. Author manuscript; available in PMC: 2022 Jun 8.

Published in final edited form as: J Chem Theory Comput. 2021 May 19;17(6):3554–3570. doi: 10.1021/acs.jctc.1c00254

Table 5.

Selected average non-bond distances (Å) in MD simulations of proteins with the nonstandard amino acids.

Residue	^aAtom pair	X-Ray str.	^b,c MD simulation	^cAbs. diff.
MDO	N2_MDO66-O_Val61	2.89	3.04 (0.22)/2.84 (0.12)	0.15/0.05
MDO	O _MDO66-NE2_Gln94	4.19	4.06 (0.65)/3.98 (1.07)	0.13/0.21
MDO	O2 _MDO66-NH2_Arg96	2.75	2.91 (0.25)/2.88 (0.21)	0.16/0.13
4FW	FE3_4FW8-N_Asn10	3.27	3.45 (0.31)/3.43 (0.28)	0.18/0.16
4FW	FE3_4FW8-N_Phe9	2.94	3.18 (0.22)/3.13 (0.18)	0.24/0.19
CSO	N_CSO29-O_Arg25	3.05	3.04 (0.21)/3.04 (0.20)	0.01/0.01
CSO	O_CSO29-N_Ala33	2.93	2.95 (0.19)/2.98 (0.17)	0.02/0.05

Protein atoms (left) are labeled by their amino acid;

values in parenthesis are the RMS fluctuations;

MD simulations were performed with the initial and optimized parameters, respectively.