FMO DATABASE

FMODB ID: J3189

Calculation Name: 3EBK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EBK

Chain ID: A

ChEMBL ID:

UniProt ID: P54962

Base Structure: X-ray

Registration Date: 2023-06-20

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1896491.428328
FMO2-HF: Nuclear repulsion	1826826.846148
FMO2-HF: Total energy	-69664.58218
FMO2-MP2: Total energy	-69867.560619

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:7:ASN)

Summations of interaction energy for fragment #1(A:7:ASN)

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.
-4.249	-0.458	12.169	-5.64	-10.321	-0.008

Interaction energy analysis for fragmet #1(A:7:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.019

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	9	ASP	-1	-0.865	-0.936	2.743	-6.327	-2.647	0.205	-1.447	-2.438	-0.006
4	A	10	CYS	0	-0.154	-0.082	2.154	0.219	0.956	5.503	-2.494	-3.747	-0.008
5	A	11	PHE	0	-0.048	-0.019	3.691	0.512	0.805	0.010	-0.023	-0.280	0.000
6	A	12	ARG	1	0.927	0.961	6.599	-0.548	-0.548	0.000	0.000	0.000	0.000
7	A	13	HIS	0	-0.035	-0.005	9.897	0.141	0.141	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.954	-0.963	11.452	-1.404	-1.404	0.000	0.000	0.000	0.000
9	A	15	SER	0	-0.059	-0.063	12.864	0.218	0.218	0.000	0.000	0.000	0.000
10	A	16	LEU	0	0.029	0.013	14.680	0.018	0.018	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.076	-0.044	15.849	0.087	0.087	0.000	0.000	0.000	0.000
12	A	18	PRO	0	0.028	0.016	14.343	-0.077	-0.077	0.000	0.000	0.000	0.000
13	A	19	ASN	0	-0.055	-0.032	14.940	-0.153	-0.153	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.037	-0.003	14.157	0.102	0.102	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.835	-0.920	16.996	-0.533	-0.533	0.000	0.000	0.000	0.000
16	A	22	TYR	0	0.007	-0.019	16.215	0.052	0.052	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.822	-0.901	18.042	-0.336	-0.336	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.843	0.919	21.574	0.418	0.418	0.000	0.000	0.000	0.000
19	A	25	PHE	0	-0.018	-0.007	15.365	0.030	0.030	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.783	0.899	19.673	0.418	0.418	0.000	0.000	0.000	0.000
21	A	27	GLY	0	0.021	0.022	20.559	0.028	0.028	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.061	-0.040	21.247	0.002	0.002	0.000	0.000	0.000	0.000
23	A	29	TRP	0	-0.002	0.023	19.742	0.006	0.006	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.026	-0.012	21.421	0.034	0.034	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.015	0.008	16.229	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	32	ALA	0	-0.029	-0.017	20.335	0.037	0.037	0.000	0.000	0.000	0.000
27	A	33	ALA	0	0.005	0.011	20.574	0.027	0.027	0.000	0.000	0.000	0.000
28	A	34	GLY	0	0.058	0.024	17.203	-0.045	-0.045	0.000	0.000	0.000	0.000
29	A	35	THR	0	0.056	0.037	14.315	0.019	0.019	0.000	0.000	0.000	0.000
30	A	36	SER	0	-0.018	0.008	14.251	0.047	0.047	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.868	-0.941	16.351	0.535	0.535	0.000	0.000	0.000	0.000
32	A	38	ALA	0	0.006	0.027	15.893	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	39	LEU	0	0.040	0.009	13.486	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	40	THR	0	-0.044	-0.017	17.721	-0.085	-0.085	0.000	0.000	0.000	0.000
