FMO DATABASE

FMODB ID: V5ML1

Calculation Name: 5T01-A-Xray372

Preferred Name: Proto-oncogene c-JUN

Target Type: SINGLE PROTEIN

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

ligand 3-letter code: 5CM

PDB ID: 5T01

Chain ID: A

ChEMBL ID: CHEMBL4977

UniProt ID: P05412

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	OptH
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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-270508.261969
FMO2-HF: Nuclear repulsion	244422.168407
FMO2-HF: Total energy	-26086.093562
FMO2-MP2: Total energy	-26160.148872

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(A:252:HIS)

Summations of interaction energy for fragment #1(A:252:HIS)

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.
-0.114	2.697	1.025	-1.476	-2.359	0.003

Interaction energy analysis for fragmet #1(A:252:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.029

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

Sort

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	A	254	LYS	1	1.068	1.021	2.944	-1.205	1.347	1.027	-1.465	-2.114	0.003
4	A	255	ALA	0	0.081	0.029	4.363	1.273	1.462	-0.001	-0.011	-0.177	0.000
5	A	256	GLU	-1	-0.885	-0.947	5.365	-0.291	-0.221	-0.001	0.000	-0.068	0.000
6	A	257	ARG	1	0.970	0.991	7.638	0.021	0.021	0.000	0.000	0.000	0.000
7	A	258	LYS	1	0.999	0.990	6.094	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	259	ARG	1	0.957	0.995	8.632	1.113	1.113	0.000	0.000	0.000	0.000
9	A	260	MET	0	0.029	0.008	10.978	0.172	0.172	0.000	0.000	0.000	0.000
10	A	261	ARG	1	0.950	0.964	9.977	-0.699	-0.699	0.000	0.000	0.000	0.000
11	A	262	ASN	0	0.033	0.004	11.077	0.258	0.258	0.000	0.000	0.000	0.000
12	A	263	ARG	1	0.980	1.005	13.977	0.317	0.317	0.000	0.000	0.000	0.000
13	A	264	ILE	0	0.000	-0.002	16.153	0.037	0.037	0.000	0.000	0.000	0.000
14	A	265	ALA	0	0.001	0.005	15.802	0.014	0.014	0.000	0.000	0.000	0.000
15	A	266	ALA	0	0.021	0.004	17.899	0.005	0.005	0.000	0.000	0.000	0.000
16	A	267	SER	0	-0.039	-0.020	19.898	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	268	LYS	1	0.978	0.978	19.031	-0.262	-0.262	0.000	0.000	0.000	0.000
18	A	269	SER	0	-0.040	-0.012	21.888	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	270	ARG	1	0.984	0.992	21.766	0.003	0.003	0.000	0.000	0.000	0.000
20	A	271	LYS	1	0.981	1.004	26.073	-0.106	-0.106	0.000	0.000	0.000	0.000
21	A	272	ARG	1	1.003	0.995	21.344	-0.287	-0.287	0.000	0.000	0.000	0.000
22	A	273	LYS	1	0.921	0.962	24.637	-0.119	-0.119	0.000	0.000	0.000	0.000
23	A	274	LEU	0	0.045	0.021	29.542	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	275	GLU	-1	-0.880	-0.945	29.849	0.142	0.142	0.000	0.000	0.000	0.000
25	A	276	ARG	1	0.936	0.966	30.856	-0.157	-0.157	0.000	0.000	0.000	0.000
26	A	277	ILE	0	0.010	0.008	33.447	0.000	0.000	0.000	0.000	0.000	0.000
27	A	278	ALA	0	0.070	0.043	35.803	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	279	ARG	1	0.931	0.966	35.326	-0.130	-0.130	0.000	0.000	0.000	0.000
29	A	280	LEU	0	-0.006	-0.010	36.570	0.000	0.000	0.000	0.000	0.000	0.000
30	A	281	GLU	-1	-0.916	-0.952	39.399	0.052	0.052	0.000	0.000	0.000	0.000
31	A	282	GLU	-1	-0.920	-0.961	41.174	0.064	0.064	0.000	0.000	0.000	0.000
32	A	283	LYS	1	0.915	0.967	41.484	-0.109	-0.109	0.000	0.000	0.000	0.000
33	A	284	VAL	0	0.018	0.000	43.444	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	285	LYS	1	0.954	0.982	45.604	-0.052	-0.052	0.000	0.000	0.000	0.000
35	A	286	THR	0	0.004	-0.017	45.742	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	287	LEU	0	-0.003	-0.004	46.191	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	288	LYS	1	0.944	0.976	48.909	-0.053	-0.053	0.000	0.000	0.000	0.000
38	A	289	ALA	0	0.021	0.020	51.407	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	290	GLN	0	0.054	0.014	49.537	0.000	0.000	0.000	0.000	0.000	0.000
40	A	291	ASN	0	-0.068	-0.028	53.485	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	292	SER	0	0.015	0.009	55.201	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	293	GLU	-1	-0.921	-0.953	55.925	0.055	0.055	0.000	0.000	0.000	0.000
43	A	294	LEU	0	-0.008	-0.014	55.373	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	295	ALA	0	0.010	0.017	59.086	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	296	SER	0	-0.015	0.001	61.143	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	297	THR	0	0.044	0.003	61.688	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	298	ALA	0	-0.025	-0.003	62.658	0.000	0.000	0.000	0.000	0.000	0.000
48	A	299	ASN	0	-0.077	-0.072	64.537	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	300	MET	0	0.056	0.051	66.882	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	301	LEU	0	0.026	0.002	65.758	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	302	ARG	1	0.902	0.955	65.917	-0.041	-0.041	0.000	0.000	0.000	0.000
52	A	303	GLU	-1	-0.935	-0.963	70.508	0.032	0.032	0.000	0.000	0.000	0.000
53	A	304	GLN	0	0.039	0.028	71.521	0.000	0.000	0.000	0.000	0.000	0.000
54	A	305	VAL	0	-0.025	-0.019	71.884	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	306	ALA	0	-0.035	-0.020	74.603	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	307	GLN	0	-0.008	0.000	76.517	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	308	LEU	0	-0.002	-0.019	75.750	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	309	LYS	1	0.947	0.977	76.519	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	310	GLN	0	0.037	0.020	80.304	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	311	LYS	1	0.929	0.971	81.755	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	312	VAL	0	-0.036	-0.008	81.697	0.000	0.000	0.000	0.000	0.000	0.000
62	A	313	MET	0	-0.047	0.001	84.610	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:252:HIS)