FMO DATABASE

FMODB ID: R82Z8

Calculation Name: 4EZA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EZA

Chain ID: B

ChEMBL ID:

UniProt ID: Q13576

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	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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-702809.312465
FMO2-HF: Nuclear repulsion	664886.67647
FMO2-HF: Total energy	-37922.635994
FMO2-MP2: Total energy	-38032.805144

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(B:2:LYS)

Summations of interaction energy for fragment #1(B:2:LYS)

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.
-23.746	-17.876	3.894	-4.828	-4.934	-0.054

Interaction energy analysis for fragmet #1(B:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.964 / q_NPA : 0.986

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	B	4	VAL	0	-0.006	0.008	2.168	-39.277	-33.961	3.886	-4.729	-4.471	-0.054
4	B	5	LYS	1	0.911	0.961	3.330	59.431	59.903	0.008	-0.074	-0.406	0.000
5	B	6	TYR	0	0.046	0.011	6.112	1.603	1.603	0.000	0.000	0.000	0.000
6	B	7	THR	0	0.037	0.027	9.625	0.982	0.982	0.000	0.000	0.000	0.000
7	B	8	ALA	0	0.087	0.026	12.269	0.327	0.327	0.000	0.000	0.000	0.000
8	B	9	ALA	0	0.003	0.006	15.728	0.784	0.784	0.000	0.000	0.000	0.000
9	B	10	LYS	1	0.959	0.991	12.062	21.964	21.964	0.000	0.000	0.000	0.000
10	B	11	LEU	0	-0.013	-0.023	12.844	0.523	0.523	0.000	0.000	0.000	0.000
11	B	12	HIS	0	-0.051	-0.004	16.027	1.078	1.078	0.000	0.000	0.000	0.000
12	B	13	GLU	-1	-0.937	-0.978	17.447	-17.120	-17.120	0.000	0.000	0.000	0.000
13	B	14	LYS	1	0.821	0.918	13.062	23.206	23.206	0.000	0.000	0.000	0.000
14	B	15	GLY	0	0.051	0.043	18.901	0.378	0.378	0.000	0.000	0.000	0.000
15	B	16	VAL	0	-0.041	-0.017	16.044	0.214	0.214	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.007	0.003	17.691	0.181	0.181	0.000	0.000	0.000	0.000
17	B	18	LEU	0	-0.054	-0.042	19.842	0.421	0.421	0.000	0.000	0.000	0.000
18	B	19	ASP	-1	-0.838	-0.943	23.147	-12.114	-12.114	0.000	0.000	0.000	0.000
19	B	20	ILE	0	-0.094	-0.045	18.805	-0.707	-0.707	0.000	0.000	0.000	0.000
20	B	21	ASP	-1	-0.801	-0.903	23.352	-11.507	-11.507	0.000	0.000	0.000	0.000
21	B	22	ASP	-1	-0.953	-0.990	25.894	-11.388	-11.388	0.000	0.000	0.000	0.000
22	B	23	LEU	0	-0.074	-0.020	20.631	-0.227	-0.227	0.000	0.000	0.000	0.000
23	B	24	GLN	0	0.072	0.036	25.219	-0.246	-0.246	0.000	0.000	0.000	0.000
24	B	25	THR	0	0.124	0.055	23.756	-0.490	-0.490	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.067	-0.032	22.564	-0.878	-0.878	0.000	0.000	0.000	0.000
