FMO DATABASE

FMODB ID: R84V8

Calculation Name: 4YEW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YEW

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACF0

Base Structure: X-ray

Registration Date: 2023-09-23

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-323448.393682
FMO2-HF: Nuclear repulsion	298306.328886
FMO2-HF: Total energy	-25142.064797
FMO2-MP2: Total energy	-25216.25189

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-18.994	-14.149	12.995	-7.284	-10.557	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.019

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	3	LYS	1	0.891	0.910	3.345	-1.636	1.882	0.019	-1.995	-1.543	0.006
4	A	4	SER	0	0.003	-0.011	5.842	0.851	0.851	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.029	0.006	2.234	-4.402	-2.807	4.335	-2.424	-3.505	-0.021
6	A	6	LEU	0	-0.013	-0.009	2.529	0.707	2.667	0.553	-0.575	-1.939	-0.003
7	A	7	ILE	0	0.033	0.015	3.878	0.542	0.822	0.009	-0.023	-0.266	0.000
8	A	8	ASP	-1	-0.802	-0.884	6.924	1.140	1.140	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.926	0.962	2.376	-13.760	-16.268	8.079	-2.267	-3.304	0.021
10	A	10	ILE	0	-0.005	0.002	7.154	-0.456	-0.456	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.042	-0.030	9.274	-0.326	-0.326	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.016	-0.006	10.272	-0.159	-0.159	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.009	0.005	10.574	-0.186	-0.186	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.027	-0.009	11.910	-0.152	-0.152	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.926	-0.951	14.449	0.774	0.774	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.056	-0.010	14.395	-0.174	-0.174	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.019	-0.009	15.301	0.068	0.068	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.920	0.932	10.584	-0.725	-0.725	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.001	0.004	13.463	-0.061	-0.061	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.041	-0.023	15.907	-0.076	-0.076	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.049	0.030	11.187	-0.049	-0.049	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.012	-0.004	11.300	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.951	0.971	12.339	-0.256	-0.256	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.016	0.024	13.449	-0.061	-0.061	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.008	0.000	7.147	-0.070	-0.070	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.789	-0.880	11.409	-0.665	-0.665	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.012	-0.007	13.736	-0.045	-0.045	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.003	0.015	12.236	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.001	0.004	9.531	-0.072	-0.072	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.004	0.008	13.868	-0.030	-0.030	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.008	-0.017	17.490	0.008	0.008	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.005	0.001	15.036	0.007	0.007	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.060	-0.042	16.705	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.836	-0.913	19.002	-0.207	-0.207	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.024	-0.001	21.081	0.008	0.008	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.000	-0.012	18.455	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.752	0.868	22.682	0.218	0.218	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.970	-0.984	24.795	-0.108	-0.108	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.083	-0.038	26.128	0.019	0.019	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.921	-0.951	25.146	-0.062	-0.062	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.867	-0.941	22.813	-0.163	-0.163	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.026	0.011	18.196	0.032	0.032	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.038	-0.021	19.129	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.010	0.013	14.567	0.047	0.047	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.040	0.001	17.336	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.009	0.005	16.981	0.063	0.063	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.017	0.000	9.262	0.015	0.015	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.006	-0.013	14.390	-0.079	-0.079	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.042	-0.016	16.416	0.042	0.042	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.012	-0.006	12.191	-0.064	-0.064	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.033	0.027	18.273	0.036	0.036	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.032	0.016	21.215	-0.062	-0.062	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.858	0.927	21.250	0.345	0.345	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.792	-0.864	25.519	-0.205	-0.205	0.000	0.000	0.000	0.000
55	A	74	ALA	0	0.024	0.010	27.903	0.001	0.001	0.000	0.000	0.000	0.000
56	A	75	LYS	1	0.793	0.870	27.198	0.203	0.203	0.000	0.000	0.000	0.000
57	A	76	VAL	0	0.001	0.005	21.593	-0.027	-0.027	0.000	0.000	0.000	0.000
58	A	77	PRO	0	0.053	0.027	18.636	0.029	0.029	0.000	0.000	0.000	0.000
59	A	78	SER	0	-0.004	-0.012	19.167	-0.030	-0.030	0.000	0.000	0.000	0.000
60	A	79	PHE	0	0.027	0.023	13.185	0.002	0.002	0.000	0.000	0.000	0.000
61	A	80	ARG	1	0.914	0.969	17.255	0.137	0.137	0.000	0.000	0.000	0.000
62	A	81	ALA	0	0.060	0.041	14.651	0.033	0.033	0.000	0.000	0.000	0.000
63	A	82	GLY	0	-0.019	-0.023	15.902	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	83	LYS	1	0.944	0.954	16.218	-0.141	-0.141	0.000	0.000	0.000	0.000
65	A	84	ALA	0	0.084	0.050	14.828	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	85	LEU	0	-0.001	0.018	9.446	0.072	0.072	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.880	0.926	12.559	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	87	ASP	-1	-0.905	-0.967	15.233	0.218	0.218	0.000	0.000	0.000	0.000
69	A	88	ALA	0	-0.067	-0.023	10.435	0.014	0.014	0.000	0.000	0.000	0.000
70	A	89	VAL	0	-0.060	-0.025	9.911	0.032	0.032	0.000	0.000	0.000	0.000
71	A	90	ASN	0	-0.027	0.008	12.488	-0.051	-0.051	0.000	0.000	0.000	0.000

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