FMO DATABASE

FMODB ID: R93V8

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	OptAll
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	-383758.622892
FMO2-HF: Nuclear repulsion	357924.399957
FMO2-HF: Total energy	-25834.222936
FMO2-MP2: Total energy	-25912.255104

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.
226.375	229.513	0.189	-1.607	-1.72	-0.003

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 : 1.040 / q_NPA : 1.022

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	0.983	0.984	2.941	20.350	23.488	0.189	-1.607	-1.720	-0.003
4	B	220	ARG	1	0.975	0.983	5.043	34.087	34.087	0.000	0.000	0.000	0.000
5	B	221	ILE	0	0.031	0.002	6.334	2.225	2.225	0.000	0.000	0.000	0.000
6	B	222	PRO	0	-0.027	0.003	9.975	-1.067	-1.067	0.000	0.000	0.000	0.000
7	B	223	TYR	0	0.007	-0.008	10.485	0.025	0.025	0.000	0.000	0.000	0.000
8	B	224	SER	0	0.070	0.020	14.722	0.688	0.688	0.000	0.000	0.000	0.000
9	B	225	LYS	1	1.010	0.975	18.420	12.883	12.883	0.000	0.000	0.000	0.000
10	B	226	GLY	0	0.036	0.032	20.881	0.338	0.338	0.000	0.000	0.000	0.000
11	B	227	GLN	0	0.057	0.029	16.632	-0.064	-0.064	0.000	0.000	0.000	0.000
12	B	228	LEU	0	-0.035	-0.019	15.087	-0.092	-0.092	0.000	0.000	0.000	0.000
13	B	229	ARG	1	0.970	0.994	18.907	11.159	11.159	0.000	0.000	0.000	0.000
14	B	230	GLU	-1	-0.799	-0.863	21.758	-11.623	-11.623	0.000	0.000	0.000	0.000
15	B	231	LEU	0	-0.024	-0.017	15.925	0.119	0.119	0.000	0.000	0.000	0.000
16	B	232	GLU	-1	-0.788	-0.891	19.375	-15.239	-15.239	0.000	0.000	0.000	0.000
17	B	233	ARG	1	0.847	0.906	21.301	11.849	11.849	0.000	0.000	0.000	0.000
18	B	234	GLU	-1	-0.780	-0.877	22.525	-11.743	-11.743	0.000	0.000	0.000	0.000
19	B	235	TYR	0	-0.079	-0.081	18.753	-0.160	-0.160	0.000	0.000	0.000	0.000
20	B	236	ALA	0	-0.060	-0.033	22.399	0.139	0.139	0.000	0.000	0.000	0.000
21	B	237	ALA	0	0.008	0.036	25.584	0.399	0.399	0.000	0.000	0.000	0.000
22	B	238	ASN	0	-0.003	-0.007	24.161	0.698	0.698	0.000	0.000	0.000	0.000
23	B	239	LYS	1	0.957	0.963	21.693	12.106	12.106	0.000	0.000	0.000	0.000
24	B	240	PHE	0	-0.026	-0.026	19.717	-1.079	-1.079	0.000	0.000	0.000	0.000
25	B	241	ILE	0	0.021	0.036	18.333	0.509	0.509	0.000	0.000	0.000	0.000
26	B	242	THR	0	0.111	0.049	21.585	-0.456	-0.456	0.000	0.000	0.000	0.000
27	B	243	LYS	1	0.986	0.979	22.645	12.284	12.284	0.000	0.000	0.000	0.000
28	B	244	ASP	-1	-0.797	-0.898	23.677	-11.410	-11.410	0.000	0.000	0.000	0.000
29	B	245	LYS	1	0.766	0.865	24.414	11.523	11.523	0.000	0.000	0.000	0.000
