FMO DATABASE

FMODB ID: 17RKZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-270766.656107
FMO2-HF: Nuclear repulsion	244680.285736
FMO2-HF: Total energy	-26086.370371
FMO2-MP2: Total energy	-26160.407727

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.
-1.28	1.836	0.838	-1.583	-2.372	0.005

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 : 0.068 / q_NPA : 0.031

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	A	254	LYS	1	1.061	1.021	3.267	-1.380	1.429	0.840	-1.561	-2.088	0.005
4	A	255	ALA	0	0.086	0.030	4.115	1.323	1.546	-0.001	-0.021	-0.202	0.000
5	A	256	GLU	-1	-0.816	-0.891	5.155	-0.205	-0.121	-0.001	-0.001	-0.082	0.000
6	A	257	ARG	1	0.972	0.984	7.945	-0.185	-0.185	0.000	0.000	0.000	0.000
7	A	258	LYS	1	0.976	0.972	5.842	-0.304	-0.304	0.000	0.000	0.000	0.000
8	A	259	ARG	1	0.877	0.941	8.475	1.111	1.111	0.000	0.000	0.000	0.000
9	A	260	MET	0	0.035	0.013	10.827	0.167	0.167	0.000	0.000	0.000	0.000
10	A	261	ARG	1	0.963	0.971	9.948	-0.946	-0.946	0.000	0.000	0.000	0.000
11	A	262	ASN	0	0.040	0.013	10.750	0.287	0.287	0.000	0.000	0.000	0.000
12	A	263	ARG	1	0.986	1.005	13.504	0.276	0.276	0.000	0.000	0.000	0.000
13	A	264	ILE	0	0.012	0.002	16.329	0.029	0.029	0.000	0.000	0.000	0.000
14	A	265	ALA	0	-0.006	0.002	15.603	0.006	0.006	0.000	0.000	0.000	0.000
15	A	266	ALA	0	0.019	0.007	17.467	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	267	SER	0	0.006	-0.008	19.200	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	268	LYS	1	0.955	0.975	19.197	-0.325	-0.325	0.000	0.000	0.000	0.000
18	A	269	SER	0	-0.042	-0.017	20.955	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	270	ARG	1	0.972	0.991	21.698	-0.037	-0.037	0.000	0.000	0.000	0.000
20	A	271	LYS	1	0.958	0.998	25.429	-0.159	-0.159	0.000	0.000	0.000	0.000
21	A	272	ARG	1	0.993	0.989	20.906	-0.370	-0.370	0.000	0.000	0.000	0.000
22	A	273	LYS	1	0.923	0.962	24.032	-0.175	-0.175	0.000	0.000	0.000	0.000
23	A	274	LEU	0	0.045	0.024	28.823	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	275	GLU	-1	-0.867	-0.944	29.640	0.174	0.174	0.000	0.000	0.000	0.000
25	A	276	ARG	1	0.933	0.965	30.206	-0.191	-0.191	0.000	0.000	0.000	0.000
26	A	277	ILE	0	0.022	0.012	33.068	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	278	ALA	0	0.071	0.046	35.326	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	279	ARG	1	0.932	0.964	34.648	-0.160	-0.160	0.000	0.000	0.000	0.000
29	A	280	LEU	0	-0.014	-0.010	35.603	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	281	GLU	-1	-0.895	-0.944	39.058	0.070	0.070	0.000	0.000	0.000	0.000
31	A	282	GLU	-1	-0.820	-0.894	40.891	0.077	0.077	0.000	0.000	0.000	0.000
32	A	283	LYS	1	0.925	0.967	41.468	-0.124	-0.124	0.000	0.000	0.000	0.000
33	A	284	VAL	0	0.024	-0.003	43.053	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	285	LYS	1	0.833	0.906	45.274	-0.077	-0.077	0.000	0.000	0.000	0.000
35	A	286	THR	0	-0.014	-0.014	45.935	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	287	LEU	0	-0.008	-0.006	45.725	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	288	LYS	1	0.951	0.981	47.939	-0.069	-0.069	0.000	0.000	0.000	0.000
38	A	289	ALA	0	0.026	0.023	51.272	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	290	GLN	0	0.060	0.022	49.576	0.001	0.001	0.000	0.000	0.000	0.000
40	A	291	ASN	0	-0.075	-0.034	53.266	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	292	SER	0	0.011	0.004	55.087	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	293	GLU	-1	-0.901	-0.948	55.469	0.067	0.067	0.000	0.000	0.000	0.000
43	A	294	LEU	0	-0.015	-0.010	55.205	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	295	ALA	0	0.014	0.019	59.078	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	296	SER	0	-0.017	0.001	61.037	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	297	THR	0	0.034	-0.008	61.471	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	298	ALA	0	-0.015	0.003	62.664	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	299	ASN	0	-0.046	-0.055	64.530	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	300	MET	0	0.050	0.048	66.872	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	301	LEU	0	0.028	0.005	65.451	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	302	ARG	1	0.866	0.933	65.742	-0.049	-0.049	0.000	0.000	0.000	0.000
52	A	303	GLU	-1	-0.930	-0.961	70.500	0.039	0.039	0.000	0.000	0.000	0.000
53	A	304	GLN	0	0.035	0.026	71.457	0.000	0.000	0.000	0.000	0.000	0.000
54	A	305	VAL	0	-0.016	-0.017	71.874	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	306	ALA	0	-0.035	-0.020	74.594	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	307	GLN	0	-0.007	0.002	75.912	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	308	LEU	0	-0.013	-0.021	75.531	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	309	LYS	1	0.950	0.980	76.051	-0.043	-0.043	0.000	0.000	0.000	0.000
59	A	310	GLN	0	0.041	0.023	80.295	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	311	LYS	1	0.919	0.970	81.748	-0.038	-0.038	0.000	0.000	0.000	0.000
61	A	312	VAL	0	-0.030	-0.008	81.639	0.000	0.000	0.000	0.000	0.000	0.000
62	A	313	MET	0	-0.047	-0.002	84.600	-0.001	-0.001	0.000	0.000	0.000	0.000

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