FMO DATABASE

FMODB ID: QY28Y

Calculation Name: 1XEB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XEB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I717

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	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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1459129.370769
FMO2-HF: Nuclear repulsion	1399773.584854
FMO2-HF: Total energy	-59355.785915
FMO2-MP2: Total energy	-59529.593325

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.
-1.541	0.829	-0.027	-1.199	-1.145	0.001

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 : -0.034 / 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	ASP	-1	-0.857	-0.910	3.822	-2.767	-0.554	-0.027	-1.145	-1.041	0.001
4	A	5	TRP	0	-0.033	-0.039	5.616	0.313	0.313	0.000	0.000	0.000	0.000
5	A	6	THR	0	-0.013	-0.004	9.158	0.068	0.068	0.000	0.000	0.000	0.000
6	A	7	CYS	0	0.004	-0.008	12.898	0.056	0.056	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.814	0.919	16.045	0.289	0.289	0.000	0.000	0.000	0.000
8	A	9	HIS	0	0.100	0.052	19.158	0.006	0.006	0.000	0.000	0.000	0.000
9	A	10	HIS	0	-0.015	-0.025	22.756	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.027	-0.011	24.368	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.896	-0.936	22.453	-0.155	-0.155	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.086	-0.034	20.131	-0.029	-0.029	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.015	-0.008	19.419	0.013	0.013	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.013	-0.024	21.816	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.930	0.962	18.729	0.219	0.219	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.748	-0.860	16.456	-0.336	-0.336	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.042	0.032	18.653	0.004	0.004	0.000	0.000	0.000	0.000
18	A	19	TYR	0	0.017	0.006	21.293	0.013	0.013	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.028	0.010	16.399	0.011	0.011	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.011	-0.010	18.068	0.010	0.010	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.007	-0.006	18.915	0.027	0.027	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.017	0.002	18.924	0.000	0.000	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.012	-0.003	14.731	0.017	0.017	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.742	0.827	18.682	0.113	0.113	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.018	0.007	21.149	0.019	0.019	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.974	-0.977	17.849	-0.081	-0.081	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.037	-0.026	17.918	0.017	0.017	0.000	0.000	0.000	0.000
28	A	29	PHE	0	-0.021	-0.021	20.916	0.010	0.010	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.002	0.018	24.275	0.003	0.003	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.029	-0.024	24.252	0.006	0.006	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.883	-0.924	19.872	0.038	0.038	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.051	-0.035	22.616	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.889	0.954	26.172	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	35	CYS	0	0.030	0.046	28.671	0.001	0.001	0.000	0.000	0.000	0.000
35	A	36	PRO	0	-0.024	-0.005	29.848	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	37	TYR	0	-0.053	-0.078	25.952	0.002	0.002	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.002	-0.005	30.974	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.684	-0.779	24.806	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.004	-0.011	27.681	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.789	-0.905	28.753	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.003	0.010	30.602	0.004	0.004	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.048	-0.021	28.584	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.795	-0.889	24.716	-0.091	-0.091	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.011	-0.007	26.103	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.008	0.004	28.558	0.006	0.006	0.000	0.000	0.000	0.000
46	A	47	GLY	0	-0.038	-0.021	29.100	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.817	-0.911	26.788	-0.081	-0.081	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.056	-0.023	23.888	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	50	HIS	0	-0.054	-0.045	20.176	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	51	HIS	0	-0.018	0.022	18.786	0.010	0.010	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.016	0.004	12.720	-0.036	-0.036	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.032	-0.015	13.091	0.023	0.023	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.018	0.014	7.813	-0.045	-0.045	0.000	0.000	0.000	0.000
54	A	55	TRP	0	-0.027	-0.030	8.540	0.194	0.194	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.980	0.978	3.568	0.496	0.653	0.000	-0.054	-0.104	0.000
56	A	57	ASP	-1	-0.901	-0.942	6.256	-0.367	-0.367	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.009	-0.004	8.432	0.190	0.190	0.000	0.000	0.000	0.000
58	A	59	GLN	0	-0.005	0.003	10.081	0.142	0.142	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.007	0.010	9.938	-0.219	-0.219	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.017	-0.014	6.706	0.146	0.146	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.011	-0.001	10.452	0.197	0.197	0.000	0.000	0.000	0.000
62	A	63	TYR	0	-0.014	-0.055	12.120	-0.097	-0.097	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.006	0.011	15.101	0.057	0.057	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.819	0.920	17.642	0.031	0.031	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.001	-0.008	18.552	0.019	0.019	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.010	-0.006	22.441	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.765	-0.883	26.240	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	69	PRO	0	0.065	0.021	27.950	0.003	0.003	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.004	0.014	30.724	0.004	0.004	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.902	0.946	31.907	0.050	0.050	0.000	0.000	0.000	0.000
