FMO DATABASE

FMODB ID: YVNR2

Calculation Name: 3KZ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KZ3

Chain ID: A

ChEMBL ID:

UniProt ID: P03034

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-514494.112385
FMO2-HF: Nuclear repulsion	483767.219493
FMO2-HF: Total energy	-30726.892892
FMO2-MP2: Total energy	-30817.143323

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-1.076	1.411	-0.014	-1.297	-1.176	0.006

Interaction energy analysis for fragmet #1(A:5:SER)

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 : 0.005

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	7	THR	0	0.015	0.008	3.714	-0.736	1.751	-0.014	-1.297	-1.176	0.006
4	A	8	GLN	0	0.051	0.004	5.988	0.203	0.203	0.000	0.000	0.000	0.000
5	A	9	GLU	-1	-0.838	-0.922	8.622	-0.759	-0.759	0.000	0.000	0.000	0.000
6	A	10	GLN	0	0.029	0.017	6.438	-0.933	-0.933	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.016	-0.010	5.805	0.228	0.228	0.000	0.000	0.000	0.000
8	A	12	GLU	-1	-0.897	-0.949	9.233	-0.191	-0.191	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.806	-0.891	12.061	-1.011	-1.011	0.000	0.000	0.000	0.000
10	A	14	ALA	0	-0.014	0.008	10.450	0.137	0.137	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.933	0.982	12.471	0.491	0.491	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.780	0.880	14.501	0.764	0.764	0.000	0.000	0.000	0.000
13	A	17	LEU	0	0.011	0.007	14.725	0.069	0.069	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.922	0.967	15.331	0.226	0.226	0.000	0.000	0.000	0.000
15	A	19	ALA	0	0.008	0.001	17.478	0.055	0.055	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.013	-0.009	20.236	0.044	0.044	0.000	0.000	0.000	0.000
17	A	21	TRP	0	0.022	0.015	19.914	0.022	0.022	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.922	-0.977	20.714	-0.116	-0.116	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.836	0.924	22.831	0.269	0.269	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.931	0.977	25.293	0.242	0.242	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.912	0.966	23.385	0.135	0.135	0.000	0.000	0.000	0.000
22	A	26	ASN	0	-0.008	-0.015	26.516	0.011	0.011	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.948	-0.963	29.888	-0.151	-0.151	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.068	-0.032	27.231	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	29	GLY	0	-0.018	0.010	30.655	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.094	-0.039	24.802	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	31	SER	0	0.033	0.013	25.801	0.014	0.014	0.000	0.000	0.000	0.000
28	A	32	TYR	0	0.028	-0.005	17.886	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	33	GLU	-1	-0.844	-0.935	22.333	-0.137	-0.137	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.052	0.030	24.721	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.090	-0.046	20.417	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	36	ALA	0	-0.001	-0.011	20.471	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.877	-0.931	21.444	-0.192	-0.192	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.882	0.931	24.372	0.227	0.227	0.000	0.000	0.000	0.000
35	A	39	MET	0	-0.088	-0.045	16.831	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	40	GLY	0	0.010	0.030	19.795	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	41	MET	0	-0.064	-0.023	15.889	-0.032	-0.032	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.073	0.037	17.884	0.036	0.036	0.000	0.000	0.000	0.000
39	A	43	GLN	0	0.077	0.016	17.893	-0.058	-0.058	0.000	0.000	0.000	0.000
40	A	44	SER	0	0.033	0.004	15.273	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.015	0.003	13.188	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.031	0.012	13.515	-0.106	-0.106	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.003	0.005	15.030	-0.054	-0.054	0.000	0.000	0.000	0.000
44	A	48	ALA	0	-0.020	-0.010	9.898	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.004	0.007	10.216	-0.169	-0.169	0.000	0.000	0.000	0.000
46	A	50	PHE	0	-0.012	-0.015	11.900	-0.067	-0.067	0.000	0.000	0.000	0.000
47	A	51	ASN	0	-0.031	-0.030	11.707	0.015	0.015	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.017	0.015	8.629	0.141	0.141	0.000	0.000	0.000	0.000
49	A	53	ILE	0	-0.039	-0.014	6.196	-0.136	-0.136	0.000	0.000	0.000	0.000
50	A	54	ASN	0	-0.005	-0.007	5.357	-0.721	-0.721	0.000	0.000	0.000	0.000
51	A	55	ALA	0	-0.002	0.001	6.415	0.280	0.280	0.000	0.000	0.000	0.000
52	A	56	LEU	0	0.004	0.005	7.888	0.307	0.307	0.000	0.000	0.000	0.000
53	A	57	ASN	0	0.056	0.030	11.130	-0.116	-0.116	0.000	0.000	0.000	0.000
54	A	58	ALA	0	0.111	0.043	13.533	0.092	0.092	0.000	0.000	0.000	0.000
55	A	59	TYR	0	-0.002	0.003	17.249	0.076	0.076	0.000	0.000	0.000	0.000
56	A	60	ASN	0	0.049	-0.003	13.877	0.146	0.146	0.000	0.000	0.000	0.000
57	A	61	ALA	0	0.015	0.024	16.034	0.060	0.060	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.045	0.011	17.680	0.079	0.079	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.069	-0.018	20.480	0.055	0.055	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.068	0.011	16.749	0.050	0.050	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.012	0.020	20.817	0.041	0.041	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.953	0.973	22.851	0.398	0.398	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.096	-0.047	22.384	0.039	0.039	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.048	0.020	20.958	0.030	0.030	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.860	0.943	25.293	0.247	0.247	0.000	0.000	0.000	0.000
66	A	70	VAL	0	-0.002	0.010	22.920	0.019	0.019	0.000	0.000	0.000	0.000
67	A	71	SER	0	-0.034	-0.012	25.419	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.038	0.006	19.242	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.899	-0.951	20.377	-0.467	-0.467	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.904	-0.943	21.364	-0.304	-0.304	0.000	0.000	0.000	0.000
71	A	75	PHE	0	-0.040	-0.039	16.412	0.008	0.008	0.000	0.000	0.000	0.000
72	A	76	SER	0	0.012	-0.009	14.813	-0.052	-0.052	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.051	0.020	17.232	0.022	0.022	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.019	-0.016	14.811	0.037	0.037	0.000	0.000	0.000	0.000
75	A	79	ILE	0	0.023	0.004	13.050	0.039	0.039	0.000	0.000	0.000	0.000
76	A	80	ALA	0	0.012	0.013	17.287	0.055	0.055	0.000	0.000	0.000	0.000
77	A	81	ARG	1	0.907	0.929	18.260	0.682	0.682	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-0.930	-0.969	15.873	-0.940	-0.940	0.000	0.000	0.000	0.000
79	A	83	ILE	0	-0.052	-0.013	19.746	0.034	0.034	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.883	0.983	22.288	0.457	0.457	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)