FMO DATABASE

FMODB ID: N1GKQ

Calculation Name: 4YVQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YVQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q940U6

Base Structure: X-ray

Registration Date: 2023-06-19

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-575683.737917
FMO2-HF: Nuclear repulsion	538277.321031
FMO2-HF: Total energy	-37406.416887
FMO2-MP2: Total energy	-37510.01509

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:439:MET)

Summations of interaction energy for fragment #1(A:439:MET)

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.
-20.826	-13.8	5.573	-3.88	-8.72	-0.015

Interaction energy analysis for fragmet #1(A:439:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.005

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	441	GLU	-1	-0.866	-0.927	2.766	-7.610	-3.548	0.393	-1.925	-2.530	-0.010
4	A	442	THR	0	-0.029	-0.032	3.901	0.289	0.642	0.000	-0.062	-0.292	0.000
5	A	443	VAL	0	-0.016	-0.009	5.220	0.731	0.731	0.000	0.000	0.000	0.000
6	A	444	PRO	0	0.013	-0.007	7.269	0.184	0.184	0.000	0.000	0.000	0.000
7	A	445	THR	0	0.060	0.025	9.271	0.075	0.075	0.000	0.000	0.000	0.000
8	A	446	ILE	0	0.033	0.024	6.583	0.070	0.070	0.000	0.000	0.000	0.000
9	A	447	LYS	1	0.924	0.969	10.663	-0.171	-0.171	0.000	0.000	0.000	0.000
10	A	448	LYS	1	0.774	0.862	13.419	0.090	0.090	0.000	0.000	0.000	0.000
11	A	449	LEU	0	0.047	0.033	13.507	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	450	ARG	1	0.958	0.976	13.886	-0.460	-0.460	0.000	0.000	0.000	0.000
13	A	451	ALA	0	-0.010	-0.001	16.640	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	452	TYR	0	-0.018	-0.002	18.603	-0.023	-0.023	0.000	0.000	0.000	0.000
15	A	453	ALA	0	0.021	0.001	18.989	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	454	GLU	-1	-0.802	-0.877	20.806	0.214	0.214	0.000	0.000	0.000	0.000
17	A	455	ARG	1	0.965	0.974	22.760	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	456	ILE	0	-0.026	0.000	23.493	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	457	ARG	1	0.791	0.873	24.182	-0.208	-0.208	0.000	0.000	0.000	0.000
20	A	458	VAL	0	-0.001	0.000	26.485	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	459	ALA	0	0.034	0.025	28.653	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	460	GLU	-1	-0.895	-0.957	29.877	0.081	0.081	0.000	0.000	0.000	0.000
23	A	461	LEU	0	-0.029	-0.008	30.120	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	462	GLU	-1	-0.911	-0.960	32.201	0.100	0.100	0.000	0.000	0.000	0.000
25	A	463	LYS	1	0.864	0.932	33.969	-0.082	-0.082	0.000	0.000	0.000	0.000
26	A	464	CYS	0	-0.048	-0.025	35.114	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	465	MET	0	-0.006	-0.009	35.724	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	466	SER	0	0.002	0.001	38.269	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	467	LYS	1	0.853	0.933	38.281	-0.077	-0.077	0.000	0.000	0.000	0.000
30	A	468	MET	0	-0.021	-0.007	39.401	0.001	0.001	0.000	0.000	0.000	0.000
31	A	469	GLY	0	0.025	0.027	42.836	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	470	ASP	-1	-0.914	-0.956	44.878	0.068	0.068	0.000	0.000	0.000	0.000
33	A	471	ASP	-1	-0.880	-0.937	43.967	0.076	0.076	0.000	0.000	0.000	0.000
34	A	472	ILE	0	-0.102	-0.031	39.862	0.006	0.006	0.000	0.000	0.000	0.000
35	A	473	ASN	0	0.025	-0.002	41.712	0.002	0.002	0.000	0.000	0.000	0.000
36	A	474	LYS	1	0.969	0.981	39.585	-0.103	-0.103	0.000	0.000	0.000	0.000
37	A	475	LYS	1	1.012	0.997	38.127	-0.105	-0.105	0.000	0.000	0.000	0.000
38	A	476	THR	0	0.035	0.034	37.741	0.007	0.007	0.000	0.000	0.000	0.000
39	A	477	THR	0	0.024	-0.010	35.626	0.002	0.002	0.000	0.000	0.000	0.000
