FMO DATABASE

FMODB ID: 2JZKR

Calculation Name: 4DYW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DYW

Chain ID: A

ChEMBL ID:

UniProt ID: Q3JWU2

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptAll
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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1092674.41462
FMO2-HF: Nuclear repulsion	1042904.174187
FMO2-HF: Total energy	-49770.240433
FMO2-MP2: Total energy	-49915.898416

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:GLU)

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

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.
64.342	66.249	-0.018	-1.035	-0.853	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.952 / q_NPA : -0.981

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	PRO	0	-0.015	-0.002	3.865	-1.023	0.884	-0.018	-1.035	-0.853	0.003
4	A	8	ARG	1	0.920	0.978	6.531	-27.078	-27.078	0.000	0.000	0.000	0.000
5	A	9	VAL	0	0.024	0.012	8.647	-1.407	-1.407	0.000	0.000	0.000	0.000
6	A	10	GLY	0	0.013	0.000	12.320	0.237	0.237	0.000	0.000	0.000	0.000
7	A	11	CYS	0	-0.073	-0.030	15.102	-0.547	-0.547	0.000	0.000	0.000	0.000
8	A	12	GLY	0	0.086	0.028	18.890	0.143	0.143	0.000	0.000	0.000	0.000
9	A	13	ALA	0	-0.008	0.005	22.151	-0.158	-0.158	0.000	0.000	0.000	0.000
10	A	14	ALA	0	0.028	0.017	25.964	-0.135	-0.135	0.000	0.000	0.000	0.000
11	A	15	ILE	0	0.001	0.003	28.496	-0.287	-0.287	0.000	0.000	0.000	0.000
12	A	16	VAL	0	-0.009	-0.010	31.338	-0.099	-0.099	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.889	0.949	34.417	-8.063	-8.063	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.919	-0.954	38.209	7.274	7.274	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.000	-0.002	39.177	-0.096	-0.096	0.000	0.000	0.000	0.000
16	A	20	ARG	1	0.883	0.942	36.684	-7.261	-7.261	0.000	0.000	0.000	0.000
17	A	21	ILE	0	0.019	0.005	29.260	0.062	0.062	0.000	0.000	0.000	0.000
18	A	22	LEU	0	-0.026	-0.004	31.568	-0.118	-0.118	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.042	-0.009	27.939	0.354	0.354	0.000	0.000	0.000	0.000
20	A	24	ILE	0	0.021	-0.003	25.895	-0.392	-0.392	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.835	0.927	26.770	-9.422	-9.422	0.000	0.000	0.000	0.000
22	A	26	ARG	1	0.941	0.978	18.000	-14.286	-14.286	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.842	0.901	24.404	-10.118	-10.118	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.781	0.877	20.027	-12.315	-12.315	0.000	0.000	0.000	0.000
25	A	29	ALA	0	0.010	0.015	16.931	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	30	PRO	0	0.053	0.024	13.774	-0.093	-0.093	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.784	-0.901	16.299	13.256	13.256	0.000	0.000	0.000	0.000
28	A	32	ALA	0	0.029	0.022	19.352	-0.389	-0.389	0.000	0.000	0.000	0.000
29	A	33	GLY	0	-0.026	-0.019	21.883	-0.168	-0.168	0.000	0.000	0.000	0.000
30	A	34	CYS	0	-0.075	-0.025	22.929	-0.390	-0.390	0.000	0.000	0.000	0.000
31	A	35	TRP	0	0.035	0.005	24.986	0.045	0.045	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.005	-0.016	24.296	0.261	0.261	0.000	0.000	0.000	0.000
33	A	37	LEU	0	0.017	0.004	23.671	-0.363	-0.363	0.000	0.000	0.000	0.000
34	A	38	PRO	0	-0.006	0.022	23.726	0.355	0.355	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.013	-0.023	21.150	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	40	GLY	0	-0.012	0.012	17.574	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	41	LYS	1	0.848	0.912	13.840	-15.723	-15.723	0.000	0.000	0.000	0.000