71	A	72	HIS	1	0.817	0.917	29.884	0.035	0.035	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.891	-0.951	33.060	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	74	GLY	0	0.002	0.016	33.633	0.003	0.003	0.000	0.000	0.000	0.000
74	A	75	GLN	0	-0.012	-0.013	30.246	0.007	0.007	0.000	0.000	0.000	0.000
75	A	76	VAL	0	0.032	0.034	24.309	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.012	-0.007	26.442	0.008	0.008	0.000	0.000	0.000	0.000
77	A	78	ILE	0	0.007	0.012	20.220	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.003	-0.013	22.200	0.010	0.010	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.819	0.897	21.201	0.032	0.032	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.001	0.009	16.995	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.035	0.017	16.387	0.015	0.015	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.003	-0.007	12.190	0.012	0.012	0.000	0.000	0.000	0.000
83	A	84	SER	0	0.091	0.026	11.966	0.006	0.006	0.000	0.000	0.000	0.000
84	A	85	SER	0	0.024	-0.005	12.994	0.061	0.061	0.000	0.000	0.000	0.000
85	A	86	ALA	0	0.020	0.012	12.409	0.039	0.039	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.052	-0.018	8.229	0.024	0.024	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.792	0.900	9.873	0.082	0.082	0.000	0.000	0.000	0.000
88	A	89	GLY	0	-0.006	-0.001	12.241	0.008	0.008	0.000	0.000	0.000	0.000
89	A	90	GLN	0	0.017	0.004	7.747	-0.123	-0.123	0.000	0.000	0.000	0.000
90	A	91	GLY	0	0.007	0.008	8.639	0.256	0.256	0.000	0.000	0.000	0.000
91	A	92	LEU	0	0.026	0.006	7.534	0.037	0.037	0.000	0.000	0.000	0.000
92	A	93	GLY	0	0.011	0.011	9.998	-0.119	-0.119	0.000	0.000	0.000	0.000
93	A	94	HIS	0	0.045	0.029	12.548	-0.074	-0.074	0.000	0.000	0.000	0.000
94	A	95	GLN	0	0.016	0.017	6.157	0.001	0.001	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.024	-0.004	10.663	-0.121	-0.121	0.000	0.000	0.000	0.000
96	A	97	MET	0	-0.006	0.000	12.984	-0.069	-0.069	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.932	-0.959	11.934	0.165	0.165	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.975	0.980	7.151	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.020	-0.005	13.886	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.018	-0.015	17.020	-0.016	-0.016	0.000	0.000	0.000	0.000
101	A	102	GLN	0	0.008	0.018	14.532	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.036	-0.024	17.080	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.006	-0.005	18.753	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.934	-0.950	21.122	-0.015	-0.015	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.909	0.954	17.398	0.132	0.132	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.088	-0.043	21.276	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	108	TRP	0	-0.005	-0.021	23.034	0.001	0.001	0.000	0.000	0.000	0.000
108	A	109	LEU	0	0.057	0.047	26.028	0.006	0.006	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.929	-0.959	27.174	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	111	THR	0	-0.073	-0.030	27.991	0.002	0.002	0.000	0.000	0.000	0.000
111	A	112	PRO	0	-0.064	-0.031	27.456	0.002	0.002	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.036	0.014	23.104	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	114	TYR	0	-0.030	-0.011	26.446	0.009	0.009	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.004	0.010	22.843	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.001	0.013	26.399	0.004	0.004	0.000	0.000	0.000	0.000
116	A	117	ALA	0	0.007	0.001	25.644	0.002	0.002	0.000	0.000	0.000	0.000
117	A	118	GLN	0	0.034	0.002	24.896	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	ALA	0	0.007	-0.027	27.478	0.006	0.006	0.000	0.000	0.000	0.000
119	A	120	HIS	0	0.039	0.029	24.465	0.007	0.007	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.038	0.020	22.088	0.005	0.005	0.000	0.000	0.000	0.000
121	A	122	GLN	0	0.051	-0.015	24.974	0.002	0.002	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.005	-0.017	26.541	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	TYR	0	-0.070	-0.037	16.806	0.014	0.014	0.000	0.000	0.000	0.000
124	A	125	TYR	0	0.094	0.035	20.757	0.011	0.011	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.063	0.055	23.783	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	127	ARG	1	0.888	0.943	22.596	-0.111	-0.111	0.000	0.000	0.000	0.000
127	A	128	TYR	0	-0.050	-0.045	16.320	0.003	0.003	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.002	0.011	22.500	-0.010	-0.010	0.000	0.000	0.000	0.000
129	A	130	PHE	0	-0.042	-0.020	22.198	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	131	VAL	0	0.022	0.003	27.169	0.005	0.005	0.000	0.000	0.000	0.000
131	A	132	ALA	0	-0.009	-0.006	30.810	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	133	VAL	0	-0.035	-0.023	32.264	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	134	THR	0	0.002	0.010	34.624	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.890	-0.931	36.243	0.021	0.021	0.000	0.000	0.000	0.000
135	A	136	VAL	0	-0.048	-0.034	34.612	0.000	0.000	0.000	0.000	0.000	0.000
136	A	137	TYR	0	-0.067	-0.038	31.118	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	138	LEU	0	-0.003	-0.017	34.525	0.003	0.003	0.000	0.000	0.000	0.000
138	A	139	GLU	-1	-0.844	-0.931	29.229	0.005	0.005	0.000	0.000	0.000	0.000
139	A	140	ASP	-1	-0.892	-0.951	30.757	0.009	0.009	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.905	-0.955	33.043	0.015	0.015	0.000	0.000	0.000	0.000
141	A	142	ILE	0	-0.048	-0.018	28.740	0.005	0.005	0.000	0.000	0.000	0.000
142	A	143	PRO	0	0.004	0.006	32.122	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	144	HIS	1	0.855	0.937	27.448	-0.015	-0.015	0.000	0.000	0.000	0.000
144	A	145	ILE	0	0.025	0.008	30.088	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	146	GLY	0	0.037	0.033	30.030	0.003	0.003	0.000	0.000	0.000	0.000
146	A	147	MET	0	-0.050	-0.026	27.689	0.005	0.005	0.000	0.000	0.000	0.000
147	A	148	ARG	1	0.957	0.981	28.522	-0.009	-0.009	0.000	0.000	0.000	0.000
148	A	149	ARG	1	0.891	0.931	22.964	-0.037	-0.037	0.000	0.000	0.000	0.000
149	A	150	ALA	0	0.016	0.013	27.682	-0.007	-0.007	0.000	0.000	0.000	0.000

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