5	H4	119.6°	120.0°
C5	C9	H6	120.0°	120.0°
C5	C2	N1	122.4°	120.1°
C5	C2	C4	118.8°	119.8°
C2	C5	H4	119.6°	120.0°
N1	C2	C4	118.8°	120.1°
C2	N1	H7	117.5°	120.0°
C9	C12	C8	119.7°	120.1°
C9	C12	H2	120.1°	119.9°
C12	C9	H6	120.0°	120.0°
C2	C4	C8	120.6°	119.9°
C2	C4	H3	119.7°	120.1°
C12	C8	C4	120.2°	120.0°
C12	C8	CL13	119.8°	120.0°
C8	C12	H2	120.2°	119.9°
C4	C8	CL13	120.0°	120.0°
C8	C4	H3	119.7°	120.0°
H8	N15	H9	109.5°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N14	C11	N7	H1	180.0°	179.6°
N14	C11	N7	C3	0.1°	0.1°
C11	N14	C10	N15	180.0°	179.9°
C11	N14	C10	C6	0.0°	0.6°
N7	C11	N14	C10	0.1°	0.4°
C11	N7	C3	C6	0.1°	0.0°
C11	N7	C3	N1	179.9°	179.7°
N14	C10	N15	C6	180.0°	179.4°
N14	C10	C6	C3	0.0°	0.5°
C10	N14	C11	H1	179.9°	180.0°
N14	C10	C6	H5	180.0°	179.4°
N14	C10	N15	H8	0.0°	179.4°
N14	C10	N15	H9	120.0°	0.6°
N7	C3	C6	C10	0.1°	0.2°
N7	C3	C6	N1	180.0°	179.7°
N7	C3	N1	C2	5.6°	5.7°
C3	N7	C11	H1	179.9°	179.7°
N7	C3	C6	H5	180.0°	179.7°
N7	C3	N1	H7	174.4°	174.2°
N15	C10	C6	C3	180.0°	180.0°
N15	C10	C6	H5	0.1°	0.0°
C10	N15	H8	H9	120.0°	180.0°
C10	C6	C3	H5	180.0°	180.0°
C10	C6	C3	N1	180.0°	180.0°
C6	C10	N15	H8	179.9°	0.0°
C6	C10	N15	H9	60.0°	180.0°
C6	C3	N1	C2	174.5°	174.0°
C6	C3	N1	H7	5.5°	6.0°
C3	N1	C2	C5	44.3°	35.9°
C3	N1	C2	H7	180.0°	180.0°
C3	N1	C2	C4	136.5°	144.4°
N1	C3	C6	H5	0.0°	0.0°
C9	C5	C2	H4	180.0°	180.0°
C9	C5	C2	N1	179.7°	179.7°
C5	C9	C12	H6	180.0°	180.0°
C9	C5	C2	C4	0.6°	0.0°
C5	C9	C12	C8	0.1°	0.0°
C5	C9	C12	H2	179.9°	180.0°
C5	C2	N1	C4	179.2°	179.7°
C2	C5	C9	C12	0.3°	0.0°
C5	C2	C4	C8	0.5°	0.0°
C5	C2	C4	H3	179.5°	180.0°
C2	C5	C9	H6	179.7°	180.0°
C5	C2	N1	H7	135.7°	144.1°
N1	C2	C4	C8	179.7°	179.7°
N1	C2	C4	H3	0.3°	0.3°
N1	C2	C5	H4	0.3°	0.2°
C9	C12	C8	H2	180.0°	180.0°
C9	C12	C8	C4	0.0°	0.0°
C9	C12	C8	CL13	180.0°	180.0°
C12	C9	C5	H4	179.6°	180.0°
C2	C4	C8	C12	0.2°	0.0°
C2	C4	C8	H3	180.0°	179.9°
C2	C4	C8	CL13	179.8°	180.0°
C4	C2	C5	H4	179.4°	180.0°
C4	C2	N1	H7	43.5°	35.6°
C12	C8	C4	CL13	180.0°	179.9°
C12	C8	C4	H3	179.8°	180.0°
C8	C12	C9	H6	180.0°	180.0°
C4	C8	C12	H2	180.0°	180.0°
CL13	C8	C12	H2	0.0°	0.0°
CL13	C8	C4	H3	0.2°	0.1°
H2	C12	C9	H6	0.1°	0.0°
H4	C5	C9	H6	0.3°	0.0°

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PDB entries from 2026-02-04

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