FMO DATABASE

FMODB ID: N14RQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1897109.675963
FMO2-HF: Nuclear repulsion	1827446.271912
FMO2-HF: Total energy	-69663.404051
FMO2-MP2: Total energy	-69866.498215

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.
-0.312	-2.947	21.375	-7.209	-11.532	-0.002

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 : -0.018 / q_NPA : -0.024

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	-0.857	-0.930	2.761	-3.349	-0.450	0.176	-1.032	-2.043	-0.003
4	A	10	CYS	0	-0.169	-0.086	2.143	0.286	-0.760	9.174	-3.564	-4.564	-0.011
5	A	11	PHE	0	-0.049	-0.027	3.721	0.040	0.381	0.009	-0.042	-0.308	0.000
6	A	12	ARG	1	0.916	0.945	6.254	-0.956	-0.956	0.000	0.000	0.000	0.000
7	A	13	HIS	0	-0.031	-0.005	9.842	0.107	0.107	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.957	-0.965	11.062	-1.410	-1.410	0.000	0.000	0.000	0.000
9	A	15	SER	0	-0.068	-0.069	12.758	0.224	0.224	0.000	0.000	0.000	0.000
10	A	16	LEU	0	0.039	0.016	14.414	0.011	0.011	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.073	-0.043	15.663	0.082	0.082	0.000	0.000	0.000	0.000
12	A	18	PRO	0	0.028	0.016	14.233	-0.097	-0.097	0.000	0.000	0.000	0.000
13	A	19	ASN	0	-0.052	-0.034	14.813	-0.167	-0.167	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.039	-0.006	14.189	0.108	0.108	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.842	-0.928	16.913	-0.634	-0.634	0.000	0.000	0.000	0.000
16	A	22	TYR	0	0.015	-0.025	15.907	0.068	0.068	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.917	-0.970	17.997	-0.422	-0.422	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.847	0.924	21.509	0.470	0.470	0.000	0.000	0.000	0.000
19	A	25	PHE	0	-0.010	-0.005	15.421	0.040	0.040	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.838	0.939	19.686	0.505	0.505	0.000	0.000	0.000	0.000
21	A	27	GLY	0	0.006	0.009	20.566	0.039	0.039	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.072	-0.041	21.295	0.009	0.009	0.000	0.000	0.000	0.000
23	A	29	TRP	0	-0.001	0.031	19.624	0.015	0.015	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.028	-0.012	21.294	0.034	0.034	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.020	0.005	16.189	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	32	ALA	0	-0.018	-0.016	20.200	0.039	0.039	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.004	0.008	20.413	0.025	0.025	0.000	0.000	0.000	0.000
28	A	34	GLY	0	0.058	0.025	17.071	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	35	THR	0	0.063	0.039	14.323	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	36	SER	0	-0.022	0.013	14.217	0.036	0.036	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.857	-0.941	16.313	0.686	0.686	0.000	0.000	0.000	0.000
32	A	38	ALA	0	0.004	0.024	15.682	-0.062	-0.062	0.000	0.000	0.000	0.000
33	A	39	LEU	0	0.026	-0.009	13.455	-0.059	-0.059	0.000	0.000	0.000	0.000
34	A	40	THR	0	-0.033	-0.014	17.706	-0.113	-0.113	0.000	0.000	0.000	0.000
35	A	41	GLN	0	-0.075	-0.037	18.796	-0.133	-0.133	0.000	0.000	0.000	0.000
36	A	42	TYR	0	-0.050	-0.013	17.014	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.880	0.958	21.404	-0.384	-0.384	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.168	-0.086	22.790	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	45	TRP	0	0.035	0.001	16.425	0.014	0.014	0.000	0.000	0.000	0.000
