FMO DATABASE

FMODB ID: 3Q62L

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	OptAll
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	-1895447.424538
FMO2-HF: Nuclear repulsion	1825782.312596
FMO2-HF: Total energy	-69665.111942
FMO2-MP2: Total energy	-69868.017097

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.
-7.923	-2.249	7.55	-5.04	-8.181	-0.017

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 : -0.028 / q_NPA : -0.016

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	-0.884	-0.945	2.640	-10.823	-6.186	0.936	-2.502	-3.070	-0.016
4	A	10	CYS	0	-0.117	-0.051	2.544	0.587	2.150	1.553	-0.987	-2.129	-0.004
5	A	11	PHE	0	-0.037	-0.017	4.204	0.694	0.892	0.001	-0.034	-0.164	0.000
6	A	12	ARG	1	0.871	0.935	7.148	-0.256	-0.256	0.000	0.000	0.000	0.000
7	A	13	HIS	0	-0.025	0.001	10.673	0.163	0.163	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.935	-0.955	12.209	-1.367	-1.367	0.000	0.000	0.000	0.000
9	A	15	SER	0	-0.062	-0.053	13.633	0.190	0.190	0.000	0.000	0.000	0.000
10	A	16	LEU	0	0.026	0.011	15.428	0.019	0.019	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.081	-0.039	16.445	0.085	0.085	0.000	0.000	0.000	0.000
12	A	18	PRO	0	0.034	0.024	15.003	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	19	ASN	0	-0.038	-0.026	15.371	-0.170	-0.170	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.023	-0.001	14.464	0.109	0.109	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.818	-0.915	17.423	-0.526	-0.526	0.000	0.000	0.000	0.000
16	A	22	TYR	0	-0.012	-0.024	16.376	0.045	0.045	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.830	-0.898	18.379	-0.356	-0.356	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.848	0.920	21.915	0.432	0.432	0.000	0.000	0.000	0.000
19	A	25	PHE	0	-0.012	0.002	15.547	0.030	0.030	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.765	0.885	19.815	0.440	0.440	0.000	0.000	0.000	0.000
21	A	27	GLY	0	0.000	0.010	20.649	0.030	0.030	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.052	-0.043	21.518	0.001	0.001	0.000	0.000	0.000	0.000
23	A	29	TRP	0	-0.010	0.006	20.151	0.003	0.003	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.032	-0.023	22.322	0.032	0.032	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.021	0.020	16.796	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	32	ALA	0	-0.027	-0.007	20.943	0.039	0.039	0.000	0.000	0.000	0.000
27	A	33	ALA	0	0.013	0.005	21.330	0.031	0.031	0.000	0.000	0.000	0.000
28	A	34	GLY	0	0.051	0.019	17.572	-0.058	-0.058	0.000	0.000	0.000	0.000
29	A	35	THR	0	0.047	0.025	14.500	0.042	0.042	0.000	0.000	0.000	0.000
30	A	36	SER	0	-0.046	-0.018	14.144	0.031	0.031	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.878	-0.946	16.368	0.503	0.503	0.000	0.000	0.000	0.000
32	A	38	ALA	0	0.006	0.032	16.157	-0.041	-0.041	0.000	0.000	0.000	0.000
33	A	39	LEU	0	0.052	0.014	14.100	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	40	THR	0	-0.045	-0.024	18.178	-0.070	-0.070	0.000	0.000	0.000	0.000
35	A	41	GLN	0	-0.051	-0.023	18.976	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	42	TYR	0	-0.067	-0.031	17.476	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.884	0.939	21.621	-0.267	-0.267	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.173	-0.087	23.140	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	45	TRP	0	0.034	0.019	16.378	0.024	0.024	0.000	0.000	0.000	0.000