35	A	41	GLN	0	-0.078	-0.038	18.882	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	42	TYR	0	-0.041	-0.014	17.032	0.000	0.000	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.879	0.936	21.404	-0.303	-0.303	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.172	-0.084	22.863	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	45	TRP	0	0.040	0.009	15.928	0.019	0.019	0.000	0.000	0.000	0.000
40	A	46	ILE	0	-0.037	-0.025	21.323	-0.041	-0.041	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.771	-0.840	16.308	0.051	0.051	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.913	0.936	19.565	0.069	0.069	0.000	0.000	0.000	0.000
43	A	49	PHE	0	0.072	0.045	13.605	0.028	0.028	0.000	0.000	0.000	0.000
44	A	50	SER	0	-0.061	-0.053	19.011	0.024	0.024	0.000	0.000	0.000	0.000
45	A	51	TYR	0	0.009	-0.009	20.268	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	52	ASP	-1	-0.829	-0.915	19.445	-0.392	-0.392	0.000	0.000	0.000	0.000
47	A	53	ASP	-1	-0.920	-0.944	15.402	-0.427	-0.427	0.000	0.000	0.000	0.000
48	A	54	ALA	0	0.000	0.015	16.325	0.043	0.043	0.000	0.000	0.000	0.000
49	A	55	LEU	0	0.021	0.016	14.314	-0.032	-0.032	0.000	0.000	0.000	0.000
50	A	56	VAL	0	-0.110	-0.052	17.847	0.069	0.069	0.000	0.000	0.000	0.000
51	A	57	SER	0	0.056	0.017	17.355	-0.027	-0.027	0.000	0.000	0.000	0.000
52	A	58	LYS	1	0.829	0.892	19.847	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	59	TYR	0	0.077	0.056	19.496	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	60	THR	0	-0.087	-0.052	23.374	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	61	ASP	-1	-0.768	-0.866	24.850	0.334	0.334	0.000	0.000	0.000	0.000
56	A	62	SER	0	-0.002	-0.025	26.595	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.022	-0.014	28.321	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	64	GLY	0	-0.018	0.011	30.040	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	65	LYN	0	0.045	0.026	30.943	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	66	ASN	0	0.011	-0.012	27.056	0.004	0.004	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.936	0.978	26.993	-0.107	-0.107	0.000	0.000	0.000	0.000
62	A	68	THR	0	0.006	0.017	21.982	0.006	0.006	0.000	0.000	0.000	0.000
63	A	69	THR	0	-0.083	-0.042	22.861	-0.037	-0.037	0.000	0.000	0.000	0.000
64	A	70	ILE	0	-0.007	0.018	16.170	0.015	0.015	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.949	0.957	19.076	-0.131	-0.131	0.000	0.000	0.000	0.000
66	A	72	GLY	0	0.071	0.039	15.217	0.082	0.082	0.000	0.000	0.000	0.000
67	A	73	ARG	1	0.856	0.931	12.457	0.161	0.161	0.000	0.000	0.000	0.000
68	A	74	THR	0	-0.037	-0.025	11.631	0.001	0.001	0.000	0.000	0.000	0.000
69	A	75	LYS	1	0.881	0.931	9.406	1.571	1.571	0.000	0.000	0.000	0.000
70	A	76	PHE	0	0.022	0.007	9.480	-0.273	-0.273	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.893	-0.938	8.632	-2.341	-2.341	0.000	0.000	0.000	0.000
72	A	78	GLY	0	0.054	0.037	10.720	-0.227	-0.227	0.000	0.000	0.000	0.000
73	A	79	ASN	0	-0.012	-0.020	10.251	0.081	0.081	0.000	0.000	0.000	0.000
74	A	80	LYS	1	0.895	0.956	6.199	4.420	4.420	0.000	0.000	0.000	0.000
75	A	81	PHE	0	0.017	-0.002	7.689	0.339	0.339	0.000	0.000	0.000	0.000
76	A	82	THR	0	-0.004	0.009	4.432	-0.231	-0.203	-0.001	-0.009	-0.017	0.000
77	A	83	ILE	0	0.008	0.004	7.173	0.142	0.142	0.000	0.000	0.000	0.000
78	A	84	ASP	-1	-0.869	-0.908	9.423	0.580	0.580	0.000	0.000	0.000	0.000
79	A	85	TYR	0	-0.044	-0.070	11.179	-0.131	-0.131	0.000	0.000	0.000	0.000
