FMO DATABASE

FMODB ID: 1JGGZ

Calculation Name: 2YV4-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YV4

Chain ID: A

ChEMBL ID:

UniProt ID: O73972

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	105
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-792606.023327
FMO2-HF: Nuclear repulsion	752923.878606
FMO2-HF: Total energy	-39682.144721
FMO2-MP2: Total energy	-39799.546703

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:236:ALA )

Summations of interaction energy for fragment #1(A:236:ALA )

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.
36	38.003	0.055	-0.791	-1.266	-0.002

Interaction energy analysis for fragmet #1(A:236:ALA )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.792 / q_NPA : 0.876

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	238	ASN	0	-0.025	-0.021	3.826	1.895	3.302	-0.008	-0.585	-0.814	-0.001
4	A	239	ALA	0	0.024	0.035	6.243	3.503	3.503	0.000	0.000	0.000	0.000
5	A	240	GLU	-1	-0.955	-0.969	7.292	-25.609	-25.609	0.000	0.000	0.000	0.000
6	A	241	VAL	0	-0.007	-0.007	6.441	0.787	0.787	0.000	0.000	0.000	0.000
7	A	242	ILE	0	-0.002	-0.005	9.399	1.327	1.327	0.000	0.000	0.000	0.000
8	A	243	VAL	0	-0.007	0.000	11.743	0.070	0.070	0.000	0.000	0.000	0.000
9	A	244	VAL	0	-0.006	0.005	14.216	0.853	0.853	0.000	0.000	0.000	0.000
10	A	245	GLU	-1	-0.914	-0.971	17.989	-15.536	-15.536	0.000	0.000	0.000	0.000
11	A	246	GLY	0	0.053	0.026	19.981	0.541	0.541	0.000	0.000	0.000	0.000
12	A	247	PRO	0	0.009	0.012	23.670	-0.261	-0.261	0.000	0.000	0.000	0.000
13	A	248	ARG	1	0.992	0.965	24.811	11.703	11.703	0.000	0.000	0.000	0.000
14	A	249	GLU	-1	-0.982	-0.982	25.880	-9.843	-9.843	0.000	0.000	0.000	0.000
15	A	250	LYS	1	0.988	0.987	26.731	10.409	10.409	0.000	0.000	0.000	0.000
16	A	251	VAL	0	0.006	0.014	20.935	-0.213	-0.213	0.000	0.000	0.000	0.000
17	A	252	LYS	1	0.815	0.889	23.189	12.184	12.184	0.000	0.000	0.000	0.000
18	A	253	GLY	0	0.016	0.026	24.960	-0.053	-0.053	0.000	0.000	0.000	0.000
19	A	254	LYS	1	0.902	0.959	21.715	12.432	12.432	0.000	0.000	0.000	0.000
20	A	255	ILE	0	-0.001	-0.003	19.155	-0.384	-0.384	0.000	0.000	0.000	0.000
21	A	256	THR	0	-0.037	-0.041	21.670	-0.105	-0.105	0.000	0.000	0.000	0.000
22	A	257	GLU	-1	-0.921	-0.951	24.590	-11.833	-11.833	0.000	0.000	0.000	0.000
23	A	258	LEU	0	0.028	0.004	18.502	-0.194	-0.194	0.000	0.000	0.000	0.000
24	A	259	VAL	0	-0.004	0.013	19.843	-0.358	-0.358	0.000	0.000	0.000	0.000
25	A	260	LYS	1	0.933	0.968	21.557	10.982	10.982	0.000	0.000	0.000	0.000
26	A	261	GLU	-1	-0.876	-0.940	22.970	-12.783	-12.783	0.000	0.000	0.000	0.000
27	A	262	LEU	0	-0.079	-0.055	17.066	-0.156	-0.156	0.000	0.000	0.000	0.000
28	A	263	LYS	1	0.922	0.962	21.000	13.177	13.177	0.000	0.000	0.000	0.000
29	A	264	GLU	-1	-0.961	-0.960	23.077	-10.820	-10.820	0.000	0.000	0.000	0.000