40	A	46	ILE	0	-0.036	-0.021	21.239	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.763	-0.844	15.923	0.038	0.038	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.906	0.941	19.486	0.097	0.097	0.000	0.000	0.000	0.000
43	A	49	PHE	0	0.074	0.040	13.756	0.018	0.018	0.000	0.000	0.000	0.000
44	A	50	SER	0	-0.068	-0.054	19.061	0.033	0.033	0.000	0.000	0.000	0.000
45	A	51	TYR	0	0.024	-0.003	20.301	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	52	ASP	-1	-0.822	-0.897	19.300	-0.507	-0.507	0.000	0.000	0.000	0.000
47	A	53	ASP	-1	-0.936	-0.952	15.364	-0.626	-0.626	0.000	0.000	0.000	0.000
48	A	54	ALA	0	0.012	0.022	16.373	0.033	0.033	0.000	0.000	0.000	0.000
49	A	55	LEU	0	0.028	0.018	14.359	-0.026	-0.026	0.000	0.000	0.000	0.000
50	A	56	VAL	0	-0.111	-0.049	17.931	0.072	0.072	0.000	0.000	0.000	0.000
51	A	57	SER	0	0.045	0.024	17.346	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	58	LYS	1	0.840	0.887	19.857	-0.043	-0.043	0.000	0.000	0.000	0.000
53	A	59	TYR	0	0.071	0.058	19.349	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	60	THR	0	-0.067	-0.041	23.400	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	61	ASP	-1	-0.805	-0.893	24.869	0.386	0.386	0.000	0.000	0.000	0.000
56	A	62	SER	0	-0.002	-0.045	26.377	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.024	-0.016	28.264	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	64	GLY	0	-0.022	0.006	30.075	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	65	LYN	0	0.065	0.051	30.688	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	66	ASN	0	0.036	0.001	25.945	0.001	0.001	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.921	0.964	26.725	-0.120	-0.120	0.000	0.000	0.000	0.000
62	A	68	THR	0	0.008	0.021	21.649	0.001	0.001	0.000	0.000	0.000	0.000
63	A	69	THR	0	-0.103	-0.048	22.538	-0.040	-0.040	0.000	0.000	0.000	0.000
64	A	70	ILE	0	-0.026	-0.001	15.854	0.014	0.014	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.942	0.953	18.775	-0.099	-0.099	0.000	0.000	0.000	0.000
66	A	72	GLY	0	0.079	0.045	15.084	0.084	0.084	0.000	0.000	0.000	0.000
67	A	73	ARG	1	0.872	0.956	12.119	0.436	0.436	0.000	0.000	0.000	0.000
68	A	74	THR	0	-0.044	-0.015	11.701	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	75	LYS	1	0.998	0.994	9.354	1.585	1.585	0.000	0.000	0.000	0.000
70	A	76	PHE	0	0.017	0.002	9.461	-0.312	-0.312	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.977	-0.991	8.358	-3.104	-3.104	0.000	0.000	0.000	0.000
72	A	78	GLY	0	0.047	0.034	10.603	-0.229	-0.229	0.000	0.000	0.000	0.000
73	A	79	ASN	0	-0.025	-0.026	10.227	0.066	0.066	0.000	0.000	0.000	0.000
74	A	80	LYS	1	0.962	0.989	6.325	4.473	4.473	0.000	0.000	0.000	0.000
75	A	81	PHE	0	0.026	0.009	7.661	0.344	0.344	0.000	0.000	0.000	0.000
76	A	82	THR	0	0.003	0.012	4.571	-0.124	-0.119	-0.001	-0.006	0.002	0.000
77	A	83	ILE	0	0.009	0.002	7.232	0.221	0.221	0.000	0.000	0.000	0.000
78	A	84	ASP	-1	-0.903	-0.941	9.141	0.188	0.188	0.000	0.000	0.000	0.000
79	A	85	TYR	0	-0.048	-0.086	10.899	-0.094	-0.094	0.000	0.000	0.000	0.000
80	A	86	ASN	0	0.003	-0.007	13.460	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.898	-0.958	15.117	0.648	0.648	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.882	0.974	15.958	-0.194	-0.194	0.000	0.000	0.000	0.000