80	A	86	ASN	0	-0.001	-0.008	13.691	0.023	0.023	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.900	-0.960	15.255	0.692	0.692	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.863	0.954	16.149	-0.229	-0.229	0.000	0.000	0.000	0.000
83	A	89	GLY	0	0.061	-0.001	15.778	-0.069	-0.069	0.000	0.000	0.000	0.000
84	A	90	LYS	1	0.991	1.002	10.227	-1.436	-1.436	0.000	0.000	0.000	0.000
85	A	91	ALA	0	-0.031	-0.007	10.631	0.253	0.253	0.000	0.000	0.000	0.000
86	A	92	PHE	0	0.032	-0.002	10.969	0.262	0.262	0.000	0.000	0.000	0.000
87	A	93	SER	0	0.017	0.031	8.795	-0.270	-0.270	0.000	0.000	0.000	0.000
88	A	94	ALA	0	0.000	0.009	5.515	0.970	0.970	0.000	0.000	0.000	0.000
89	A	95	PRO	0	0.000	-0.004	2.059	-1.292	-2.433	6.453	-1.628	-3.685	0.006
90	A	96	TYR	0	-0.017	-0.035	4.466	0.830	1.024	-0.001	-0.039	-0.154	0.000
91	A	97	SER	0	0.019	0.013	7.380	-0.587	-0.587	0.000	0.000	0.000	0.000
92	A	98	VAL	0	0.010	0.005	9.486	0.339	0.339	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.003	0.025	11.518	-0.105	-0.105	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.069	0.038	14.697	0.026	0.026	0.000	0.000	0.000	0.000
95	A	101	THR	0	-0.005	-0.033	18.276	0.031	0.031	0.000	0.000	0.000	0.000
96	A	102	ASP	-1	-0.731	-0.822	20.490	-0.289	-0.289	0.000	0.000	0.000	0.000
97	A	103	TYR	0	-0.020	0.009	19.515	0.010	0.010	0.000	0.000	0.000	0.000
98	A	104	GLU	-1	-0.866	-0.940	22.971	-0.241	-0.241	0.000	0.000	0.000	0.000
99	A	105	ASN	0	-0.098	-0.069	25.495	0.047	0.047	0.000	0.000	0.000	0.000
100	A	106	TYR	0	-0.035	-0.040	21.552	0.048	0.048	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.014	0.027	17.728	-0.049	-0.049	0.000	0.000	0.000	0.000
102	A	108	ILE	0	-0.015	0.012	15.732	0.082	0.082	0.000	0.000	0.000	0.000
103	A	109	VAL	0	-0.011	-0.008	11.232	-0.146	-0.146	0.000	0.000	0.000	0.000
104	A	110	GLU	-1	-0.722	-0.834	8.103	-0.856	-0.856	0.000	0.000	0.000	0.000
105	A	111	GLY	0	0.020	0.001	6.668	-0.497	-0.497	0.000	0.000	0.000	0.000
106	A	113	PRO	0	0.009	0.032	5.862	1.766	1.766	0.000	0.000	0.000	0.000
107	A	114	ALA	0	0.054	0.010	8.351	-0.070	-0.070	0.000	0.000	0.000	0.000
108	A	115	ALA	0	-0.023	-0.015	9.429	-0.313	-0.313	0.000	0.000	0.000	0.000
109	A	116	ALA	0	-0.042	-0.018	11.032	-0.274	-0.274	0.000	0.000	0.000	0.000
110	A	117	ASN	0	-0.024	-0.025	11.685	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	118	GLY	0	0.001	-0.005	7.504	0.029	0.029	0.000	0.000	0.000	0.000
112	A	119	HIS	0	-0.105	-0.055	7.350	0.557	0.557	0.000	0.000	0.000	0.000
113	A	120	VAL	0	-0.037	-0.015	9.371	-0.092	-0.092	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.046	0.030	10.818	-0.181	-0.181	0.000	0.000	0.000	0.000
115	A	122	TYR	0	-0.037	-0.030	12.096	0.073	0.073	0.000	0.000	0.000	0.000
116	A	123	VAL	0	0.039	0.023	16.004	-0.101	-0.101	0.000	0.000	0.000	0.000
117	A	124	GLN	0	-0.031	-0.014	17.449	0.098	0.098	0.000	0.000	0.000	0.000
118	A	125	LEU	0	0.031	0.004	20.275	-0.038	-0.038	0.000	0.000	0.000	0.000
119	A	126	ARG	1	0.774	0.879	22.815	0.303	0.303	0.000	0.000	0.000	0.000
120	A	127	MET	0	-0.035	-0.006	24.896	0.023	0.023	0.000	0.000	0.000	0.000
121	A	128	THR	0	-0.015	-0.025	26.774	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	129	LEU	0	0.057	0.020	29.632	0.008	0.008	0.000	0.000	0.000	0.000
123	A	130	ARG	1	0.933	0.981	29.869	0.162	0.162	0.000	0.000	0.000	0.000
124	A	131	ARG	1	0.849	0.914	28.303	0.150	0.150	0.000	0.000	0.000	0.000