40	A	46	ILE	0	-0.043	-0.019	21.935	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.776	-0.846	17.309	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.897	0.923	19.848	0.120	0.120	0.000	0.000	0.000	0.000
43	A	49	PHE	0	0.109	0.065	13.728	0.024	0.024	0.000	0.000	0.000	0.000
44	A	50	SER	0	-0.077	-0.051	19.039	0.029	0.029	0.000	0.000	0.000	0.000
45	A	51	TYR	0	0.007	-0.011	20.443	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	52	ASP	-1	-0.843	-0.903	19.677	-0.398	-0.398	0.000	0.000	0.000	0.000
47	A	53	ASP	-1	-0.862	-0.940	15.300	-0.428	-0.428	0.000	0.000	0.000	0.000
48	A	54	ALA	0	-0.001	0.026	16.124	0.017	0.017	0.000	0.000	0.000	0.000
49	A	55	LEU	0	0.005	0.010	14.573	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	56	VAL	0	-0.110	-0.058	18.018	0.071	0.071	0.000	0.000	0.000	0.000
51	A	57	SER	0	0.053	0.008	17.548	-0.031	-0.031	0.000	0.000	0.000	0.000
52	A	58	LYS	1	0.832	0.894	19.967	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	59	TYR	0	0.079	0.052	19.848	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	60	THR	0	-0.082	-0.038	23.888	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	61	ASP	-1	-0.760	-0.865	25.467	0.296	0.296	0.000	0.000	0.000	0.000
56	A	62	SER	0	-0.019	-0.027	27.426	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.005	-0.002	29.093	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	64	GLY	0	-0.008	0.013	30.495	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	65	LYN	0	0.044	0.033	31.424	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	66	ASN	0	0.003	-0.035	27.131	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.893	0.952	27.286	-0.083	-0.083	0.000	0.000	0.000	0.000
62	A	68	THR	0	0.016	0.033	22.327	0.003	0.003	0.000	0.000	0.000	0.000
63	A	69	THR	0	-0.082	-0.046	23.222	-0.046	-0.046	0.000	0.000	0.000	0.000
64	A	70	ILE	0	0.000	0.026	16.643	0.025	0.025	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.941	0.953	19.251	-0.106	-0.106	0.000	0.000	0.000	0.000
66	A	72	GLY	0	0.058	0.032	15.504	0.088	0.088	0.000	0.000	0.000	0.000
67	A	73	ARG	1	0.854	0.952	12.578	0.232	0.232	0.000	0.000	0.000	0.000
68	A	74	THR	0	-0.027	-0.029	11.519	0.007	0.007	0.000	0.000	0.000	0.000
69	A	75	LYS	1	0.858	0.920	9.327	1.689	1.689	0.000	0.000	0.000	0.000
70	A	76	PHE	0	0.046	0.024	9.453	-0.349	-0.349	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.893	-0.948	8.120	-2.750	-2.750	0.000	0.000	0.000	0.000
72	A	78	GLY	0	0.063	0.045	11.397	-0.180	-0.180	0.000	0.000	0.000	0.000
73	A	79	ASN	0	-0.025	-0.025	10.996	0.068	0.068	0.000	0.000	0.000	0.000
74	A	80	LYS	1	0.854	0.937	6.375	4.151	4.151	0.000	0.000	0.000	0.000
75	A	81	PHE	0	-0.007	-0.014	7.983	0.420	0.420	0.000	0.000	0.000	0.000
76	A	82	THR	0	0.004	0.006	4.418	-0.377	-0.354	-0.001	-0.009	-0.012	0.000
77	A	83	ILE	0	0.005	-0.002	7.168	0.209	0.209	0.000	0.000	0.000	0.000
78	A	84	ASP	-1	-0.865	-0.921	9.180	0.414	0.414	0.000	0.000	0.000	0.000
79	A	85	TYR	0	-0.021	-0.041	11.449	-0.094	-0.094	0.000	0.000	0.000	0.000
80	A	86	ASN	0	-0.007	-0.019	13.807	0.054	0.054	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.889	-0.952	15.231	0.735	0.735	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.900	0.951	16.247	-0.197	-0.197	0.000	0.000	0.000	0.000