40	A	478	ARG	1	0.892	0.945	29.828	-0.195	-0.195	0.000	0.000	0.000	0.000
41	A	479	ALA	0	0.013	0.016	32.796	0.010	0.010	0.000	0.000	0.000	0.000
42	A	480	VAL	0	0.039	0.014	32.811	0.007	0.007	0.000	0.000	0.000	0.000
43	A	481	ASP	-1	-0.861	-0.923	29.444	0.198	0.198	0.000	0.000	0.000	0.000
44	A	482	ASP	-1	-0.842	-0.931	28.518	0.212	0.212	0.000	0.000	0.000	0.000
45	A	483	LEU	0	-0.019	0.003	27.978	0.014	0.014	0.000	0.000	0.000	0.000
46	A	484	SER	0	-0.040	-0.028	27.992	0.010	0.010	0.000	0.000	0.000	0.000
47	A	485	ARG	1	0.895	0.932	23.790	-0.234	-0.234	0.000	0.000	0.000	0.000
48	A	486	GLY	0	0.004	0.009	23.318	0.027	0.027	0.000	0.000	0.000	0.000
49	A	487	ILE	0	-0.014	-0.018	23.958	0.015	0.015	0.000	0.000	0.000	0.000
50	A	488	VAL	0	0.036	0.018	20.462	0.008	0.008	0.000	0.000	0.000	0.000
51	A	489	ASN	0	0.001	-0.013	19.177	0.016	0.016	0.000	0.000	0.000	0.000
52	A	490	ARG	1	0.930	0.964	18.581	-0.191	-0.191	0.000	0.000	0.000	0.000
53	A	491	PHE	0	-0.011	0.007	19.794	0.002	0.002	0.000	0.000	0.000	0.000
54	A	492	LEU	0	-0.031	-0.022	15.606	0.003	0.003	0.000	0.000	0.000	0.000
55	A	493	HIS	0	0.009	0.014	14.412	0.078	0.078	0.000	0.000	0.000	0.000
56	A	494	GLY	0	0.045	0.028	13.430	0.087	0.087	0.000	0.000	0.000	0.000
57	A	495	PRO	0	0.047	0.006	12.569	0.068	0.068	0.000	0.000	0.000	0.000
58	A	496	MET	0	-0.009	-0.010	10.018	0.044	0.044	0.000	0.000	0.000	0.000
59	A	497	GLN	0	-0.013	0.013	8.754	0.202	0.202	0.000	0.000	0.000	0.000
60	A	498	HIS	0	-0.053	-0.026	8.450	0.242	0.242	0.000	0.000	0.000	0.000
61	A	499	LEU	0	-0.013	0.006	6.527	-0.096	-0.096	0.000	0.000	0.000	0.000
62	A	500	ARG	1	0.946	0.982	3.421	-6.472	-6.072	0.007	-0.108	-0.300	0.000
63	A	501	CYS	0	-0.053	0.036	3.646	-1.993	-1.513	0.007	-0.149	-0.338	0.001
64	A	502	ASP	-1	-0.684	-0.902	3.530	-2.658	-1.061	0.109	-0.677	-1.029	-0.006
65	A	503	GLY	0	-0.102	-0.085	5.503	0.372	0.372	0.000	0.000	0.000	0.000
66	A	504	SER	0	-0.092	-0.039	8.093	0.001	0.001	0.000	0.000	0.000	0.000
67	A	505	ASP	-1	-0.871	-0.917	9.025	-0.242	-0.242	0.000	0.000	0.000	0.000
68	A	506	SER	0	-0.068	-0.040	8.016	0.061	0.061	0.000	0.000	0.000	0.000
69	A	507	ARG	1	0.835	0.962	6.241	-1.404	-1.404	0.000	0.000	0.000	0.000
70	A	508	THR	0	0.090	0.037	4.740	-0.749	-0.607	-0.001	-0.004	-0.136	0.000
71	A	509	LEU	0	0.060	0.003	2.186	-0.793	-1.108	5.057	-0.942	-3.800	0.000
72	A	510	SER	0	0.017	-0.008	4.582	-0.007	0.077	0.001	0.008	-0.093	0.000
73	A	511	GLU	-1	-0.886	-0.940	8.154	-0.114	-0.114	0.000	0.000	0.000	0.000
74	A	512	THR	0	-0.031	-0.002	4.266	-0.026	0.197	0.000	-0.021	-0.202	0.000
75	A	513	LEU	0	-0.002	-0.012	4.988	-0.155	-0.155	0.000	0.000	0.000	0.000
76	A	514	GLU	-1	-0.885	-0.938	7.442	-0.341	-0.341	0.000	0.000	0.000	0.000
77	A	515	ASN	0	-0.045	-0.018	9.377	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	516	MET	0	-0.025	-0.009	8.077	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	517	HIS	0	0.006	0.003	10.086	0.083	0.083	0.000	0.000	0.000	0.000
80	A	518	ALA	0	-0.014	-0.008	12.734	0.028	0.028	0.000	0.000	0.000	0.000
81	A	519	LEU	0	0.015	0.005	11.496	0.028	0.028	0.000	0.000	0.000	0.000
82	A	520	ASN	0	0.002	-0.009	11.986	0.066	0.066	0.000	0.000	0.000	0.000
83	A	521	ARG	1	0.932	0.968	15.595	0.175	0.175	0.000	0.000	0.000	0.000
84	A	522	MET	0	-0.045	-0.017	18.127	0.015	0.015	0.000	0.000	0.000	0.000
85	A	523	TYR	0	0.007	0.003	17.098	0.013	0.013	0.000	0.000	0.000	0.000
86	A	524	GLY	0	0.002	0.016	19.680	0.009	0.009	0.000	0.000	0.000	0.000
87	A	525	LEU	0	-0.039	-0.016	14.389	0.012	0.012	0.000	0.000	0.000	0.000
88	A	526	GLU	-1	-0.854	-0.908	13.865	-0.176	-0.176	0.000	0.000	0.000	0.000
89	A	527	LYS	1	0.892	0.951	17.790	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:439:MET)