FMO DATABASE

FMODB ID: R5RR8

Calculation Name: 4JPN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JPN

Chain ID: A

ChEMBL ID:

UniProt ID: P03646

Base Structure: X-ray

Registration Date: 2023-06-20

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-325573.900047
FMO2-HF: Nuclear repulsion	294716.161229
FMO2-HF: Total energy	-30857.738819
FMO2-MP2: Total energy	-30944.985926

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:144:VAL)

Summations of interaction energy for fragment #1(A:144:VAL)

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.
3.44	4.981	-0.015	-0.467	-1.06	0.002

Interaction energy analysis for fragmet #1(A:144:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.015

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	146	ALA	0	0.034	0.007	3.799	1.113	2.377	-0.015	-0.435	-0.815	0.002
4	A	147	GLY	0	0.029	0.018	5.859	0.270	0.270	0.000	0.000	0.000	0.000
5	A	148	PHE	0	-0.018	-0.017	5.303	-0.216	-0.216	0.000	0.000	0.000	0.000
6	A	149	GLU	-1	-0.906	-0.964	4.401	4.063	4.340	0.000	-0.032	-0.245	0.000
7	A	150	ASN	0	0.004	0.005	7.207	-0.370	-0.370	0.000	0.000	0.000	0.000
8	A	151	GLN	0	-0.013	-0.007	10.418	-0.144	-0.144	0.000	0.000	0.000	0.000
9	A	152	LYS	1	0.934	1.008	8.699	-1.321	-1.321	0.000	0.000	0.000	0.000
10	A	153	GLU	-1	-0.929	-0.961	11.215	0.448	0.448	0.000	0.000	0.000	0.000
11	A	154	LEU	0	0.009	-0.014	13.056	-0.109	-0.109	0.000	0.000	0.000	0.000
12	A	155	THR	0	-0.023	-0.037	14.477	-0.078	-0.078	0.000	0.000	0.000	0.000
13	A	156	LYS	1	0.846	0.911	15.151	-0.411	-0.411	0.000	0.000	0.000	0.000
14	A	157	MET	0	0.003	0.012	16.810	-0.043	-0.043	0.000	0.000	0.000	0.000
15	A	158	GLN	0	-0.023	-0.012	19.212	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	159	LEU	0	-0.015	-0.011	17.931	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	160	ASP	-1	-0.863	-0.915	19.894	0.272	0.272	0.000	0.000	0.000	0.000
18	A	161	ASN	0	-0.004	0.008	22.430	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	162	GLN	0	0.006	-0.011	23.861	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	163	LYS	1	0.895	0.958	23.616	-0.197	-0.197	0.000	0.000	0.000	0.000
21	A	164	GLU	-1	-0.888	-0.949	24.941	0.168	0.168	0.000	0.000	0.000	0.000
22	A	165	ILE	0	-0.018	-0.015	28.428	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	166	ALA	0	-0.031	-0.012	29.893	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	167	GLU	-1	-0.924	-0.973	28.645	0.129	0.129	0.000	0.000	0.000	0.000
25	A	168	MET	0	0.040	0.027	31.573	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	169	GLN	0	-0.018	0.009	34.464	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	170	ASN	0	-0.027	-0.027	33.653	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	171	GLU	-1	-0.961	-0.970	36.532	0.076	0.076	0.000	0.000	0.000	0.000
29	A	172	THR	0	0.030	0.013	38.332	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	173	GLN	0	-0.040	-0.033	39.112	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	174	LYS	1	0.921	0.958	39.951	-0.068	-0.068	0.000	0.000	0.000	0.000
32	A	175	GLU	-1	-0.896	-0.941	41.489	0.060	0.060	0.000	0.000	0.000	0.000
33	A	176	ILE	0	-0.014	-0.007	44.424	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	177	ALA	0	-0.002	0.001	45.692	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	178	GLY	0	-0.011	-0.007	46.834	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	179	ILE	0	0.020	0.008	48.300	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	180	GLN	0	-0.004	0.003	49.472	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	181	SER	0	-0.029	-0.007	51.318	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	182	ALA	0	0.006	-0.004	52.682	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	183	THR	0	0.002	-0.005	54.598	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	184	SER	0	-0.009	0.003	56.060	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	185	ARG	1	0.942	0.966	56.304	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	186	GLN	0	-0.031	-0.018	58.781	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	187	ASN	0	0.061	0.026	60.523	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	188	THR	0	-0.042	-0.019	61.245	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	189	LYS	1	0.879	0.930	59.983	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	190	ASP	-1	-0.849	-0.917	64.913	0.025	0.025	0.000	0.000	0.000	0.000
48	A	191	GLN	0	-0.066	-0.037	64.561	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	192	VAL	0	-0.044	-0.020	67.187	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	193	TYR	0	0.017	0.018	69.466	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	194	ALA	0	0.059	0.025	71.045	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	195	GLN	0	0.012	-0.005	70.594	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	196	ASN	0	-0.028	-0.025	69.307	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	197	GLU	-1	-0.941	-0.958	73.728	0.019	0.019	0.000	0.000	0.000	0.000
55	A	198	MET	0	-0.043	-0.020	76.241	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	199	LEU	0	0.021	0.027	74.708	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	200	ALA	0	0.051	0.015	78.346	0.000	0.000	0.000	0.000	0.000	0.000
58	A	201	TYR	0	-0.021	-0.009	80.571	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	202	GLN	0	0.024	0.009	79.641	0.000	0.000	0.000	0.000	0.000	0.000
60	A	203	GLN	0	-0.014	-0.006	78.069	0.000	0.000	0.000	0.000	0.000	0.000
61	A	204	LYS	1	0.985	1.002	83.307	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	205	GLU	-1	-0.907	-0.959	86.276	0.014	0.014	0.000	0.000	0.000	0.000
63	A	206	SER	0	-0.056	-0.029	85.533	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	207	THR	0	0.008	-0.008	86.410	0.000	0.000	0.000	0.000	0.000	0.000
65	A	208	ALA	0	-0.012	-0.003	88.853	0.000	0.000	0.000	0.000	0.000	0.000
66	A	209	ARG	1	0.928	0.960	86.839	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	210	VAL	0	0.007	0.008	89.179	0.000	0.000	0.000	0.000	0.000	0.000
68	A	211	ALA	0	0.002	0.006	92.304	0.000	0.000	0.000	0.000	0.000	0.000
69	A	212	SER	0	0.016	0.007	94.733	0.000	0.000	0.000	0.000	0.000	0.000
70	A	213	ILE	0	-0.011	0.004	92.901	0.000	0.000	0.000	0.000	0.000	0.000
71	A	214	MET	0	-0.051	-0.035	93.933	0.000	0.000	0.000	0.000	0.000	0.000
72	A	215	GLU	-1	-0.975	-0.970	97.341	0.010	0.010	0.000	0.000	0.000	0.000
73	A	216	ASN	0	-0.053	-0.032	100.026	0.000	0.000	0.000	0.000	0.000	0.000
74	A	217	THR	0	-0.090	-0.038	99.064	0.000	0.000	0.000	0.000	0.000	0.000
75	A	218	ASN	0	-0.019	-0.008	101.331	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:144:VAL)