30	A	265	ARG	1	0.882	0.941	18.496	14.992	14.992	0.000	0.000	0.000	0.000
31	A	266	GLY	0	-0.015	-0.006	22.430	-0.150	-0.150	0.000	0.000	0.000	0.000
32	A	267	LYS	1	0.839	0.933	16.096	17.094	17.094	0.000	0.000	0.000	0.000
33	A	268	LYS	1	0.931	0.973	16.950	18.335	18.335	0.000	0.000	0.000	0.000
34	A	269	VAL	0	-0.004	-0.020	16.092	-1.393	-1.393	0.000	0.000	0.000	0.000
35	A	270	GLY	0	0.039	0.005	14.899	0.752	0.752	0.000	0.000	0.000	0.000
36	A	271	VAL	0	-0.024	-0.005	15.032	-0.653	-0.653	0.000	0.000	0.000	0.000
37	A	272	ILE	0	-0.026	-0.013	10.758	-0.123	-0.123	0.000	0.000	0.000	0.000
38	A	273	GLY	0	0.032	-0.016	15.125	-0.090	-0.090	0.000	0.000	0.000	0.000
39	A	274	SER	0	-0.098	-0.077	18.247	0.269	0.269	0.000	0.000	0.000	0.000
40	A	275	GLU	-1	-0.834	-0.901	21.566	-11.489	-11.489	0.000	0.000	0.000	0.000
41	A	276	SER	0	0.038	0.015	21.007	-0.472	-0.472	0.000	0.000	0.000	0.000
42	A	277	TYR	0	0.033	0.007	20.833	-0.082	-0.082	0.000	0.000	0.000	0.000
43	A	278	ASN	0	-0.051	-0.038	23.942	0.028	0.028	0.000	0.000	0.000	0.000
44	A	279	ALA	0	-0.020	-0.001	18.958	0.170	0.170	0.000	0.000	0.000	0.000
45	A	280	ASP	-1	-0.856	-0.925	19.150	-14.647	-14.647	0.000	0.000	0.000	0.000
46	A	281	GLU	-1	-0.898	-0.957	16.489	-17.773	-17.773	0.000	0.000	0.000	0.000
47	A	282	PHE	0	-0.025	-0.018	17.745	-0.164	-0.164	0.000	0.000	0.000	0.000
48	A	283	PHE	0	-0.016	-0.009	14.454	-0.386	-0.386	0.000	0.000	0.000	0.000
49	A	284	PHE	0	-0.002	0.013	16.537	-0.294	-0.294	0.000	0.000	0.000	0.000
50	A	285	LEU	0	0.000	0.004	14.416	-1.012	-1.012	0.000	0.000	0.000	0.000
51	A	286	GLY	0	0.031	0.007	16.354	-0.642	-0.642	0.000	0.000	0.000	0.000
52	A	287	SER	0	-0.081	-0.030	19.092	0.339	0.339	0.000	0.000	0.000	0.000
53	A	288	SER	0	0.031	0.005	20.690	0.411	0.411	0.000	0.000	0.000	0.000
54	A	289	VAL	0	0.067	0.021	18.411	-0.825	-0.825	0.000	0.000	0.000	0.000
55	A	290	GLU	-1	-0.941	-0.969	17.607	-15.416	-15.416	0.000	0.000	0.000	0.000
56	A	291	GLU	-1	-0.888	-0.959	17.319	-15.470	-15.470	0.000	0.000	0.000	0.000
57	A	292	VAL	0	0.011	0.027	14.001	-1.311	-1.311	0.000	0.000	0.000	0.000
58	A	293	ALA	0	-0.036	-0.027	13.029	-2.096	-2.096	0.000	0.000	0.000	0.000
59	A	294	LYS	1	0.924	0.974	12.338	14.752	14.752	0.000	0.000	0.000	0.000
60	A	295	ASN	0	-0.029	-0.025	12.923	-1.147	-1.147	0.000	0.000	0.000	0.000
61	A	296	LEU	0	0.045	0.040	8.718	-1.682	-1.682	0.000	0.000	0.000	0.000
62	A	297	PHE	0	0.014	-0.015	4.878	-3.131	-3.131	0.000	0.000	0.000	0.000
63	A	298	LYS	1	0.899	0.952	7.418	19.195	19.195	0.000	0.000	0.000	0.000
64	A	299	ALA	0	0.034	0.021	10.053	0.171	0.171	0.000	0.000	0.000	0.000
65	A	300	LEU	0	0.024	-0.003	5.477	0.109	0.109	0.000	0.000	0.000	0.000
66	A	301	ARG	1	0.924	0.976	6.236	37.125	37.125	0.000	0.000	0.000	0.000
67	A	302	TYR	0	-0.061	-0.016	7.984	1.466	1.466	0.000	0.000	0.000	0.000
