FMO DATABASE

FMODB ID: R9YV8

Calculation Name: 4E2U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E2U

Chain ID: A

ChEMBL ID:

UniProt ID: O58001

Base Structure: X-ray

Registration Date: 2023-06-22

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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1798157.300323
FMO2-HF: Nuclear repulsion	1731546.256567
FMO2-HF: Total energy	-66611.043756
FMO2-MP2: Total energy	-66807.399761

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:-4:SER)

Summations of interaction energy for fragment #1(A:-4: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.
-3.243	-0.574	3.349	-3.254	-2.765	0.002

Interaction energy analysis for fragmet #1(A:-4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.020

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	-2	HIS	0	0.060	0.029	3.805	-1.657	1.300	-0.025	-1.551	-1.382	0.005
4	A	-1	MET	0	-0.046	0.007	6.225	0.342	0.342	0.000	0.000	0.000	0.000
5	A	1	ALA	0	-0.027	-0.030	8.334	-0.261	-0.261	0.000	0.000	0.000	0.000
6	A	2	PHE	0	-0.003	0.000	10.666	0.010	0.010	0.000	0.000	0.000	0.000
7	A	3	ALA	0	0.031	0.008	14.491	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	4	ARG	1	0.925	0.961	17.287	0.303	0.303	0.000	0.000	0.000	0.000
9	A	5	ASP	-1	-0.935	-0.966	19.614	-0.198	-0.198	0.000	0.000	0.000	0.000
10	A	6	THR	0	-0.049	-0.027	18.075	0.015	0.015	0.000	0.000	0.000	0.000
11	A	7	GLU	-1	-0.894	-0.945	20.674	-0.100	-0.100	0.000	0.000	0.000	0.000
12	A	8	VAL	0	-0.049	-0.037	19.029	0.004	0.004	0.000	0.000	0.000	0.000
13	A	9	TYR	0	-0.032	-0.050	22.093	0.001	0.001	0.000	0.000	0.000	0.000
14	A	10	TYR	0	-0.091	-0.078	22.220	0.012	0.012	0.000	0.000	0.000	0.000
15	A	11	GLU	-1	-0.808	-0.862	24.155	0.018	0.018	0.000	0.000	0.000	0.000
16	A	12	ASN	0	0.010	0.030	25.492	0.014	0.014	0.000	0.000	0.000	0.000
17	A	13	ASP	-1	-0.895	-0.943	27.323	0.027	0.027	0.000	0.000	0.000	0.000
18	A	14	THR	0	-0.068	-0.042	29.142	0.001	0.001	0.000	0.000	0.000	0.000
19	A	15	VAL	0	-0.054	-0.018	30.873	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	16	PRO	0	0.012	0.016	28.938	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	17	HIS	0	-0.026	-0.022	26.848	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	18	MET	0	-0.035	-0.028	26.330	0.004	0.004	0.000	0.000	0.000	0.000
23	A	19	GLU	-1	-0.800	-0.848	24.455	-0.064	-0.064	0.000	0.000	0.000	0.000
24	A	20	SER	0	0.068	0.038	22.946	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	21	ILE	0	-0.025	-0.017	15.669	0.004	0.004	0.000	0.000	0.000	0.000
26	A	22	GLU	-1	-0.928	-0.978	19.913	-0.213	-0.213	0.000	0.000	0.000	0.000
27	A	23	GLU	-1	-0.877	-0.935	21.104	-0.107	-0.107	0.000	0.000	0.000	0.000
28	A	24	MET	0	0.001	0.017	20.515	0.009	0.009	0.000	0.000	0.000	0.000
29	A	25	TYR	0	-0.084	-0.090	16.155	0.006	0.006	0.000	0.000	0.000	0.000
30	A	26	SER	0	-0.024	-0.010	20.510	0.013	0.013	0.000	0.000	0.000	0.000
31	A	27	LYS	1	0.921	0.972	23.775	0.048	0.048	0.000	0.000	0.000	0.000
32	A	28	TYR	0	-0.009	-0.080	21.766	0.014	0.014	0.000	0.000	0.000	0.000
33	A	29	ALA	0	0.005	0.021	21.469	0.011	0.011	0.000	0.000	0.000	0.000
34	A	30	SER	0	-0.072	-0.030	22.930	0.007	0.007	0.000	0.000	0.000	0.000
35	A	31	MET	0	-0.106	-0.035	26.034	0.009	0.009	0.000	0.000	0.000	0.000
36	A	32	ASN	0	-0.042	-0.038	22.414	0.007	0.007	0.000	0.000	0.000	0.000
