FMO DATABASE

FMODB ID: Z6M1N

Calculation Name: 5EGO-B-Xray372

Preferred Name:

Target Type:

Ligand Name: 5-methyl-2'-deoxy-cytidine-5'-monophosphate

ligand 3-letter code: 5CM

PDB ID: 5EGO

Chain ID: B

ChEMBL ID:

UniProt ID: Q92826

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-383506.975911
FMO2-HF: Nuclear repulsion	357673.017248
FMO2-HF: Total energy	-25833.958663
FMO2-MP2: Total energy	-25912.019194

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:217:ARG)

Summations of interaction energy for fragment #1(B:217:ARG)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
228.44	231.957	0.104	-1.748	-1.872	0.002

Interaction energy analysis for fragmet #1(B:217:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.035 / q_NPA : 1.019

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	219	LYS	1	0.976	0.979	3.083	21.121	24.638	0.104	-1.748	-1.872	0.002
4	B	220	ARG	1	0.975	0.991	4.930	34.280	34.280	0.000	0.000	0.000	0.000
5	B	221	ILE	0	0.028	-0.009	6.085	2.391	2.391	0.000	0.000	0.000	0.000
6	B	222	PRO	0	-0.031	0.003	9.837	-0.405	-0.405	0.000	0.000	0.000	0.000
7	B	223	TYR	0	0.010	0.001	10.595	0.034	0.034	0.000	0.000	0.000	0.000
8	B	224	SER	0	0.079	0.029	14.613	0.767	0.767	0.000	0.000	0.000	0.000
9	B	225	LYS	1	1.026	0.986	18.341	12.850	12.850	0.000	0.000	0.000	0.000
10	B	226	GLY	0	0.025	0.019	20.651	0.304	0.304	0.000	0.000	0.000	0.000
11	B	227	GLN	0	0.046	0.020	16.339	-0.187	-0.187	0.000	0.000	0.000	0.000
12	B	228	LEU	0	-0.036	-0.019	14.795	0.072	0.072	0.000	0.000	0.000	0.000
13	B	229	ARG	1	0.960	0.983	18.607	11.302	11.302	0.000	0.000	0.000	0.000
14	B	230	GLU	-1	-0.804	-0.874	21.470	-11.690	-11.690	0.000	0.000	0.000	0.000
15	B	231	LEU	0	-0.012	-0.007	15.731	0.161	0.161	0.000	0.000	0.000	0.000
16	B	232	GLU	-1	-0.819	-0.911	19.369	-15.094	-15.094	0.000	0.000	0.000	0.000
17	B	233	ARG	1	0.855	0.920	21.511	11.808	11.808	0.000	0.000	0.000	0.000
18	B	234	GLU	-1	-0.755	-0.873	22.470	-11.729	-11.729	0.000	0.000	0.000	0.000
19	B	235	TYR	0	-0.126	-0.106	18.712	-0.270	-0.270	0.000	0.000	0.000	0.000
20	B	236	ALA	0	-0.051	-0.029	22.216	0.087	0.087	0.000	0.000	0.000	0.000
21	B	237	ALA	0	-0.010	0.025	25.382	0.397	0.397	0.000	0.000	0.000	0.000
22	B	238	ASN	0	-0.034	-0.026	24.196	0.679	0.679	0.000	0.000	0.000	0.000
23	B	239	LYS	1	0.967	0.964	21.115	12.116	12.116	0.000	0.000	0.000	0.000
24	B	240	PHE	0	-0.022	-0.014	19.631	-1.166	-1.166	0.000	0.000	0.000	0.000
25	B	241	ILE	0	0.001	0.026	18.480	0.523	0.523	0.000	0.000	0.000	0.000
26	B	242	THR	0	0.100	0.038	21.628	-0.269	-0.269	0.000	0.000	0.000	0.000
27	B	243	LYS	1	0.965	0.954	22.211	12.577	12.577	0.000	0.000	0.000	0.000