38	A	42	VAL	0	0.008	0.011	14.255	-1.092	-1.092	0.000	0.000	0.000	0.000
39	A	43	ASP	-1	-0.859	-0.907	14.001	17.766	17.766	0.000	0.000	0.000	0.000
40	A	44	TRP	0	-0.001	-0.022	12.442	0.370	0.370	0.000	0.000	0.000	0.000
41	A	45	LEU	0	-0.033	-0.022	15.375	-0.940	-0.940	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.750	-0.830	17.654	13.271	13.271	0.000	0.000	0.000	0.000
43	A	47	PRO	0	-0.009	-0.013	18.772	0.423	0.423	0.000	0.000	0.000	0.000
44	A	48	VAL	0	0.067	0.030	19.027	-0.186	-0.186	0.000	0.000	0.000	0.000
45	A	49	GLU	-1	-0.815	-0.882	20.465	11.482	11.482	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.843	0.907	21.435	-13.357	-13.357	0.000	0.000	0.000	0.000
47	A	51	ALA	0	-0.004	0.014	19.271	-0.209	-0.209	0.000	0.000	0.000	0.000
48	A	52	VAL	0	0.021	0.003	21.267	-0.172	-0.172	0.000	0.000	0.000	0.000
49	A	53	CYS	0	-0.068	-0.040	23.445	-0.444	-0.444	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.721	0.828	18.845	-14.345	-14.345	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.810	-0.897	19.184	14.516	14.516	0.000	0.000	0.000	0.000
52	A	56	ILE	0	-0.022	-0.012	23.074	-0.223	-0.223	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.922	-0.959	26.343	9.145	9.145	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.879	-0.951	22.705	12.412	12.412	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.821	-0.896	22.849	12.407	12.407	0.000	0.000	0.000	0.000
56	A	60	LEU	0	-0.059	-0.046	26.691	-0.297	-0.297	0.000	0.000	0.000	0.000
57	A	61	GLY	0	-0.028	0.001	30.040	-0.354	-0.354	0.000	0.000	0.000	0.000
58	A	62	ILE	0	-0.056	-0.024	31.246	-0.340	-0.340	0.000	0.000	0.000	0.000
59	A	63	ALA	0	0.083	0.054	31.139	0.327	0.327	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.005	-0.013	27.679	-0.291	-0.291	0.000	0.000	0.000	0.000
61	A	65	GLU	-1	-0.814	-0.889	31.698	8.010	8.010	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.757	0.851	33.568	-8.101	-8.101	0.000	0.000	0.000	0.000
63	A	67	ALA	0	0.041	0.040	29.112	-0.094	-0.094	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.010	-0.005	29.730	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.037	-0.014	23.209	0.034	0.034	0.000	0.000	0.000	0.000
66	A	70	LEU	0	-0.058	-0.018	26.201	-0.339	-0.339	0.000	0.000	0.000	0.000
67	A	71	CYS	0	0.003	0.006	23.903	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.005	-0.011	17.997	0.242	0.242	0.000	0.000	0.000	0.000
69	A	73	VAL	0	-0.002	0.016	16.867	-0.219	-0.219	0.000	0.000	0.000	0.000
70	A	74	ASP	-1	-0.848	-0.922	14.038	19.098	19.098	0.000	0.000	0.000	0.000
71	A	75	HIS	0	-0.064	-0.034	12.019	-1.582	-1.582	0.000	0.000	0.000	0.000
72	A	76	ILE	0	-0.018	-0.016	9.673	1.686	1.686	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.778	-0.871	9.919	17.126	17.126	0.000	0.000	0.000	0.000
74	A	78	ALA	0	-0.002	-0.015	8.331	1.540	1.540	0.000	0.000	0.000	0.000
75	A	79	ALA	0	-0.065	-0.018	9.351	0.685	0.685	0.000	0.000	0.000	0.000
76	A	80	ASN	0	-0.099	-0.079	11.091	-0.228	-0.228	0.000	0.000	0.000	0.000
77	A	81	GLY	0	-0.028	0.005	6.877	0.542	0.542	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-0.873	-0.931	5.658	24.846	24.846	0.000	0.000	0.000	0.000
79	A	83	HIS	0	0.009	-0.015	6.800	-1.030	-1.030	0.000	0.000	0.000	0.000
80	A	84	TRP	0	-0.059	-0.035	8.253	2.517	2.517	0.000	0.000	0.000	0.000
81	A	85	VAL	0	0.029	0.026	11.171	-1.201	-1.201	0.000	0.000	0.000	0.000
82	A	86	ALA	0	0.004	-0.013	13.860	0.227	0.227	0.000	0.000	0.000	0.000
83	A	87	PRO	0	-0.028	-0.005	16.854	-0.731	-0.731	0.000	0.000	0.000	0.000