26	B	27	GLN	0	-0.011	-0.031	21.671	-0.417	-0.417	0.000	0.000	0.000	0.000
27	B	28	PHE	0	0.060	0.029	18.755	-1.017	-1.017	0.000	0.000	0.000	0.000
28	B	29	LYS	1	0.895	0.952	16.352	13.782	13.782	0.000	0.000	0.000	0.000
29	B	30	ASN	0	-0.029	-0.013	15.458	-1.525	-1.525	0.000	0.000	0.000	0.000
30	B	31	VAL	0	0.049	0.046	15.380	-0.367	-0.367	0.000	0.000	0.000	0.000
31	B	32	THR	0	-0.100	-0.051	8.799	-1.375	-1.375	0.000	0.000	0.000	0.000
32	B	33	PHE	0	0.026	0.019	10.956	1.107	1.107	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.866	-0.943	7.183	-44.698	-44.698	0.000	0.000	0.000	0.000
34	B	35	ILE	0	-0.011	-0.012	7.217	3.521	3.521	0.000	0.000	0.000	0.000
35	B	36	ILE	0	-0.036	-0.031	4.144	-8.021	-7.939	0.000	-0.025	-0.057	0.000
36	B	37	ALA	0	0.030	0.028	5.035	3.468	3.468	0.000	0.000	0.000	0.000
37	B	38	THR	0	0.000	-0.017	6.667	-0.332	-0.332	0.000	0.000	0.000	0.000
38	B	39	GLU	-1	-0.955	-0.978	9.190	-16.873	-16.873	0.000	0.000	0.000	0.000
39	B	40	ASP	-1	-0.887	-0.927	11.424	-14.738	-14.738	0.000	0.000	0.000	0.000
40	B	41	VAL	0	-0.022	-0.035	11.964	-0.938	-0.938	0.000	0.000	0.000	0.000
41	B	42	GLY	0	-0.037	-0.012	12.975	-0.549	-0.549	0.000	0.000	0.000	0.000
42	B	43	ILE	0	-0.002	0.009	13.267	0.228	0.228	0.000	0.000	0.000	0.000
43	B	44	PHE	0	0.003	0.005	8.921	-1.783	-1.783	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.747	-0.838	9.046	-22.367	-22.367	0.000	0.000	0.000	0.000
45	B	46	VAL	0	-0.017	-0.018	9.682	-3.414	-3.414	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.743	0.845	9.735	27.204	27.204	0.000	0.000	0.000	0.000
47	B	48	SER	0	0.019	0.015	12.033	-1.967	-1.967	0.000	0.000	0.000	0.000
48	B	49	LYS	1	0.898	0.938	8.154	32.680	32.680	0.000	0.000	0.000	0.000
49	B	50	PHE	0	0.045	0.012	13.890	0.167	0.167	0.000	0.000	0.000	0.000
50	B	51	LEU	0	-0.009	-0.010	16.009	0.160	0.160	0.000	0.000	0.000	0.000
51	B	52	GLY	0	-0.034	-0.013	12.313	0.168	0.168	0.000	0.000	0.000	0.000
52	B	53	VAL	0	-0.012	0.001	13.098	-1.046	-1.046	0.000	0.000	0.000	0.000
53	B	54	GLU	-1	-0.878	-0.941	12.656	-22.935	-22.935	0.000	0.000	0.000	0.000
54	B	55	MET	0	-0.039	-0.021	14.962	0.967	0.967	0.000	0.000	0.000	0.000
55	B	56	GLU	-1	-0.889	-0.943	16.933	-14.065	-14.065	0.000	0.000	0.000	0.000
56	B	57	LYS	1	0.905	0.944	12.982	18.082	18.082	0.000	0.000	0.000	0.000
57	B	58	VAL	0	0.009	0.016	14.884	1.193	1.193	0.000	0.000	0.000	0.000
58	B	59	GLN	0	-0.032	-0.023	12.962	-1.931	-1.931	0.000	0.000	0.000	0.000
59	B	60	LEU	0	-0.015	-0.009	14.696	1.074	1.074	0.000	0.000	0.000	0.000
60	B	61	ASN	0	0.103	0.056	15.143	-1.255	-1.255	0.000	0.000	0.000	0.000