125	A	132	PHE	0	-0.028	-0.008	31.675	0.011	0.011	0.000	0.000	0.000	0.000
126	A	133	HIS	0	0.048	0.021	33.808	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	134	PRO	0	-0.032	-0.015	35.465	0.007	0.007	0.000	0.000	0.000	0.000
128	A	135	LYS	1	0.911	0.964	36.669	-0.025	-0.025	0.000	0.000	0.000	0.000
129	A	136	LEU	0	-0.011	-0.011	40.216	0.000	0.000	0.000	0.000	0.000	0.000
130	A	137	GLY	0	0.016	-0.005	38.921	0.005	0.005	0.000	0.000	0.000	0.000
131	A	138	ASP	-1	-0.837	-0.904	38.765	0.058	0.058	0.000	0.000	0.000	0.000
132	A	139	LYS	1	0.832	0.898	38.372	-0.055	-0.055	0.000	0.000	0.000	0.000
133	A	140	GLU	-1	-0.831	-0.887	34.432	0.060	0.060	0.000	0.000	0.000	0.000
134	A	141	MET	0	-0.040	-0.023	33.176	-0.016	-0.016	0.000	0.000	0.000	0.000
135	A	142	LEU	0	0.035	0.013	27.578	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	143	GLN	0	0.064	0.031	29.525	-0.024	-0.024	0.000	0.000	0.000	0.000
137	A	144	HIS	0	-0.032	-0.022	30.575	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	145	TYR	0	-0.013	-0.031	27.777	-0.009	-0.009	0.000	0.000	0.000	0.000
139	A	146	THR	0	0.004	-0.023	25.557	-0.015	-0.015	0.000	0.000	0.000	0.000
140	A	147	LEU	0	0.020	0.020	28.429	-0.012	-0.012	0.000	0.000	0.000	0.000
141	A	148	ASP	-1	-0.878	-0.938	30.405	-0.028	-0.028	0.000	0.000	0.000	0.000
142	A	149	GLN	0	-0.057	-0.027	28.132	-0.028	-0.028	0.000	0.000	0.000	0.000
143	A	150	VAL	0	0.023	0.015	25.443	-0.021	-0.021	0.000	0.000	0.000	0.000
144	A	151	ASN	0	-0.011	-0.020	28.020	-0.012	-0.012	0.000	0.000	0.000	0.000
145	A	152	GLN	0	-0.054	-0.030	31.431	-0.017	-0.017	0.000	0.000	0.000	0.000
146	A	153	ASN	0	-0.048	-0.030	27.340	-0.025	-0.025	0.000	0.000	0.000	0.000
147	A	154	LYS	1	0.869	0.956	27.251	0.024	0.024	0.000	0.000	0.000	0.000
148	A	155	LYS	1	0.956	0.965	27.937	0.127	0.127	0.000	0.000	0.000	0.000
149	A	156	ALA	0	0.027	0.018	26.525	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	157	ILE	0	0.026	0.023	22.542	-0.018	-0.018	0.000	0.000	0.000	0.000
151	A	158	GLU	-1	-0.779	-0.898	23.364	-0.073	-0.073	0.000	0.000	0.000	0.000
152	A	159	GLU	-1	-0.838	-0.898	24.916	-0.198	-0.198	0.000	0.000	0.000	0.000
153	A	160	ASP	-1	-0.787	-0.884	20.550	-0.390	-0.390	0.000	0.000	0.000	0.000
154	A	161	LEU	0	-0.031	-0.029	19.399	-0.028	-0.028	0.000	0.000	0.000	0.000
155	A	162	LYS	1	0.817	0.907	20.814	0.182	0.182	0.000	0.000	0.000	0.000
156	A	163	HIS	0	-0.046	-0.015	18.929	0.019	0.019	0.000	0.000	0.000	0.000
157	A	164	PHE	0	-0.048	-0.020	16.468	-0.046	-0.046	0.000	0.000	0.000	0.000
158	A	165	ASN	0	-0.074	-0.039	18.133	0.057	0.057	0.000	0.000	0.000	0.000
159	A	166	LEU	0	-0.011	-0.002	16.513	0.059	0.059	0.000	0.000	0.000	0.000
160	A	167	LYS	1	0.835	0.880	21.068	-0.049	-0.049	0.000	0.000	0.000	0.000
161	A	168	TYR	0	0.007	-0.020	23.134	0.033	0.033	0.000	0.000	0.000	0.000
162	A	169	GLU	-1	-0.931	-0.953	24.248	0.044	0.044	0.000	0.000	0.000	0.000
163	A	170	ASP	-1	-0.854	-0.907	22.629	0.073	0.073	0.000	0.000	0.000	0.000
164	A	171	LEU	0	-0.088	-0.026	18.693	0.039	0.039	0.000	0.000	0.000	0.000
165	A	172	HIS	0	0.035	0.020	19.619	-0.027	-0.027	0.000	0.000	0.000	0.000
166	A	173	SER	0	0.035	0.014	21.772	-0.010	-0.010	0.000	0.000	0.000	0.000
167	A	174	THR	0	0.010	-0.022	19.472	0.029	0.029	0.000	0.000	0.000	0.000
168	A	176	HIS	0	0.020	0.010	25.814	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ASN)