84	A	88	VAL	0	0.009	0.010	20.118	0.004	0.004	0.000	0.000	0.000	0.000
85	A	89	TYR	0	-0.042	-0.058	22.404	-0.111	-0.111	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.000	0.012	26.379	-0.057	-0.057	0.000	0.000	0.000	0.000
87	A	91	ALA	0	0.029	-0.001	29.964	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	92	HIS	0	0.060	0.037	32.060	-0.048	-0.048	0.000	0.000	0.000	0.000
89	A	93	ALA	0	-0.082	-0.034	35.167	-0.253	-0.253	0.000	0.000	0.000	0.000
90	A	94	PHE	0	0.029	0.001	33.703	0.292	0.292	0.000	0.000	0.000	0.000
91	A	95	SER	0	-0.019	-0.014	35.558	-0.244	-0.244	0.000	0.000	0.000	0.000
92	A	96	GLY	0	0.007	0.005	35.944	0.205	0.205	0.000	0.000	0.000	0.000
93	A	97	GLU	-1	-0.914	-0.982	37.639	7.672	7.672	0.000	0.000	0.000	0.000
94	A	98	PRO	0	-0.053	0.006	33.362	0.067	0.067	0.000	0.000	0.000	0.000
95	A	99	ARG	1	0.916	0.961	33.161	-9.095	-9.095	0.000	0.000	0.000	0.000
96	A	100	VAL	0	0.034	0.006	29.753	0.254	0.254	0.000	0.000	0.000	0.000
97	A	101	VAL	0	-0.050	-0.010	28.884	-0.322	-0.322	0.000	0.000	0.000	0.000
98	A	102	GLU	-1	-0.816	-0.900	24.790	11.829	11.829	0.000	0.000	0.000	0.000
99	A	103	PRO	0	-0.034	-0.027	27.987	0.228	0.228	0.000	0.000	0.000	0.000
100	A	104	ASP	-1	-0.847	-0.902	26.264	11.127	11.127	0.000	0.000	0.000	0.000
101	A	105	ARG	1	0.802	0.880	21.478	-12.301	-12.301	0.000	0.000	0.000	0.000
102	A	106	HIS	0	-0.008	-0.022	23.601	0.033	0.033	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.864	-0.915	27.007	9.539	9.539	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.036	-0.005	30.188	-0.345	-0.345	0.000	0.000	0.000	0.000
105	A	109	LEU	0	0.023	0.006	30.581	0.342	0.342	0.000	0.000	0.000	0.000
106	A	110	GLY	0	-0.009	0.006	32.749	-0.296	-0.296	0.000	0.000	0.000	0.000
107	A	111	TRP	0	0.021	0.013	33.730	0.282	0.282	0.000	0.000	0.000	0.000
108	A	112	PHE	0	0.005	-0.002	32.951	-0.214	-0.214	0.000	0.000	0.000	0.000
109	A	113	ALA	0	0.041	0.022	35.514	0.113	0.113	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.016	-0.024	33.172	0.146	0.146	0.000	0.000	0.000	0.000
111	A	115	ASP	-1	-0.934	-0.967	34.681	7.684	7.684	0.000	0.000	0.000	0.000
112	A	116	ASP	-1	-0.983	-0.980	36.900	7.553	7.553	0.000	0.000	0.000	0.000
113	A	117	LEU	0	-0.009	0.010	30.723	0.128	0.128	0.000	0.000	0.000	0.000
114	A	118	PRO	0	0.009	0.021	30.794	-0.054	-0.054	0.000	0.000	0.000	0.000
115	A	119	GLN	0	-0.031	-0.023	29.478	0.512	0.512	0.000	0.000	0.000	0.000
116	A	120	PRO	0	-0.011	-0.022	25.503	-0.182	-0.182	0.000	0.000	0.000	0.000
117	A	121	LEU	0	0.045	0.022	25.680	0.047	0.047	0.000	0.000	0.000	0.000
118	A	122	THR	0	0.008	0.007	20.553	0.084	0.084	0.000	0.000	0.000	0.000
119	A	123	HIS	0	-0.015	-0.043	16.742	-0.888	-0.888	0.000	0.000	0.000	0.000
120	A	124	ALA	0	0.017	-0.003	18.899	-0.244	-0.244	0.000	0.000	0.000	0.000
121	A	125	THR	0	0.000	-0.005	20.515	-0.375	-0.375	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.813	0.922	20.166	-12.911	-12.911	0.000	0.000	0.000	0.000
123	A	127	ILE	0	0.082	0.039	19.641	-0.282	-0.282	0.000	0.000	0.000	0.000
124	A	128	ALA	0	0.014	0.009	23.734	-0.244	-0.244	0.000	0.000	0.000	0.000
125	A	129	LEU	0	0.004	-0.009	25.592	-0.404	-0.404	0.000	0.000	0.000	0.000
126	A	130	GLU	-1	-0.951	-0.979	25.370	10.832	10.832	0.000	0.000	0.000	0.000
127	A	131	GLN	0	-0.087	-0.046	26.470	0.003	0.003	0.000	0.000	0.000	0.000
128	A	132	VAL	0	-0.062	-0.017	29.350	-0.224	-0.224	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.046	-0.013	31.816	-0.354	-0.354	0.000	0.000	0.000	0.000

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