37	A	33	GLY	0	0.001	0.021	23.234	0.011	0.011	0.000	0.000	0.000	0.000
38	A	34	GLU	-1	-0.883	-0.938	18.592	-0.176	-0.176	0.000	0.000	0.000	0.000
39	A	35	LEU	0	-0.047	-0.032	16.003	0.010	0.010	0.000	0.000	0.000	0.000
40	A	36	PRO	0	0.002	-0.007	15.148	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	37	PHE	0	-0.050	-0.027	8.579	0.092	0.092	0.000	0.000	0.000	0.000
42	A	38	ASP	-1	-0.876	-0.931	5.508	-0.167	-0.223	-0.001	-0.005	0.062	0.000
43	A	39	ASN	0	-0.028	-0.011	6.482	0.360	0.360	0.000	0.000	0.000	0.000
44	A	40	GLY	0	-0.011	-0.013	9.785	-0.063	-0.063	0.000	0.000	0.000	0.000
45	A	41	TYR	0	-0.063	-0.016	12.325	0.103	0.103	0.000	0.000	0.000	0.000
46	A	42	ALA	0	0.037	0.009	12.831	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	43	VAL	0	-0.002	0.017	14.802	0.012	0.012	0.000	0.000	0.000	0.000
48	A	44	PRO	0	0.006	0.003	17.539	0.016	0.016	0.000	0.000	0.000	0.000
49	A	45	LEU	0	-0.030	-0.010	18.019	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	46	ASP	-1	-0.909	-0.960	20.620	0.089	0.089	0.000	0.000	0.000	0.000
51	A	47	ASN	0	-0.043	-0.021	23.624	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	48	VAL	0	0.047	0.044	21.354	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	49	PHE	0	-0.044	-0.036	21.836	0.019	0.019	0.000	0.000	0.000	0.000
54	A	50	VAL	0	0.041	0.026	18.764	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	51	TYR	0	-0.052	-0.052	22.130	0.016	0.016	0.000	0.000	0.000	0.000
56	A	52	THR	0	-0.023	-0.002	18.492	0.000	0.000	0.000	0.000	0.000	0.000
57	A	53	LEU	0	0.028	0.009	20.266	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	54	ASP	-1	-0.853	-0.914	20.086	0.150	0.150	0.000	0.000	0.000	0.000
59	A	55	ILE	0	-0.033	-0.041	18.794	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	56	ALA	0	-0.029	-0.005	22.005	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	57	SER	0	-0.024	-0.009	24.004	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	58	GLY	0	0.000	-0.001	25.306	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	59	GLU	-1	-0.944	-0.974	26.041	0.086	0.086	0.000	0.000	0.000	0.000
64	A	60	ILE	0	0.002	0.010	24.824	0.005	0.005	0.000	0.000	0.000	0.000
65	A	61	LYS	1	0.910	0.958	23.682	-0.118	-0.118	0.000	0.000	0.000	0.000
66	A	62	LYS	1	0.936	0.974	24.120	-0.059	-0.059	0.000	0.000	0.000	0.000
67	A	63	THR	0	-0.030	-0.044	19.071	0.012	0.012	0.000	0.000	0.000	0.000
68	A	64	ARG	1	0.960	0.982	17.443	-0.199	-0.199	0.000	0.000	0.000	0.000
69	A	65	ALA	0	0.038	0.012	17.064	0.016	0.016	0.000	0.000	0.000	0.000
70	A	66	SER	0	-0.085	-0.047	13.868	0.008	0.008	0.000	0.000	0.000	0.000
71	A	67	TYR	0	-0.005	-0.016	8.841	0.034	0.034	0.000	0.000	0.000	0.000
72	A	68	ILE	0	0.023	0.032	14.585	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	69	TYR	0	-0.045	-0.058	8.931	0.174	0.174	0.000	0.000	0.000	0.000
74	A	70	ARG	1	0.916	0.960	12.818	0.239	0.239	0.000	0.000	0.000	0.000
75	A	71	GLU	-1	-0.803	-0.891	8.598	-1.805	-1.805	0.000	0.000	0.000	0.000
76	A	72	LYS	1	0.878	0.948	12.709	0.448	0.448	0.000	0.000	0.000	0.000
77	A	73	VAL	0	0.034	0.026	10.759	-0.147	-0.147	0.000	0.000	0.000	0.000
78	A	74	GLU	-1	-0.907	-0.956	13.212	-0.441	-0.441	0.000	0.000	0.000	0.000
79	A	75	LYS	1	0.868	0.936	14.017	0.513	0.513	0.000	0.000	0.000	0.000
80	A	76	LEU	0	-0.017	-0.001	13.339	-0.102	-0.102	0.000	0.000	0.000	0.000
