FMO DATABASE

FMODB ID: J39N9

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:

Apendix: None

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-576462.112282
FMO2-HF: Nuclear repulsion	539055.192904
FMO2-HF: Total energy	-37406.919378
FMO2-MP2: Total energy	-37510.510359

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.
-42.59	-36.268	14.911	-8.077	-13.155	0.01

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 : 0.044 / 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	441	GLU	-1	-0.859	-0.927	2.400	-9.913	-5.556	1.705	-2.641	-3.422	-0.022
4	A	442	THR	0	-0.010	-0.026	4.098	0.307	0.621	-0.001	-0.053	-0.261	0.000
5	A	443	VAL	0	-0.022	-0.010	5.296	0.419	0.531	-0.001	-0.014	-0.096	0.000
6	A	444	PRO	0	0.012	-0.004	7.560	-0.007	-0.007	0.000	0.000	0.000	0.000
7	A	445	THR	0	0.043	0.012	9.442	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	446	ILE	0	0.030	0.023	6.741	-0.031	-0.031	0.000	0.000	0.000	0.000
9	A	447	LYS	1	0.934	0.973	10.913	-0.573	-0.573	0.000	0.000	0.000	0.000
10	A	448	LYS	1	0.779	0.861	13.701	-0.182	-0.182	0.000	0.000	0.000	0.000
11	A	449	LEU	0	0.045	0.029	13.616	-0.052	-0.052	0.000	0.000	0.000	0.000
12	A	450	ARG	1	0.968	0.980	14.262	-0.815	-0.815	0.000	0.000	0.000	0.000
13	A	451	ALA	0	-0.018	-0.004	16.899	-0.047	-0.047	0.000	0.000	0.000	0.000
14	A	452	TYR	0	-0.018	-0.005	18.829	-0.049	-0.049	0.000	0.000	0.000	0.000
15	A	453	ALA	0	0.015	-0.001	19.211	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	454	GLU	-1	-0.797	-0.868	21.029	0.350	0.350	0.000	0.000	0.000	0.000
17	A	455	ARG	1	0.953	0.974	23.015	-0.208	-0.208	0.000	0.000	0.000	0.000
18	A	456	ILE	0	-0.016	-0.002	23.455	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	457	ARG	1	0.760	0.843	24.500	-0.345	-0.345	0.000	0.000	0.000	0.000
20	A	458	VAL	0	0.000	-0.004	26.729	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	459	ALA	0	0.040	0.032	28.910	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	460	GLU	-1	-0.828	-0.904	30.082	0.143	0.143	0.000	0.000	0.000	0.000
23	A	461	LEU	0	-0.036	-0.009	30.277	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	462	GLU	-1	-0.910	-0.958	32.442	0.175	0.175	0.000	0.000	0.000	0.000
25	A	463	LYS	1	0.796	0.883	33.931	-0.156	-0.156	0.000	0.000	0.000	0.000
26	A	464	CYS	0	-0.061	-0.036	35.211	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	465	MET	0	0.013	0.003	35.950	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	466	SER	0	-0.006	-0.009	38.519	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	467	LYS	1	0.857	0.936	38.078	-0.136	-0.136	0.000	0.000	0.000	0.000
30	A	468	MET	0	-0.021	-0.006	39.733	0.002	0.002	0.000	0.000	0.000	0.000
31	A	469	GLY	0	0.005	0.016	43.072	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	470	ASP	-1	-0.919	-0.961	45.142	0.106	0.106	0.000	0.000	0.000	0.000
33	A	471	ASP	-1	-0.916	-0.953	44.114	0.125	0.125	0.000	0.000	0.000	0.000
34	A	472	ILE	0	-0.059	-0.009	39.529	0.009	0.009	0.000	0.000	0.000	0.000
35	A	473	ASN	0	0.069	0.040	41.997	0.004	0.004	0.000	0.000	0.000	0.000
36	A	474	LYS	1	0.978	0.987	39.869	-0.152	-0.152	0.000	0.000	0.000	0.000
37	A	475	LYS	1	1.000	0.992	38.405	-0.150	-0.150	0.000	0.000	0.000	0.000
38	A	476	THR	0	0.019	0.006	37.996	0.009	0.009	0.000	0.000	0.000	0.000
39	A	477	THR	0	0.016	-0.019	35.949	0.005	0.005	0.000	0.000	0.000	0.000
40	A	478	ARG	1	0.782	0.852	29.324	-0.289	-0.289	0.000	0.000	0.000	0.000
41	A	479	ALA	0	0.010	0.013	33.056	0.016	0.016	0.000	0.000	0.000	0.000
42	A	480	VAL	0	0.043	0.016	33.045	0.012	0.012	0.000	0.000	0.000	0.000
