FMO DATABASE

FMODB ID: YY122

Calculation Name: 2XZE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XZE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y3E7

Base Structure: X-ray

Registration Date: 2023-03-14

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1213153.834882
FMO2-HF: Nuclear repulsion	1156137.088324
FMO2-HF: Total energy	-57016.746558
FMO2-MP2: Total energy	-57186.095758

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-1.244	2.78	3.09	-2.566	-4.547	-0.011

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.035

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

Sort

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	4	HIS	0	0.021	-0.003	3.803	-0.190	0.970	-0.013	-0.397	-0.750	0.002
4	A	5	GLY	0	0.017	0.033	6.018	0.772	0.772	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.805	-0.858	5.583	-0.728	-0.728	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.021	-0.026	7.027	-0.070	-0.070	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.065	-0.060	8.285	0.255	0.255	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.044	-0.016	2.461	-0.469	-0.057	1.194	-0.491	-1.114	-0.005
9	A	10	PRO	0	0.010	0.003	4.876	-0.223	-0.223	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.048	0.016	5.691	-0.221	-0.221	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.913	-0.964	7.404	0.360	0.360	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.880	-0.942	2.344	2.749	3.302	1.112	-0.657	-1.008	0.000
13	A	14	ARG	1	0.778	0.887	2.788	-1.490	-0.288	0.534	-0.735	-1.001	-0.008
14	A	15	VAL	0	-0.006	-0.012	4.538	0.181	0.165	-0.001	-0.001	0.018	0.000
15	A	16	ARG	1	0.867	0.924	4.777	-1.450	-1.367	-0.001	-0.003	-0.079	0.000
16	A	17	ALA	0	0.045	0.042	2.532	0.175	0.712	0.265	-0.259	-0.543	0.000
17	A	18	LEU	0	0.016	0.008	4.327	0.281	0.374	0.000	-0.023	-0.070	0.000
18	A	19	SER	0	-0.074	-0.034	7.840	0.169	0.169	0.000	0.000	0.000	0.000
19	A	20	GLN	0	-0.020	-0.009	6.461	0.042	0.042	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.016	0.019	7.725	0.012	0.012	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.026	-0.016	10.211	0.002	0.002	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.068	-0.037	11.698	0.025	0.025	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.018	0.017	12.504	0.025	0.025	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.101	-0.060	14.475	-0.049	-0.049	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.796	-0.917	18.117	0.072	0.072	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.093	-0.042	20.950	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.011	-0.004	24.645	0.009	0.009	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.790	-0.940	27.275	0.027	0.027	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.879	-0.909	30.087	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.119	-0.046	28.626	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.018	0.000	32.101	0.004	0.004	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.112	0.054	31.009	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.832	0.895	31.319	0.012	0.012	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.927	0.962	31.474	0.029	0.029	0.000	0.000	0.000	0.000
35	A	36	TYR	0	0.134	0.065	25.212	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.005	-0.006	28.283	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.925	0.960	30.319	0.025	0.025	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.023	0.012	27.484	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.017	0.011	25.579	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.037	-0.029	25.862	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.895	-0.953	26.925	-0.098	-0.098	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.018	0.005	20.764	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.007	-0.007	22.566	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.897	0.949	24.052	0.071	0.071	0.000	0.000	0.000	0.000
45	A	46	MET	0	0.055	0.028	22.807	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.008	0.003	20.083	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.012	-0.013	21.309	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.010	0.018	24.093	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.018	0.008	19.365	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.018	-0.026	20.370	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-1.024	-1.005	21.321	-0.128	-0.128	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.943	-0.970	22.871	-0.221	-0.221	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.014	0.004	21.287	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.016	0.002	16.395	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.036	-0.012	15.002	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.799	-0.865	11.311	-0.933	-0.933	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.017	-0.002	13.196	0.022	0.022	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.020	0.006	15.314	0.047	0.047	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.012	0.001	10.041	0.067	0.067	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.025	0.025	10.871	0.075	0.075	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.016	-0.010	13.581	0.068	0.068	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.020	-0.005	17.287	0.039	0.039	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.019	-0.013	13.362	0.083	0.083	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.995	1.032	15.770	0.165	0.165	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.043	-0.036	17.403	0.027	0.027	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.008	-0.008	18.142	0.014	0.014	0.000	0.000	0.000	0.000
