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Summary Geometry Related PDB entries

V99

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C5	C4	sing	1.53Å	1.52Å
C4	S	sing	1.81Å	1.82Å
S	C3	sing	1.76Å	1.69Å
N1	C3	doub	1.31Å	1.33Å	Aromatic
N1	N	sing	1.29Å	1.33Å	Aromatic
C3	N2	sing	1.36Å	1.38Å	Aromatic
N	C2	doub	1.30Å	1.35Å	Aromatic
N2	C2	sing	1.37Å	1.39Å	Aromatic
N2	N3	sing	1.37Å	1.38Å
C2	C1	sing	1.51Å	1.48Å
C1	C	sing	1.53Å	1.51Å
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C5	H3	sing	1.09Å	1.10Å
C5	H4	sing	1.09Å	1.10Å
C5	H5	sing	1.09Å	1.10Å
N3	H6	sing	1.01Å	1.00Å
N3	H7	sing	1.01Å	1.00Å
C4	H8	sing	1.09Å	1.10Å
C4	H9	sing	1.09Å	1.10Å
C	H10	sing	1.09Å	1.10Å
C	H11	sing	1.09Å	1.10Å
C	H12	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C5	C4	S	102.8°	109.5°
C4	C5	H3	109.5°	109.5°
C4	C5	H4	109.4°	109.5°
C4	C5	H5	109.5°	109.5°
C5	C4	H8	111.1°	109.5°
C5	C4	H9	111.1°	109.5°
C4	S	C3	103.6°	100.0°
S	C4	H8	111.1°	109.5°
S	C4	H9	111.1°	109.5°
S	C3	N1	128.8°	126.4°
S	C3	N2	122.3°	126.5°
C3	N1	N	108.5°	109.8°
N1	C3	N2	108.7°	107.1°
N1	N	C2	109.9°	110.0°
C3	N2	C2	106.3°	105.7°
C3	N2	N3	129.2°	127.2°
N	C2	N2	106.6°	107.3°
N	C2	C1	129.7°	126.3°
C2	N2	N3	124.4°	127.1°
N2	C2	C1	123.6°	126.3°
N2	N3	H6	109.5°	111.0°
N2	N3	H7	109.5°	111.0°
C2	C1	C	109.5°	109.5°
C2	C1	H1	109.5°	109.5°
C2	C1	H2	109.5°	109.5°
C	C1	H1	109.5°	109.4°
C	C1	H2	109.4°	109.5°
C1	C	H10	109.5°	109.4°
C1	C	H11	109.5°	109.5°
C1	C	H12	109.4°	109.5°
H1	C1	H2	109.5°	109.5°
H3	C5	H4	109.5°	109.5°
H3	C5	H5	109.5°	109.5°
H4	C5	H5	109.5°	109.5°
H6	N3	H7	109.5°	111.0°
H8	C4	H9	109.5°	109.5°
H10	C	H11	109.4°	109.5°
H10	C	H12	109.5°	109.5°
H11	C	H12	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C5	C4	S	H8	118.9°	120.0°
C5	C4	S	H9	118.9°	120.0°
C5	C4	S	C3	97.8°	180.0°
C4	C5	H3	H4	120.0°	120.0°
C4	C5	H3	H5	120.0°	120.0°
C4	C5	H4	H5	120.0°	120.0°
C5	C4	H8	H9	123.1°	120.0°
C4	S	C3	N1	9.1°	0.1°
C4	S	C3	N2	176.1°	180.0°
S	C4	C5	H3	180.0°	60.0°
S	C4	C5	H4	60.0°	180.0°
S	C4	C5	H5	60.0°	60.0°
S	C4	H8	H9	123.1°	120.0°
S	C3	N1	N2	175.4°	179.9°
S	C3	N1	N	175.0°	179.9°
S	C3	N2	C2	175.2°	179.9°
S	C3	N2	N3	8.0°	0.0°
C3	S	C4	H8	143.2°	60.0°
C3	S	C4	H9	21.1°	60.0°
C3	N1	N	C2	0.1°	0.0°
N1	C3	N2	C2	0.5°	0.0°
N1	C3	N2	N3	176.3°	179.9°
N	N1	C3	N2	0.4°	0.0°
N1	N	C2	N2	0.3°	0.0°
N1	N	C2	C1	179.3°	180.0°
C3	N2	C2	N	0.5°	0.0°
C3	N2	C2	N3	177.0°	179.9°
C3	N2	C2	C1	179.1°	180.0°
C3	N2	N3	H6	180.0°	90.0°
C3	N2	N3	H7	60.0°	34.1°
N	C2	N2	C1	179.6°	180.0°
N	C2	N2	N3	176.5°	179.9°
N	C2	C1	C	121.6°	89.9°
N	C2	C1	H1	118.4°	30.0°
N	C2	C1	H2	1.6°	150.0°
N2	C2	C1	C	58.9°	90.0°
N2	C2	C1	H1	61.1°	150.0°
N2	C2	C1	H2	178.9°	30.0°
C2	N2	N3	H6	3.8°	89.9°
C2	N2	N3	H7	116.2°	146.0°
N3	N2	C2	C1	3.9°	0.1°
N2	N3	H6	H7	120.0°	124.0°
C2	C1	C	H1	120.0°	120.0°
C2	C1	C	H2	120.0°	120.1°
C2	C1	H1	H2	120.0°	120.0°
C2	C1	C	H10	180.0°	60.0°
C2	C1	C	H11	60.0°	59.9°
C2	C1	C	H12	60.0°	180.0°
C	C1	H1	H2	120.0°	120.0°
C1	C	H10	H11	120.0°	120.0°
C1	C	H10	H12	120.0°	120.0°
C1	C	H11	H12	120.0°	120.0°
H1	C1	C	H10	60.0°	180.0°
H1	C1	C	H11	180.0°	60.0°
H1	C1	C	H12	60.0°	60.0°
H2	C1	C	H10	60.0°	60.0°
H2	C1	C	H11	60.0°	180.0°
H2	C1	C	H12	180.0°	59.9°
H3	C5	H4	H5	120.0°	120.0°
H3	C5	C4	H8	61.1°	180.0°
H3	C5	C4	H9	61.1°	60.0°
H4	C5	C4	H8	58.9°	60.0°
H4	C5	C4	H9	178.9°	60.0°
H5	C5	C4	H8	178.9°	60.0°
H5	C5	C4	H9	58.9°	180.0°
H10	C	H11	H12	120.0°	120.0°

225681

PDB entries from 2024-10-02

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