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SummaryGeometryRelated PDB entries

5DM

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
OC1doub1.21Å1.23Å
C1CA1sing1.51Å1.52Å
N1CA1sing1.47Å1.46Å
N1Csing1.47Å1.45Å
N1HN1sing1.01Å1.00Å
SDCEsing1.81Å1.77Å
SDCG1sing1.81Å1.80Å
CEHEsing1.09Å1.10Å
CEHEAsing1.09Å1.10Å
CEHEBsing1.09Å1.10Å
CA1CB1sing1.53Å1.53Å
CA1HA1sing1.09Å1.10Å
CB1CG1sing1.53Å1.52Å
CB1HB1sing1.09Å1.10Å
CB1HB1Asing1.09Å1.10Å
CG1HG1sing1.09Å1.10Å
CG1HG1Asing1.09Å1.10Å
CCAsing1.53Å1.53Å
CHsing1.09Å1.10Å
CHAsing1.09Å1.10Å
NCAsing1.47Å1.45Å
NHNsing1.01Å1.00Å
NHNAsing1.01Å1.00Å
CACBsing1.53Å1.51Å
CAHAAsing1.09Å1.10Å
CBCGsing1.51Å1.50Å
CBHBsing1.09Å1.10Å
CBHBAsing1.09Å1.10Å
CGCD1doub1.38Å1.39ÅAromatic
CGCD2sing1.38Å1.38ÅAromatic
CZCE1doub1.38Å1.38ÅAromatic
CZCE2sing1.38Å1.38ÅAromatic
CZHZsing1.08Å1.08Å
CD1CE1sing1.38Å1.38ÅAromatic
CD1HD1sing1.08Å1.08Å
CD2CE2doub1.38Å1.38ÅAromatic
CD2HD2sing1.08Å1.08Å
CE1HE1sing1.08Å1.08Å
CE2HE2sing1.08Å1.08Å
C1OXTsing1.34Å39.20Å
OXTHXTsing0.97Å0.00Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
OC1CA1120.5°120.0°
OC1OXT121.8°120.0°
C1CA1N1110.9°109.5°
C1CA1CB1109.6°109.5°
C1CA1HA1108.3°109.4°
CA1C1OXT3.4°120.0°
CA1N1C110.9°111.0°
CA1N1HN1109.1°111.0°
N1CA1CB1110.4°109.5°
N1CA1HA1109.1°109.5°
CN1HN1109.1°111.0°
N1CCA110.4°109.5°
N1CH109.2°109.4°
N1CHA109.2°109.5°
CESDCG1102.6°103.0°
SDCEHE109.5°109.5°
SDCEHEA109.5°109.5°
SDCEHEB109.5°109.5°
SDCG1CB1114.5°109.5°
SDCG1HG1108.2°109.5°
SDCG1HG1A108.2°109.4°
HECEHEA109.4°109.5°
HECEHEB109.5°109.5°
HEACEHEB109.5°109.4°
CB1CA1HA1108.3°109.4°
CA1CB1CG1114.4°109.5°
CA1CB1HB1108.2°109.5°
CA1CB1HB1A108.2°109.5°
CG1CB1HB1108.2°109.4°
CG1CB1HB1A108.2°109.4°
CB1CG1HG1108.2°109.5°
CB1CG1HG1A108.2°109.5°
HB1CB1HB1A109.5°109.5°
HG1CG1HG1A109.4°109.5°
CACH109.2°109.5°
CACHA109.3°109.5°
CCAN112.2°109.4°
CCACB128.7°109.5°
CCAHAA98.4°109.4°
HCHA109.5°109.4°
CANHN109.5°111.0°
CANHNA109.5°111.0°
NCACB112.5°109.5°
NCAHAA98.8°109.5°
HNNHNA109.5°111.0°
CBCAHAA98.5°109.5°
CACBCG115.3°109.5°
CACBHB108.0°109.5°
CACBHBA108.0°109.5°
CGCBHB108.0°109.5°
CGCBHBA108.0°109.4°
CBCGCD1120.5°120.0°
CBCGCD2121.1°120.0°
HBCBHBA109.5°109.4°
CD1CGCD2118.4°120.0°
CGCD1CE1121.0°120.0°
CGCD1HD1119.5°120.0°
CGCD2CE2121.1°120.0°
CGCD2HD2119.5°120.0°
CE1CZCE2119.7°120.0°
CE1CZHZ120.2°120.0°
CZCE1CD1119.9°120.0°
CZCE1HE1120.0°120.0°
CE2CZHZ120.2°120.0°
CZCE2CD2119.8°120.0°
CZCE2HE2120.1°120.1°
CE1CD1HD1119.5°120.0°
CD1CE1HE1120.0°120.0°
CE2CD2HD2119.4°120.0°
CD2CE2HE2120.1°120.0°
C1OXTHXT90.0°117.0°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
OC1CA1OXT113.7°179.8°
OC1CA1N1135.3°0.1°
OC1CA1CB1102.5°120.0°
OC1CA1HA115.5°120.1°
OC1OXTHXT90.0°0.0°
C1CA1N1CB1121.8°120.0°
C1CA1N1HA1119.3°120.0°
C1CA1N1C128.9°85.0°
C1CA1N1HN1110.9°151.1°
C1CA1CB1HA1118.0°119.9°
C1CA1CB1CG1105.5°175.0°