28	B	244	ASP	-1	-0.807	-0.892	23.629	-11.277	-11.277	0.000	0.000	0.000	0.000
29	B	245	LYS	1	0.798	0.883	24.157	11.365	11.365	0.000	0.000	0.000	0.000
30	B	246	ARG	1	0.890	0.941	17.342	15.858	15.858	0.000	0.000	0.000	0.000
31	B	247	ARG	1	0.906	0.915	20.334	13.270	13.270	0.000	0.000	0.000	0.000
32	B	248	LYS	1	0.978	0.995	22.589	10.838	10.838	0.000	0.000	0.000	0.000
33	B	249	ILE	0	0.033	0.011	18.923	-0.098	-0.098	0.000	0.000	0.000	0.000
34	B	250	SER	0	-0.067	-0.021	18.021	-0.142	-0.142	0.000	0.000	0.000	0.000
35	B	251	ALA	0	0.039	0.012	19.565	-0.225	-0.225	0.000	0.000	0.000	0.000
36	B	252	ALA	0	-0.013	0.001	22.633	0.071	0.071	0.000	0.000	0.000	0.000
37	B	253	THR	0	-0.074	-0.072	18.151	-0.403	-0.403	0.000	0.000	0.000	0.000
38	B	254	SER	0	0.064	0.048	17.879	-0.234	-0.234	0.000	0.000	0.000	0.000
39	B	255	LEU	0	-0.070	-0.014	13.211	-1.182	-1.182	0.000	0.000	0.000	0.000
40	B	256	SER	0	0.046	0.013	12.045	0.421	0.421	0.000	0.000	0.000	0.000
41	B	257	GLU	-1	-0.712	-0.845	14.330	-15.701	-15.701	0.000	0.000	0.000	0.000
42	B	258	ARG	1	0.971	0.993	7.777	29.275	29.275	0.000	0.000	0.000	0.000
43	B	259	GLN	0	0.050	0.041	9.529	-0.143	-0.143	0.000	0.000	0.000	0.000
44	B	260	ILE	0	0.028	0.027	11.325	-0.818	-0.818	0.000	0.000	0.000	0.000
45	B	261	THR	0	-0.050	-0.020	13.693	1.086	1.086	0.000	0.000	0.000	0.000
46	B	262	ILE	0	-0.001	-0.002	7.551	0.177	0.177	0.000	0.000	0.000	0.000
47	B	263	TRP	0	0.005	0.018	11.052	-0.443	-0.443	0.000	0.000	0.000	0.000
48	B	264	PHE	0	0.033	0.005	12.334	0.330	0.330	0.000	0.000	0.000	0.000
49	B	265	GLN	0	-0.052	-0.025	11.533	-0.827	-0.827	0.000	0.000	0.000	0.000
50	B	266	ASN	0	-0.031	-0.028	8.050	-1.076	-1.076	0.000	0.000	0.000	0.000
51	B	267	ARG	1	0.812	0.926	11.637	15.549	15.549	0.000	0.000	0.000	0.000
52	B	268	ARG	1	0.941	0.964	15.097	17.603	17.603	0.000	0.000	0.000	0.000
53	B	269	VAL	0	-0.038	-0.012	11.902	0.691	0.691	0.000	0.000	0.000	0.000
54	B	270	LYS	1	0.936	0.965	14.782	16.789	16.789	0.000	0.000	0.000	0.000
55	B	271	GLU	-1	-0.771	-0.856	16.025	-12.950	-12.950	0.000	0.000	0.000	0.000
56	B	272	LYS	1	0.999	0.997	17.937	16.418	16.418	0.000	0.000	0.000	0.000
57	B	273	LYS	1	0.911	0.965	13.214	20.391	20.391	0.000	0.000	0.000	0.000
58	B	274	VAL	0	0.015	0.011	19.350	0.001	0.001	0.000	0.000	0.000	0.000
59	B	275	LEU	0	-0.023	0.004	21.939	0.688	0.688	0.000	0.000	0.000	0.000
60	B	276	ALA	0	-0.054	-0.039	23.452	-0.208	-0.208	0.000	0.000	0.000	0.000
61	B	277	LYS	1	0.946	0.977	25.318	11.243	11.243	0.000	0.000	0.000	0.000
62	B	278	VAL	0	0.044	0.017	27.669	-0.320	-0.320	0.000	0.000	0.000	0.000
63	B	279	LYS	1	1.002	1.023	24.458	11.764	11.764	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:217:ARG)