81	A	77	ILE	0	-0.008	0.000	14.933	0.045	0.045	0.000	0.000	0.000	0.000
82	A	78	GLU	-1	-0.868	-0.956	16.646	-0.201	-0.201	0.000	0.000	0.000	0.000
83	A	79	ILE	0	0.027	0.007	17.188	0.016	0.016	0.000	0.000	0.000	0.000
84	A	80	LYS	1	0.906	0.962	21.030	0.150	0.150	0.000	0.000	0.000	0.000
85	A	81	LEU	0	0.066	0.030	23.490	0.007	0.007	0.000	0.000	0.000	0.000
86	A	82	SER	0	0.010	0.004	26.748	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	83	SER	0	-0.004	-0.001	28.902	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	84	GLY	0	-0.009	-0.001	29.454	0.002	0.002	0.000	0.000	0.000	0.000
89	A	85	TYR	0	-0.003	-0.004	21.215	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	86	SER	0	-0.014	-0.019	22.877	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	87	LEU	0	0.037	0.041	17.079	0.000	0.000	0.000	0.000	0.000	0.000
92	A	88	LYS	1	0.913	0.959	17.904	0.223	0.223	0.000	0.000	0.000	0.000
93	A	89	VAL	0	0.051	0.030	12.791	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	90	THR	0	0.030	0.011	8.676	0.080	0.080	0.000	0.000	0.000	0.000
95	A	91	PRO	0	0.020	-0.008	10.597	0.083	0.083	0.000	0.000	0.000	0.000
96	A	92	SER	0	-0.013	0.002	5.953	0.074	0.074	0.000	0.000	0.000	0.000
97	A	93	HIS	0	-0.007	0.004	8.906	0.048	0.048	0.000	0.000	0.000	0.000
98	A	94	PRO	0	-0.012	0.005	8.801	0.064	0.064	0.000	0.000	0.000	0.000
99	A	95	VAL	0	0.001	-0.009	11.843	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	96	LEU	0	0.019	0.011	15.504	0.027	0.027	0.000	0.000	0.000	0.000
101	A	97	LEU	0	-0.012	-0.007	18.346	-0.019	-0.019	0.000	0.000	0.000	0.000
102	A	98	PHE	0	0.019	0.005	21.009	0.019	0.019	0.000	0.000	0.000	0.000
103	A	99	ARG	1	0.768	0.866	19.322	0.005	0.005	0.000	0.000	0.000	0.000
104	A	100	ASP	-1	-0.980	-0.959	23.828	0.067	0.067	0.000	0.000	0.000	0.000
105	A	101	GLY	0	0.057	0.016	24.446	0.012	0.012	0.000	0.000	0.000	0.000
106	A	102	LEU	0	-0.043	-0.023	21.724	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	103	GLN	0	0.010	0.000	18.864	0.008	0.008	0.000	0.000	0.000	0.000
108	A	104	TRP	0	0.016	0.014	13.801	-0.027	-0.027	0.000	0.000	0.000	0.000
109	A	105	VAL	0	-0.021	-0.012	15.067	0.032	0.032	0.000	0.000	0.000	0.000
110	A	106	PRO	0	0.025	0.023	11.201	-0.038	-0.038	0.000	0.000	0.000	0.000
111	A	107	ALA	0	0.065	0.022	12.500	0.009	0.009	0.000	0.000	0.000	0.000
112	A	108	ALA	0	-0.046	-0.030	13.485	0.020	0.020	0.000	0.000	0.000	0.000
113	A	109	GLU	-1	-0.980	-0.989	14.513	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	110	VAL	0	-0.046	-0.015	16.844	0.032	0.032	0.000	0.000	0.000	0.000
115	A	111	LYS	1	0.888	0.942	19.139	0.025	0.025	0.000	0.000	0.000	0.000
116	A	112	PRO	0	-0.016	-0.023	22.743	0.004	0.004	0.000	0.000	0.000	0.000
117	A	113	GLY	0	0.009	0.004	25.822	0.006	0.006	0.000	0.000	0.000	0.000
118	A	114	ASP	-1	-0.772	-0.859	22.137	-0.034	-0.034	0.000	0.000	0.000	0.000
119	A	115	VAL	0	-0.011	-0.004	24.682	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	116	VAL	0	0.002	-0.011	20.740	0.006	0.006	0.000	0.000	0.000	0.000
121	A	117	VAL	0	0.016	-0.001	21.853	0.004	0.004	0.000	0.000	0.000	0.000
122	A	118	GLY	0	-0.007	-0.011	22.356	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	119	VAL	0	-0.031	-0.006	24.575	0.008	0.008	0.000	0.000	0.000	0.000
124	A	120	ARG	1	0.879	0.916	26.857	0.013	0.013	0.000	0.000	0.000	0.000
125	A	131	ASN	0	-0.056	-0.032	30.014	0.002	0.002	0.000	0.000	0.000	0.000