83	A	89	GLY	0	0.034	-0.012	16.051	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	90	LYS	1	0.969	1.002	10.762	-1.359	-1.359	0.000	0.000	0.000	0.000
85	A	91	ALA	0	-0.020	0.000	10.837	0.249	0.249	0.000	0.000	0.000	0.000
86	A	92	PHE	0	0.033	0.001	11.520	0.231	0.231	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.007	0.014	9.299	-0.270	-0.270	0.000	0.000	0.000	0.000
88	A	94	ALA	0	0.019	0.022	5.975	0.892	0.892	0.000	0.000	0.000	0.000
89	A	95	PRO	0	0.019	0.003	2.093	-0.860	-1.742	5.062	-1.483	-2.697	0.003
90	A	96	TYR	0	-0.029	-0.040	4.616	0.987	1.122	-0.001	-0.025	-0.109	0.000
91	A	97	SER	0	0.039	0.026	7.674	-0.567	-0.567	0.000	0.000	0.000	0.000
92	A	98	VAL	0	0.007	0.003	9.948	0.323	0.323	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.007	0.031	12.103	-0.064	-0.064	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.066	0.033	15.358	0.021	0.021	0.000	0.000	0.000	0.000
95	A	101	THR	0	-0.027	-0.052	18.840	0.028	0.028	0.000	0.000	0.000	0.000
96	A	102	ASP	-1	-0.729	-0.831	21.019	-0.311	-0.311	0.000	0.000	0.000	0.000
97	A	103	TYR	0	-0.003	0.002	19.673	0.007	0.007	0.000	0.000	0.000	0.000
98	A	104	GLU	-1	-0.819	-0.897	23.490	-0.248	-0.248	0.000	0.000	0.000	0.000
99	A	105	ASN	0	-0.087	-0.051	25.953	0.048	0.048	0.000	0.000	0.000	0.000
100	A	106	TYR	0	-0.034	-0.041	22.453	0.039	0.039	0.000	0.000	0.000	0.000
101	A	107	ALA	0	-0.002	0.021	18.256	-0.047	-0.047	0.000	0.000	0.000	0.000
102	A	108	ILE	0	-0.012	0.008	16.684	0.080	0.080	0.000	0.000	0.000	0.000
103	A	109	VAL	0	-0.014	-0.005	12.105	-0.132	-0.132	0.000	0.000	0.000	0.000
104	A	110	GLU	-1	-0.705	-0.834	8.659	-0.957	-0.957	0.000	0.000	0.000	0.000
105	A	111	GLY	0	0.014	-0.005	7.335	-0.392	-0.392	0.000	0.000	0.000	0.000
106	A	113	PRO	0	0.004	0.024	6.294	1.504	1.504	0.000	0.000	0.000	0.000
107	A	114	ALA	0	0.040	0.006	8.706	-0.044	-0.044	0.000	0.000	0.000	0.000
108	A	115	ALA	0	-0.028	-0.018	10.020	-0.227	-0.227	0.000	0.000	0.000	0.000
109	A	116	ALA	0	-0.020	-0.008	11.224	-0.240	-0.240	0.000	0.000	0.000	0.000
110	A	117	ASN	0	0.000	0.002	12.250	-0.036	-0.036	0.000	0.000	0.000	0.000
111	A	118	GLY	0	0.003	0.006	7.934	0.147	0.147	0.000	0.000	0.000	0.000
112	A	119	HIS	0	-0.120	-0.077	7.523	0.428	0.428	0.000	0.000	0.000	0.000
113	A	120	VAL	0	-0.020	-0.007	9.635	-0.041	-0.041	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.038	0.030	11.163	-0.208	-0.208	0.000	0.000	0.000	0.000
115	A	122	TYR	0	-0.023	-0.021	12.890	0.100	0.100	0.000	0.000	0.000	0.000
116	A	123	VAL	0	0.037	0.023	16.620	-0.097	-0.097	0.000	0.000	0.000	0.000
117	A	124	GLN	0	-0.026	-0.008	17.575	0.081	0.081	0.000	0.000	0.000	0.000
118	A	125	LEU	0	0.022	0.004	20.942	-0.034	-0.034	0.000	0.000	0.000	0.000
119	A	126	ARG	1	0.789	0.885	23.043	0.330	0.330	0.000	0.000	0.000	0.000
120	A	127	MET	0	-0.028	0.000	25.087	0.025	0.025	0.000	0.000	0.000	0.000
121	A	128	THR	0	-0.009	-0.022	26.917	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	129	LEU	0	0.042	0.018	29.786	0.007	0.007	0.000	0.000	0.000	0.000
123	A	130	ARG	1	0.828	0.927	29.649	0.200	0.200	0.000	0.000	0.000	0.000
124	A	131	ARG	1	0.848	0.909	29.530	0.165	0.165	0.000	0.000	0.000	0.000
125	A	132	PHE	0	-0.023	-0.009	31.818	0.011	0.011	0.000	0.000	0.000	0.000