43	A	481	ASP	-1	-0.791	-0.867	29.707	0.313	0.313	0.000	0.000	0.000	0.000
44	A	482	ASP	-1	-0.779	-0.866	28.760	0.329	0.329	0.000	0.000	0.000	0.000
45	A	483	LEU	0	-0.007	0.010	28.206	0.021	0.021	0.000	0.000	0.000	0.000
46	A	484	SER	0	-0.024	-0.008	28.197	0.017	0.017	0.000	0.000	0.000	0.000
47	A	485	ARG	1	0.865	0.901	24.119	-0.356	-0.356	0.000	0.000	0.000	0.000
48	A	486	GLY	0	0.010	0.012	23.543	0.041	0.041	0.000	0.000	0.000	0.000
49	A	487	ILE	0	-0.016	-0.019	24.141	0.021	0.021	0.000	0.000	0.000	0.000
50	A	488	VAL	0	0.037	0.016	20.865	0.015	0.015	0.000	0.000	0.000	0.000
51	A	489	ASN	0	0.001	-0.010	19.387	0.056	0.056	0.000	0.000	0.000	0.000
52	A	490	ARG	1	0.930	0.965	18.759	-0.283	-0.283	0.000	0.000	0.000	0.000
53	A	491	PHE	0	-0.013	0.005	19.910	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	492	LEU	0	-0.029	-0.018	15.823	0.008	0.008	0.000	0.000	0.000	0.000
55	A	493	HIS	0	-0.012	0.001	14.563	0.118	0.118	0.000	0.000	0.000	0.000
56	A	494	GLY	0	0.044	0.026	13.542	0.129	0.129	0.000	0.000	0.000	0.000
57	A	495	PRO	0	0.053	0.011	12.604	0.101	0.101	0.000	0.000	0.000	0.000
58	A	496	MET	0	-0.016	-0.010	10.177	0.098	0.098	0.000	0.000	0.000	0.000
59	A	497	GLN	0	0.010	0.026	8.910	0.351	0.351	0.000	0.000	0.000	0.000
60	A	498	HIS	0	-0.058	-0.031	8.488	0.304	0.304	0.000	0.000	0.000	0.000
61	A	499	LEU	0	-0.009	0.007	6.538	-0.170	-0.170	0.000	0.000	0.000	0.000
62	A	500	ARG	1	0.837	0.903	2.068	-23.675	-25.034	8.328	-3.489	-3.480	0.039
63	A	501	CYS	0	-0.038	-0.021	3.733	-2.258	-1.770	0.008	-0.149	-0.346	0.001
64	A	502	ASP	-1	-0.737	-0.854	3.594	-3.028	-1.355	0.128	-0.703	-1.098	-0.007
65	A	503	GLY	0	-0.077	-0.066	5.888	0.517	0.517	0.000	0.000	0.000	0.000
66	A	504	SER	0	-0.085	-0.042	8.175	0.053	0.053	0.000	0.000	0.000	0.000
67	A	505	ASP	-1	-0.867	-0.911	9.064	-0.361	-0.361	0.000	0.000	0.000	0.000
68	A	506	SER	0	-0.069	-0.043	7.853	0.048	0.048	0.000	0.000	0.000	0.000
69	A	507	ARG	1	0.833	0.945	6.098	-1.669	-1.669	0.000	0.000	0.000	0.000
70	A	508	THR	0	0.023	-0.023	4.819	-0.934	-0.812	-0.001	-0.002	-0.118	0.000
71	A	509	LEU	0	0.050	-0.004	2.382	-1.206	-0.890	4.745	-0.996	-4.066	-0.001
72	A	510	SER	0	0.029	-0.001	4.548	0.181	0.272	0.000	-0.009	-0.082	0.000
73	A	511	GLU	-1	-0.823	-0.880	8.136	-0.326	-0.326	0.000	0.000	0.000	0.000
74	A	512	THR	0	-0.048	-0.008	4.076	0.195	0.403	0.000	-0.021	-0.186	0.000
75	A	513	LEU	0	0.017	0.001	5.008	0.087	0.087	0.000	0.000	0.000	0.000
76	A	514	GLU	-1	-0.797	-0.893	7.534	-0.255	-0.255	0.000	0.000	0.000	0.000
77	A	515	ASN	0	-0.037	-0.010	9.136	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	516	MET	0	-0.022	0.004	8.212	0.067	0.067	0.000	0.000	0.000	0.000
79	A	517	HIS	0	0.003	0.002	10.235	0.136	0.136	0.000	0.000	0.000	0.000
80	A	518	ALA	0	-0.028	-0.014	12.863	0.029	0.029	0.000	0.000	0.000	0.000
81	A	519	LEU	0	0.028	0.013	11.539	0.032	0.032	0.000	0.000	0.000	0.000
82	A	520	ASN	0	0.005	-0.013	12.196	0.092	0.092	0.000	0.000	0.000	0.000
83	A	521	ARG	1	0.848	0.920	15.202	0.180	0.180	0.000	0.000	0.000	0.000
84	A	522	MET	0	-0.034	-0.011	18.273	0.017	0.017	0.000	0.000	0.000	0.000
85	A	523	TYR	0	0.000	-0.004	16.994	0.021	0.021	0.000	0.000	0.000	0.000
86	A	524	GLY	0	0.007	0.018	19.835	0.010	0.010	0.000	0.000	0.000	0.000
87	A	525	LEU	0	-0.052	-0.023	14.441	0.015	0.015	0.000	0.000	0.000	0.000
88	A	526	GLU	-1	-0.829	-0.887	14.037	0.038	0.038	0.000	0.000	0.000	0.000
89	A	527	LYS	1	0.889	0.949	17.940	-0.129	-0.129	0.000	0.000	0.000	0.000

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