C1CA1CB1HB115.2°55.0°
C1CA1CB1HB1A133.8°65.1°
CA1C1OXTHXT90.0°179.8°
CA1N1CHN1120.2°123.9°
N1CA1CB1HA1119.4°120.0°
N1CA1CB1CG1131.9°65.0°
N1CA1CB1HB1107.3°175.0°
N1CA1CB1HB1A11.2°55.0°
CA1N1CCA75.8°180.0°
CA1N1CH44.3°60.0°
CA1N1CHA164.0°60.0°
N1CA1C1OXT111.1°179.7°
CN1CA1CB1109.3°155.0°
CN1CA1HA19.6°35.0°
N1CCAH120.1°120.0°
N1CCAHA120.1°120.0°
N1CHHA119.6°120.0°
N1CCAN130.3°55.0°
N1CCACB80.9°175.0°
N1CCAHAA27.1°65.0°
HN1N1CA1CB110.9°31.0°
HN1N1CA1HA1129.8°88.9°
HN1N1CCA163.9°56.1°
HN1N1CH75.9°176.1°
HN1N1CHA43.8°63.9°
SDCEHEHEA120.0°120.0°
SDCEHEHEB120.0°120.0°
SDCEHEAHEB120.0°120.0°
CESDCG1CB131.3°180.0°
CESDCG1HG1152.0°60.0°
CESDCG1HG1A89.5°60.0°
CG1SDCEHE180.0°60.0°
CG1SDCEHEA60.0°60.0°
CG1SDCEHEB60.0°180.0°
SDCG1CB1CA1101.1°180.0°
SDCG1CB1HG1120.8°120.0°
SDCG1CB1HG1A120.8°120.0°
SDCG1CB1HB119.7°60.0°
SDCG1CB1HB1A138.2°60.0°
SDCG1HG1HG1A117.7°120.0°
HECEHEAHEB120.0°120.0°
CA1CB1CG1HB1120.7°120.0°
CA1CB1CG1HB1A120.7°120.0°
CA1CB1HB1HB1A117.7°120.1°
CA1CB1CG1HG119.7°60.0°
CA1CB1CG1HG1A138.2°60.0°
CB1CA1C1OXT11.2°60.2°
HA1CA1CB1CG112.5°55.0°
HA1CA1CB1HB1133.2°64.9°
HA1CA1CB1HB1A108.2°175.0°
HA1CA1C1OXT129.1°59.7°
CG1CB1HB1HB1A117.7°120.0°
CB1CG1HG1HG1A117.7°120.0°
HB1CB1CG1HG1140.4°60.0°
HB1CB1CG1HG1A101.1°180.0°
HB1ACB1CG1HG1101.0°180.0°
HB1ACB1CG1HG1A17.4°60.0°
CACHHA119.6°120.0°
CCANCB154.0°120.0°
CCANHAA102.9°119.9°
CCANHN180.0°60.1°
CCANHNA60.0°176.0°
CCACBHAA108.0°120.0°
CCACBCG145.9°175.0°
CCACBHB25.0°65.0°
CCACBHBA93.3°55.0°
HCCAN10.2°65.0°
HCCACB159.0°55.0°
HCCAHAA93.0°175.0°
HACCAN109.6°175.0°
HACCACB39.2°65.0°
HACCAHAA147.3°55.1°
CANHNHNA120.0°123.9°
NCACBHAA103.3°120.0°
NCACBCG2.8°65.0°
NCACBHB123.7°55.0°
NCACBHBA118.0°175.0°
HNNCACB26.0°60.0°
HNNCAHAA77.1°180.0°
HNANCACB146.0°64.0°
HNANCAHAA42.9°56.1°
CACBCGHB120.8°120.0°
CACBCGHBA120.8°120.1°
CACBHBHBA117.4°120.1°
CACBCGCD1104.9°90.0°
CACBCGCD276.7°90.3°
HAACACBCG106.1°55.0°
HAACACBHB133.0°175.0°
HAACACBHBA14.7°65.0°
CGCBHBHBA117.4°119.9°
CBCGCD1CD2178.5°179.7°
CBCGCD1CE1179.2°180.0°
CBCGCD1HD10.8°0.0°
CBCGCD2CE2179.2°180.0°
CBCGCD2HD20.9°0.1°
HBCBCGCD116.0°30.0°
HBCBCGCD2162.5°149.6°
HBACBCGCD1134.3°149.9°
HBACBCGCD244.2°29.7°
CGCD1CE1CZ0.5°0.0°
CGCD1CE1HD1180.0°180.0°
CD1CGCD2CE20.7°0.4°
CD1CGCD2HD2179.4°179.7°
CGCD1CE1HE1179.5°179.7°
CGCD2CE2CZ0.5°0.1°
CD2CGCD1CE10.7°0.3°
CD2CGCD1HD1179.3°179.7°
CGCD2CE2HD2180.0°179.9°
CGCD2CE2HE2179.5°179.6°
CE1CZCE2HZ180.0°179.7°
CZCE1CD1HE1180.0°179.7°
CZCE1CD1HD1179.5°180.0°
CE1CZCE2CD20.4°0.2°
CE1CZCE2HE2179.6°180.0°
CE2CZCE1CD10.4°0.3°
CZCE2CD2HE2180.0°179.7°
CZCE2CD2HD2179.5°180.0°
CE2CZCE1HE1179.6°180.0°
HZCZCE1CD1179.6°180.0°
HZCZCE2CD2179.6°179.9°
HZCZCE1HE10.4°0.3°
HZCZCE2HE20.4°0.3°
HD1CD1CE1HE10.5°0.3°
HD2CD2CE2HE20.5°0.3°

248636

PDB entries from 2026-02-04

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