126	A	133	HIS	0	0.071	0.026	33.925	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	134	PRO	0	-0.016	-0.009	36.148	0.006	0.006	0.000	0.000	0.000	0.000
128	A	135	LYS	1	0.811	0.894	37.598	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	136	LEU	0	0.013	0.005	39.889	0.000	0.000	0.000	0.000	0.000	0.000
130	A	137	GLY	0	-0.003	-0.006	39.453	0.004	0.004	0.000	0.000	0.000	0.000
131	A	138	ASP	-1	-0.824	-0.895	39.398	0.043	0.043	0.000	0.000	0.000	0.000
132	A	139	LYS	1	0.822	0.894	38.704	-0.038	-0.038	0.000	0.000	0.000	0.000
133	A	140	GLU	-1	-0.791	-0.864	35.162	0.031	0.031	0.000	0.000	0.000	0.000
134	A	141	MET	0	-0.042	-0.023	33.759	-0.013	-0.013	0.000	0.000	0.000	0.000
135	A	142	LEU	0	0.030	0.018	27.989	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	143	GLN	0	0.065	0.034	30.031	-0.024	-0.024	0.000	0.000	0.000	0.000
137	A	144	HIS	0	-0.001	-0.006	31.080	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	145	TYR	0	0.002	-0.021	28.284	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	146	THR	0	0.010	-0.017	25.915	-0.018	-0.018	0.000	0.000	0.000	0.000
140	A	147	LEU	0	0.013	0.014	28.749	-0.013	-0.013	0.000	0.000	0.000	0.000
141	A	148	ASP	-1	-0.847	-0.934	30.823	-0.054	-0.054	0.000	0.000	0.000	0.000
142	A	149	GLN	0	-0.073	-0.031	28.649	-0.030	-0.030	0.000	0.000	0.000	0.000
143	A	150	VAL	0	0.030	0.015	26.032	-0.022	-0.022	0.000	0.000	0.000	0.000
144	A	151	ASN	0	-0.045	-0.033	28.603	-0.010	-0.010	0.000	0.000	0.000	0.000
145	A	152	GLN	0	-0.035	-0.023	32.182	-0.016	-0.016	0.000	0.000	0.000	0.000
146	A	153	ASN	0	-0.019	-0.016	27.788	-0.023	-0.023	0.000	0.000	0.000	0.000
147	A	154	LYS	1	0.867	0.958	27.474	0.064	0.064	0.000	0.000	0.000	0.000
148	A	155	LYS	1	0.946	0.958	28.598	0.155	0.155	0.000	0.000	0.000	0.000
149	A	156	ALA	0	0.002	0.018	26.959	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	157	ILE	0	0.026	0.010	23.334	-0.016	-0.016	0.000	0.000	0.000	0.000
151	A	158	GLU	-1	-0.762	-0.889	23.892	-0.115	-0.115	0.000	0.000	0.000	0.000
152	A	159	GLU	-1	-0.845	-0.893	25.453	-0.228	-0.228	0.000	0.000	0.000	0.000
153	A	160	ASP	-1	-0.783	-0.889	21.159	-0.431	-0.431	0.000	0.000	0.000	0.000
154	A	161	LEU	0	-0.047	-0.033	20.169	-0.027	-0.027	0.000	0.000	0.000	0.000
155	A	162	LYS	1	0.827	0.905	21.344	0.214	0.214	0.000	0.000	0.000	0.000
156	A	163	HIS	0	-0.042	-0.012	19.100	0.017	0.017	0.000	0.000	0.000	0.000
157	A	164	PHE	0	-0.040	-0.022	16.943	-0.039	-0.039	0.000	0.000	0.000	0.000
158	A	165	ASN	0	-0.067	-0.032	18.375	0.063	0.063	0.000	0.000	0.000	0.000
159	A	166	LEU	0	-0.029	-0.011	17.135	0.056	0.056	0.000	0.000	0.000	0.000
160	A	167	LYS	1	0.819	0.878	21.646	-0.005	-0.005	0.000	0.000	0.000	0.000
161	A	168	TYR	0	0.005	-0.028	23.668	0.031	0.031	0.000	0.000	0.000	0.000
162	A	169	GLU	-1	-0.909	-0.940	24.723	0.008	0.008	0.000	0.000	0.000	0.000
163	A	170	ASP	-1	-0.850	-0.904	22.692	0.021	0.021	0.000	0.000	0.000	0.000
164	A	171	LEU	0	-0.080	-0.031	19.062	0.031	0.031	0.000	0.000	0.000	0.000
165	A	172	HIS	0	0.037	0.024	19.835	-0.019	-0.019	0.000	0.000	0.000	0.000
166	A	173	SER	0	0.012	0.010	21.902	-0.009	-0.009	0.000	0.000	0.000	0.000
167	A	174	THR	0	0.019	-0.018	19.678	0.030	0.030	0.000	0.000	0.000	0.000
168	A	176	HIS	0	0.024	0.007	26.180	0.003	0.003	0.000	0.000	0.000	0.000

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