68	A	303	MET	0	0.003	0.009	9.977	1.616	1.616	0.000	0.000	0.000	0.000
69	A	304	ASP	-1	-0.754	-0.866	6.279	-46.593	-46.593	0.000	0.000	0.000	0.000
70	A	305	LYS	1	0.882	0.953	9.850	22.306	22.306	0.000	0.000	0.000	0.000
71	A	306	ALA	0	-0.025	-0.011	12.356	1.852	1.852	0.000	0.000	0.000	0.000
72	A	307	GLY	0	-0.012	-0.005	13.100	1.671	1.671	0.000	0.000	0.000	0.000
73	A	308	VAL	0	-0.061	-0.023	12.681	1.137	1.137	0.000	0.000	0.000	0.000
74	A	309	ASP	-1	-0.819	-0.891	12.058	-21.629	-21.629	0.000	0.000	0.000	0.000
75	A	310	VAL	0	-0.050	-0.031	11.901	-1.527	-1.527	0.000	0.000	0.000	0.000
76	A	311	VAL	0	0.014	-0.002	9.704	0.869	0.869	0.000	0.000	0.000	0.000
77	A	312	ILE	0	0.008	0.003	11.918	-0.590	-0.590	0.000	0.000	0.000	0.000
78	A	313	ALA	0	-0.039	-0.028	11.721	0.033	0.033	0.000	0.000	0.000	0.000
79	A	314	GLU	-1	-0.770	-0.859	13.820	-14.139	-14.139	0.000	0.000	0.000	0.000
80	A	315	GLY	0	0.002	-0.015	16.941	-0.539	-0.539	0.000	0.000	0.000	0.000
81	A	316	VAL	0	-0.014	0.000	17.917	0.564	0.564	0.000	0.000	0.000	0.000
82	A	317	GLU	-1	-0.895	-0.950	21.384	-12.327	-12.327	0.000	0.000	0.000	0.000
83	A	318	GLU	-1	-0.844	-0.929	23.661	-11.656	-11.656	0.000	0.000	0.000	0.000
84	A	319	ARG	1	0.902	0.932	23.850	11.073	11.073	0.000	0.000	0.000	0.000
85	A	320	GLY	0	0.050	0.034	22.223	-0.322	-0.322	0.000	0.000	0.000	0.000
86	A	321	LEU	0	-0.031	-0.007	19.051	-0.745	-0.745	0.000	0.000	0.000	0.000
87	A	322	GLY	0	0.089	0.043	17.266	-1.209	-1.209	0.000	0.000	0.000	0.000
88	A	323	LEU	0	0.017	0.019	16.257	-1.017	-1.017	0.000	0.000	0.000	0.000
89	A	324	ALA	0	-0.031	-0.015	16.028	-1.042	-1.042	0.000	0.000	0.000	0.000
90	A	325	VAL	0	-0.001	-0.002	11.957	-1.825	-1.825	0.000	0.000	0.000	0.000
91	A	326	MET	0	0.035	0.028	11.536	-2.338	-2.338	0.000	0.000	0.000	0.000
92	A	327	ASN	0	-0.009	-0.025	11.743	-1.856	-1.856	0.000	0.000	0.000	0.000
93	A	328	ARG	1	0.860	0.942	8.650	29.340	29.340	0.000	0.000	0.000	0.000
94	A	329	LEU	0	0.024	0.003	6.623	-4.237	-4.237	0.000	0.000	0.000	0.000
95	A	330	ARG	1	0.868	0.965	7.473	19.347	19.347	0.000	0.000	0.000	0.000
96	A	331	LYS	1	0.939	0.968	6.687	31.909	31.909	0.000	0.000	0.000	0.000
97	A	332	ALA	0	0.025	0.001	7.030	-0.144	-0.144	0.000	0.000	0.000	0.000
98	A	333	SER	0	-0.058	-0.037	3.231	-7.288	-6.703	0.063	-0.199	-0.449	-0.001
99	A	334	GLY	0	0.027	0.022	4.778	1.642	1.653	0.000	-0.007	-0.003	0.000
100	A	335	TYR	0	-0.008	0.000	7.050	-1.895	-1.895	0.000	0.000	0.000	0.000
101	A	336	LYS	1	0.983	1.003	9.586	19.073	19.073	0.000	0.000	0.000	0.000
102	A	337	ILE	0	0.013	0.010	13.262	-0.605	-0.605	0.000	0.000	0.000	0.000
103	A	338	VAL	0	-0.039	-0.026	15.891	0.797	0.797	0.000	0.000	0.000	0.000
104	A	339	LYS	1	0.967	0.991	18.961	11.445	11.445	0.000	0.000	0.000	0.000
105	A	340	ALA	-1	-0.913	-0.965	22.090	-11.626	-11.626	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:236:ALA )