83	A	89	GLY	0	0.052	-0.007	15.494	-0.078	-0.078	0.000	0.000	0.000	0.000
84	A	90	LYS	1	1.003	1.009	9.990	-1.550	-1.550	0.000	0.000	0.000	0.000
85	A	91	ALA	0	-0.040	-0.014	10.385	0.261	0.261	0.000	0.000	0.000	0.000
86	A	92	PHE	0	0.035	-0.001	10.795	0.358	0.358	0.000	0.000	0.000	0.000
87	A	93	SER	0	0.013	0.033	8.542	-0.246	-0.246	0.000	0.000	0.000	0.000
88	A	94	ALA	0	-0.009	0.004	5.257	1.076	1.076	0.000	0.000	0.000	0.000
89	A	95	PRO	0	0.004	0.011	1.803	0.449	-4.562	12.018	-2.544	-4.463	0.012
90	A	96	TYR	0	-0.013	-0.035	4.571	1.313	1.490	-0.001	-0.021	-0.156	0.000
91	A	97	SER	0	0.016	0.010	7.225	-0.763	-0.763	0.000	0.000	0.000	0.000
92	A	98	VAL	0	0.008	0.007	9.326	0.403	0.403	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.005	0.026	11.203	-0.130	-0.130	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.069	0.038	14.330	0.019	0.019	0.000	0.000	0.000	0.000
95	A	101	THR	0	0.002	-0.021	17.918	0.032	0.032	0.000	0.000	0.000	0.000
96	A	102	ASP	-1	-0.727	-0.827	20.309	-0.296	-0.296	0.000	0.000	0.000	0.000
97	A	103	TYR	0	-0.031	0.011	19.485	0.000	0.000	0.000	0.000	0.000	0.000
98	A	104	GLU	-1	-0.888	-0.969	22.948	-0.269	-0.269	0.000	0.000	0.000	0.000
99	A	105	ASN	0	-0.105	-0.070	25.393	0.052	0.052	0.000	0.000	0.000	0.000
100	A	106	TYR	0	-0.045	-0.059	21.154	0.051	0.051	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.018	0.021	17.390	-0.058	-0.058	0.000	0.000	0.000	0.000
102	A	108	ILE	0	-0.008	0.014	15.337	0.094	0.094	0.000	0.000	0.000	0.000
103	A	109	VAL	0	-0.018	-0.008	10.934	-0.166	-0.166	0.000	0.000	0.000	0.000
104	A	110	GLU	-1	-0.708	-0.828	7.718	-0.652	-0.652	0.000	0.000	0.000	0.000
105	A	111	GLY	0	0.010	-0.004	6.458	-0.623	-0.623	0.000	0.000	0.000	0.000
106	A	113	PRO	0	0.005	0.029	5.616	2.198	2.198	0.000	0.000	0.000	0.000
107	A	114	ALA	0	0.064	0.014	8.112	-0.063	-0.063	0.000	0.000	0.000	0.000
108	A	115	ALA	0	-0.020	-0.016	9.285	-0.366	-0.366	0.000	0.000	0.000	0.000
109	A	116	ALA	0	-0.059	-0.022	11.001	-0.354	-0.354	0.000	0.000	0.000	0.000
110	A	117	ASN	0	-0.032	-0.027	11.590	0.016	0.016	0.000	0.000	0.000	0.000
111	A	118	GLY	0	0.005	-0.003	7.319	0.024	0.024	0.000	0.000	0.000	0.000
112	A	119	HIS	0	-0.088	-0.040	7.138	0.834	0.834	0.000	0.000	0.000	0.000
113	A	120	VAL	0	-0.039	-0.017	9.327	-0.194	-0.194	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.058	0.040	10.629	-0.182	-0.182	0.000	0.000	0.000	0.000
115	A	122	TYR	0	-0.035	-0.034	11.779	0.078	0.078	0.000	0.000	0.000	0.000
116	A	123	VAL	0	0.039	0.026	15.806	-0.118	-0.118	0.000	0.000	0.000	0.000
117	A	124	GLN	0	-0.029	-0.010	17.219	0.111	0.111	0.000	0.000	0.000	0.000
118	A	125	LEU	0	0.029	-0.002	20.067	-0.043	-0.043	0.000	0.000	0.000	0.000
119	A	126	ARG	1	0.798	0.910	22.507	0.326	0.326	0.000	0.000	0.000	0.000
120	A	127	MET	0	-0.032	-0.002	24.684	0.026	0.026	0.000	0.000	0.000	0.000
121	A	128	THR	0	-0.014	-0.022	26.608	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	129	LEU	0	0.060	0.017	29.681	0.011	0.011	0.000	0.000	0.000	0.000
123	A	130	ARG	1	0.928	0.976	29.897	0.171	0.171	0.000	0.000	0.000	0.000
124	A	131	ARG	1	0.873	0.932	28.405	0.152	0.152	0.000	0.000	0.000	0.000
125	A	132	PHE	0	-0.035	-0.007	31.516	0.014	0.014	0.000	0.000	0.000	0.000