61	B	62	ILE	0	0.010	-0.005	15.386	0.574	0.574	0.000	0.000	0.000	0.000
62	B	63	GLN	0	0.032	-0.006	18.012	0.663	0.663	0.000	0.000	0.000	0.000
63	B	64	ASP	-1	-0.868	-0.922	20.842	-12.539	-12.539	0.000	0.000	0.000	0.000
64	B	65	LEU	0	-0.046	-0.037	17.979	0.286	0.286	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.031	-0.024	21.200	0.399	0.399	0.000	0.000	0.000	0.000
66	B	67	GLN	0	-0.014	-0.008	23.836	0.461	0.461	0.000	0.000	0.000	0.000
67	B	68	MET	0	0.003	0.009	23.742	0.207	0.207	0.000	0.000	0.000	0.000
68	B	69	GLN	0	-0.027	-0.013	24.252	0.574	0.574	0.000	0.000	0.000	0.000
69	B	70	TYR	0	-0.042	-0.023	25.921	0.341	0.341	0.000	0.000	0.000	0.000
70	B	71	GLU	-1	-0.970	-0.966	29.746	-9.442	-9.442	0.000	0.000	0.000	0.000
71	B	72	GLY	0	-0.044	-0.014	30.875	0.239	0.239	0.000	0.000	0.000	0.000
72	B	73	VAL	0	-0.009	0.011	28.061	0.093	0.093	0.000	0.000	0.000	0.000
73	B	74	ALA	0	-0.013	-0.016	27.776	-0.390	-0.390	0.000	0.000	0.000	0.000
74	B	75	VAL	0	-0.072	-0.044	25.226	-0.552	-0.552	0.000	0.000	0.000	0.000
75	B	76	MET	0	0.047	0.038	20.067	0.477	0.477	0.000	0.000	0.000	0.000
76	B	77	LYS	1	0.846	0.916	23.733	11.733	11.733	0.000	0.000	0.000	0.000
77	B	78	MET	0	-0.040	0.006	15.741	-0.216	-0.216	0.000	0.000	0.000	0.000
78	B	79	PHE	0	0.051	0.010	15.792	-0.786	-0.786	0.000	0.000	0.000	0.000
79	B	80	ASP	-1	-0.820	-0.904	21.477	-12.092	-12.092	0.000	0.000	0.000	0.000
80	B	81	LYS	1	0.910	0.962	23.433	13.195	13.195	0.000	0.000	0.000	0.000
81	B	82	VAL	0	-0.060	-0.017	18.409	-0.023	-0.023	0.000	0.000	0.000	0.000
82	B	83	LYS	1	0.948	0.989	21.865	11.428	11.428	0.000	0.000	0.000	0.000
83	B	84	VAL	0	0.027	-0.002	18.299	-0.401	-0.401	0.000	0.000	0.000	0.000
84	B	85	ASN	0	0.028	0.003	21.261	0.466	0.466	0.000	0.000	0.000	0.000
85	B	86	VAL	0	0.045	0.027	21.093	-0.878	-0.878	0.000	0.000	0.000	0.000
86	B	87	ASN	0	0.062	0.019	21.442	-0.652	-0.652	0.000	0.000	0.000	0.000
87	B	88	LEU	0	-0.037	-0.022	19.509	-0.547	-0.547	0.000	0.000	0.000	0.000
88	B	89	LEU	0	0.012	0.007	15.525	-1.239	-1.239	0.000	0.000	0.000	0.000
89	B	90	ILE	0	0.032	0.022	16.518	-1.261	-1.261	0.000	0.000	0.000	0.000
90	B	91	TYR	0	-0.016	-0.008	16.692	-1.080	-1.080	0.000	0.000	0.000	0.000
91	B	92	LEU	0	-0.077	-0.050	12.345	-0.968	-0.968	0.000	0.000	0.000	0.000
92	B	93	LEU	0	-0.038	-0.020	12.161	-2.004	-2.004	0.000	0.000	0.000	0.000
93	B	94	ASN	0	-0.044	-0.004	11.989	-0.539	-0.539	0.000	0.000	0.000	0.000
94	B	95	LYS	1	0.924	0.983	10.689	21.401	21.401	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:LYS)