67	A	68	THR	0	0.005	0.010	16.207	0.027	0.027	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.024	-0.002	18.775	0.013	0.013	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.044	-0.037	21.813	0.008	0.008	0.000	0.000	0.000	0.000
70	A	71	ILE	0	-0.050	-0.016	21.152	0.004	0.004	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.923	-0.959	17.428	0.145	0.145	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.854	0.933	16.988	-0.090	-0.090	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.014	-0.007	22.718	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	PRO	0	-0.061	-0.045	24.969	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.923	0.965	21.143	-0.104	-0.104	0.000	0.000	0.000	0.000
76	A	77	HIS	0	-0.031	0.015	27.056	0.004	0.004	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.937	0.964	29.153	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.897	-0.947	32.389	0.010	0.010	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.071	-0.037	30.090	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.936	0.962	32.938	-0.031	-0.031	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.006	-0.008	35.126	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.005	0.028	35.276	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.009	0.008	37.268	0.001	0.001	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.055	-0.045	33.086	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.007	-0.003	36.533	0.001	0.001	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.760	-0.873	33.531	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.963	0.997	31.723	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.965	0.986	32.372	0.004	0.004	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.904	-0.964	33.350	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.018	0.014	27.761	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.001	-0.002	28.493	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.967	0.987	29.134	0.028	0.028	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.963	0.987	27.605	0.054	0.054	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.011	0.005	23.434	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.916	0.971	24.605	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.885	-0.965	26.521	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.065	-0.015	24.758	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.034	-0.018	21.600	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.018	0.004	19.132	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.068	0.041	20.406	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.870	0.947	21.088	0.122	0.122	0.000	0.000	0.000	0.000
102	A	103	ALA	0	0.003	0.004	16.498	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.936	-0.980	16.354	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.864	-0.935	17.619	-0.116	-0.116	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.009	-0.016	15.732	-0.017	-0.017	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.960	0.995	11.667	-0.140	-0.140	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.004	0.002	13.698	-0.021	-0.021	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.949	-0.974	16.277	-0.224	-0.224	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.018	-0.016	11.022	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.031	0.018	10.374	-0.047	-0.047	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.953	0.992	12.917	0.172	0.172	0.000	0.000	0.000	0.000
112	A	113	ARG	1	0.874	0.934	13.893	0.386	0.386	0.000	0.000	0.000	0.000
113	A	114	TYR	0	0.001	-0.051	8.318	-0.045	-0.045	0.000	0.000	0.000	0.000
114	A	115	THR	0	-0.011	-0.016	11.708	0.027	0.027	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.906	0.956	13.365	0.218	0.218	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.798	-0.898	11.915	-0.695	-0.695	0.000	0.000	0.000	0.000
117	A	118	TYR	0	-0.004	0.007	9.167	0.070	0.070	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.096	-0.051	12.257	0.057	0.057	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.838	-0.923	15.750	-0.190	-0.190	0.000	0.000	0.000	0.000
120	A	121	TYR	0	0.022	0.019	12.417	0.024	0.024	0.000	0.000	0.000	0.000
121	A	122	ASN	0	-0.011	-0.024	12.408	0.023	0.023	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.993	-0.991	15.853	-0.043	-0.043	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.890	-0.938	18.417	-0.201	-0.201	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.791	0.897	15.494	0.213	0.213	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.917	0.970	18.771	-0.021	-0.021	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.986	0.988	21.064	0.074	0.074	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.832	-0.918	20.372	-0.137	-0.137	0.000	0.000	0.000	0.000
128	A	129	ALA	0	-0.019	-0.011	21.719	0.007	0.007	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.970	-0.994	23.675	0.006	0.006	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.963	-0.975	26.635	-0.059	-0.059	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.019	-0.004	24.878	0.002	0.002	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.001	-0.007	27.698	0.004	0.004	0.000	0.000	0.000	0.000
133	A	134	ARG	1	0.935	0.972	29.347	0.022	0.022	0.000	0.000	0.000	0.000
134	A	135	ASN	0	-0.034	-0.044	30.718	0.004	0.004	0.000	0.000	0.000	0.000
135	A	136	MET	0	-0.054	-0.012	29.111	0.001	0.001	0.000	0.000	0.000	0.000
136	A	137	ALA	0	-0.026	-0.005	33.118	0.003	0.003	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.087	-0.034	35.558	0.001	0.001	0.000	0.000	0.000	0.000
138	A	139	GLN	0	0.006	-0.005	38.041	0.001	0.001	0.000	0.000	0.000	0.000
139	A	140	GLN	0	-0.003	-0.014	40.800	0.002	0.002	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.914	-0.943	42.635	-0.010	-0.010	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.073	-0.019	42.882	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)