126	A	132	GLY	0	0.002	-0.003	30.325	0.002	0.002	0.000	0.000	0.000	0.000
127	A	133	GLU	-1	-0.942	-0.942	30.718	0.019	0.019	0.000	0.000	0.000	0.000
128	A	134	LEU	0	-0.018	-0.024	25.577	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	135	GLU	-1	-0.839	-0.904	27.637	-0.026	-0.026	0.000	0.000	0.000	0.000
130	A	136	PHE	0	-0.007	-0.017	26.579	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	137	HIS	0	0.004	0.004	25.656	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	138	GLU	-1	-0.915	-0.954	26.078	-0.050	-0.050	0.000	0.000	0.000	0.000
133	A	139	VAL	0	-0.040	-0.015	22.633	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	140	SER	0	-0.026	-0.009	25.772	0.004	0.004	0.000	0.000	0.000	0.000
135	A	141	SER	0	-0.051	-0.043	25.849	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	142	VAL	0	0.046	0.031	20.570	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	143	ARG	1	0.859	0.934	21.002	0.214	0.214	0.000	0.000	0.000	0.000
138	A	144	ILE	0	0.015	0.023	15.321	-0.015	-0.015	0.000	0.000	0.000	0.000
139	A	145	ILE	0	-0.060	-0.038	18.635	0.040	0.040	0.000	0.000	0.000	0.000
140	A	146	ASP	-1	-0.841	-0.918	18.602	-0.398	-0.398	0.000	0.000	0.000	0.000
141	A	147	TYR	0	-0.076	-0.063	16.532	0.067	0.067	0.000	0.000	0.000	0.000
142	A	148	ASN	0	-0.009	-0.015	17.735	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	149	ASN	0	-0.022	-0.008	17.332	0.053	0.053	0.000	0.000	0.000	0.000
144	A	150	TRP	0	0.015	-0.002	15.298	-0.085	-0.085	0.000	0.000	0.000	0.000
145	A	151	VAL	0	-0.019	0.024	11.811	0.063	0.063	0.000	0.000	0.000	0.000
146	A	152	TYR	0	0.067	0.022	13.496	-0.041	-0.041	0.000	0.000	0.000	0.000
147	A	153	ASP	-1	-0.732	-0.857	9.693	-0.222	-0.222	0.000	0.000	0.000	0.000
148	A	154	LEU	0	0.005	0.014	12.414	0.030	0.030	0.000	0.000	0.000	0.000
149	A	155	VAL	0	0.008	0.014	10.212	0.011	0.011	0.000	0.000	0.000	0.000
150	A	156	ILE	0	0.019	0.005	12.635	0.010	0.010	0.000	0.000	0.000	0.000
151	A	157	PRO	0	-0.056	-0.040	12.881	0.030	0.030	0.000	0.000	0.000	0.000
152	A	158	GLU	-1	-0.935	-0.921	13.968	0.207	0.207	0.000	0.000	0.000	0.000
153	A	159	THR	0	0.020	-0.017	15.950	0.023	0.023	0.000	0.000	0.000	0.000
154	A	160	HIS	0	-0.040	-0.006	11.050	-0.019	-0.019	0.000	0.000	0.000	0.000
155	A	161	ASN	0	-0.016	-0.013	12.934	-0.058	-0.058	0.000	0.000	0.000	0.000
156	A	162	PHE	0	0.039	0.020	14.528	0.016	0.016	0.000	0.000	0.000	0.000
157	A	163	ILE	0	-0.034	-0.009	18.361	-0.016	-0.016	0.000	0.000	0.000	0.000
158	A	164	ALA	0	-0.001	0.009	21.115	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	165	PRO	0	0.042	0.015	22.621	0.010	0.010	0.000	0.000	0.000	0.000
160	A	166	ASN	0	-0.061	-0.026	24.418	0.010	0.010	0.000	0.000	0.000	0.000
161	A	167	GLY	0	0.055	0.027	25.576	0.002	0.002	0.000	0.000	0.000	0.000
162	A	168	LEU	0	-0.044	-0.013	21.061	0.008	0.008	0.000	0.000	0.000	0.000
163	A	169	VAL	0	0.001	0.009	18.316	0.000	0.000	0.000	0.000	0.000	0.000
164	A	170	LEU	0	-0.031	-0.006	16.186	-0.011	-0.011	0.000	0.000	0.000	0.000
165	A	171	HIS	1	0.876	0.923	9.834	-0.089	-0.089	0.000	0.000	0.000	0.000
166	A	172	ASN	0	0.020	-0.009	9.330	0.006	0.006	0.000	0.000	0.000	0.000
167	A	173	ALA	0	-0.030	0.003	6.600	0.035	0.035	0.000	0.000	0.000	0.000
168	A	174	GLN	0	-0.008	0.003	1.936	-0.965	-1.197	3.375	-1.698	-1.445	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:SER)