30	B	246	ARG	1	0.843	0.914	17.382	15.824	15.824	0.000	0.000	0.000	0.000
31	B	247	ARG	1	0.910	0.915	20.733	13.257	13.257	0.000	0.000	0.000	0.000
32	B	248	LYS	1	0.944	0.980	22.756	10.869	10.869	0.000	0.000	0.000	0.000
33	B	249	ILE	0	0.031	0.011	19.229	-0.024	-0.024	0.000	0.000	0.000	0.000
34	B	250	SER	0	-0.078	-0.036	17.841	-0.248	-0.248	0.000	0.000	0.000	0.000
35	B	251	ALA	0	0.042	0.017	19.553	-0.218	-0.218	0.000	0.000	0.000	0.000
36	B	252	ALA	0	0.002	0.007	22.600	0.020	0.020	0.000	0.000	0.000	0.000
37	B	253	THR	0	-0.064	-0.058	18.530	-0.371	-0.371	0.000	0.000	0.000	0.000
38	B	254	SER	0	0.055	0.033	17.952	-0.414	-0.414	0.000	0.000	0.000	0.000
39	B	255	LEU	0	-0.071	-0.005	13.303	-1.115	-1.115	0.000	0.000	0.000	0.000
40	B	256	SER	0	0.062	0.013	12.095	0.396	0.396	0.000	0.000	0.000	0.000
41	B	257	GLU	-1	-0.713	-0.852	14.329	-15.593	-15.593	0.000	0.000	0.000	0.000
42	B	258	ARG	1	0.968	1.000	8.036	29.144	29.144	0.000	0.000	0.000	0.000
43	B	259	GLN	0	0.060	0.053	9.659	-0.383	-0.383	0.000	0.000	0.000	0.000
44	B	260	ILE	0	0.045	0.035	11.266	-0.785	-0.785	0.000	0.000	0.000	0.000
45	B	261	THR	0	-0.037	-0.020	13.697	0.983	0.983	0.000	0.000	0.000	0.000
46	B	262	ILE	0	0.010	0.005	7.460	0.105	0.105	0.000	0.000	0.000	0.000
47	B	263	TRP	0	-0.009	0.007	10.963	-0.288	-0.288	0.000	0.000	0.000	0.000
48	B	264	PHE	0	0.033	0.010	12.534	0.463	0.463	0.000	0.000	0.000	0.000
49	B	265	GLN	0	-0.049	-0.024	11.671	-0.491	-0.491	0.000	0.000	0.000	0.000
50	B	266	ASN	0	-0.037	-0.025	8.169	-1.214	-1.214	0.000	0.000	0.000	0.000
51	B	267	ARG	1	0.843	0.920	11.770	15.251	15.251	0.000	0.000	0.000	0.000
52	B	268	ARG	1	0.946	0.975	15.449	17.689	17.689	0.000	0.000	0.000	0.000
53	B	269	VAL	0	-0.028	-0.008	11.587	0.715	0.715	0.000	0.000	0.000	0.000
54	B	270	LYS	1	0.836	0.903	14.482	16.559	16.559	0.000	0.000	0.000	0.000
55	B	271	GLU	-1	-0.771	-0.846	15.902	-12.989	-12.989	0.000	0.000	0.000	0.000
56	B	272	LYS	1	0.974	0.974	17.696	16.525	16.525	0.000	0.000	0.000	0.000
57	B	273	LYS	1	0.921	0.962	13.016	20.469	20.469	0.000	0.000	0.000	0.000
58	B	274	VAL	0	0.015	0.018	19.256	0.206	0.206	0.000	0.000	0.000	0.000
59	B	275	LEU	0	-0.006	0.023	21.854	0.620	0.620	0.000	0.000	0.000	0.000
60	B	276	ALA	0	-0.030	-0.012	23.536	0.067	0.067	0.000	0.000	0.000	0.000
61	B	277	LYS	1	0.897	0.933	25.391	11.415	11.415	0.000	0.000	0.000	0.000
62	B	278	VAL	0	0.043	0.012	27.727	-0.347	-0.347	0.000	0.000	0.000	0.000
63	B	279	LYS	1	1.007	1.028	24.312	11.830	11.830	0.000	0.000	0.000	0.000

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