126	A	133	HIS	0	0.055	0.025	33.650	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	134	PRO	0	-0.047	-0.020	35.396	0.009	0.009	0.000	0.000	0.000	0.000
128	A	135	LYS	1	0.953	0.998	35.818	-0.031	-0.031	0.000	0.000	0.000	0.000
129	A	136	LEU	0	-0.006	-0.007	40.180	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	137	GLY	0	0.007	-0.005	38.834	0.004	0.004	0.000	0.000	0.000	0.000
131	A	138	ASP	-1	-0.847	-0.913	38.704	0.071	0.071	0.000	0.000	0.000	0.000
132	A	139	LYS	1	0.838	0.901	38.421	-0.070	-0.070	0.000	0.000	0.000	0.000
133	A	140	GLU	-1	-0.843	-0.899	34.191	0.086	0.086	0.000	0.000	0.000	0.000
134	A	141	MET	0	-0.078	-0.048	33.032	-0.020	-0.020	0.000	0.000	0.000	0.000
135	A	142	LEU	0	0.043	0.007	27.051	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	143	GLN	0	0.087	0.036	29.410	-0.026	-0.026	0.000	0.000	0.000	0.000
137	A	144	HIS	0	-0.033	-0.019	30.470	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	145	TYR	0	-0.017	-0.032	27.631	-0.012	-0.012	0.000	0.000	0.000	0.000
139	A	146	THR	0	0.003	-0.020	25.399	-0.016	-0.016	0.000	0.000	0.000	0.000
140	A	147	LEU	0	0.023	0.024	28.265	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	148	ASP	-1	-0.886	-0.946	30.226	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	149	GLN	0	-0.020	-0.011	27.892	-0.032	-0.032	0.000	0.000	0.000	0.000
143	A	150	VAL	0	0.009	0.019	25.319	-0.021	-0.021	0.000	0.000	0.000	0.000
144	A	151	ASN	0	-0.003	-0.021	27.789	-0.011	-0.011	0.000	0.000	0.000	0.000
145	A	152	GLN	0	-0.079	-0.040	31.188	-0.021	-0.021	0.000	0.000	0.000	0.000
146	A	153	ASN	0	-0.047	-0.030	27.030	-0.029	-0.029	0.000	0.000	0.000	0.000
147	A	154	LYS	1	0.922	0.992	27.116	-0.025	-0.025	0.000	0.000	0.000	0.000
148	A	155	LYS	1	0.959	0.962	27.639	0.106	0.106	0.000	0.000	0.000	0.000
149	A	156	ALA	0	0.029	0.024	26.112	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	157	ILE	0	0.014	0.020	22.239	-0.015	-0.015	0.000	0.000	0.000	0.000
151	A	158	GLU	-1	-0.845	-0.949	23.051	-0.016	-0.016	0.000	0.000	0.000	0.000
152	A	159	GLU	-1	-0.961	-0.972	24.597	-0.162	-0.162	0.000	0.000	0.000	0.000
153	A	160	ASP	-1	-0.779	-0.871	20.181	-0.361	-0.361	0.000	0.000	0.000	0.000
154	A	161	LEU	0	-0.041	-0.039	18.675	-0.021	-0.021	0.000	0.000	0.000	0.000
155	A	162	LYS	1	0.941	0.990	20.498	0.132	0.132	0.000	0.000	0.000	0.000
156	A	163	HIS	0	-0.043	-0.011	18.816	0.010	0.010	0.000	0.000	0.000	0.000
157	A	164	PHE	0	-0.060	-0.029	15.759	-0.044	-0.044	0.000	0.000	0.000	0.000
158	A	165	ASN	0	-0.064	-0.032	17.832	0.051	0.051	0.000	0.000	0.000	0.000
159	A	166	LEU	0	-0.018	-0.009	16.310	0.072	0.072	0.000	0.000	0.000	0.000
160	A	167	LYS	1	1.003	0.998	20.800	-0.107	-0.107	0.000	0.000	0.000	0.000
161	A	168	TYR	0	0.022	-0.008	22.902	0.037	0.037	0.000	0.000	0.000	0.000
162	A	169	GLU	-1	-1.013	-1.014	24.012	0.117	0.117	0.000	0.000	0.000	0.000
163	A	170	ASP	-1	-0.891	-0.937	22.630	0.188	0.188	0.000	0.000	0.000	0.000
164	A	171	LEU	0	-0.121	-0.045	18.492	0.054	0.054	0.000	0.000	0.000	0.000
165	A	172	HIS	0	0.037	0.022	19.502	-0.049	-0.049	0.000	0.000	0.000	0.000
166	A	173	SER	0	0.042	0.009	21.656	-0.012	-0.012	0.000	0.000	0.000	0.000
167	A	174	THR	0	0.006	-0.019	19.559	0.036	0.036	0.000	0.000	0.000	0.000
168	A	176	HIS	0	0.029	0.026	25.627	-0.005	-0.005	0.000	0.000	0.000	0.000

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