FMO DATABASE

FMODB ID: 9GN12

Calculation Name: 3EBK-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	169
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1907747.234995
FMO2-HF: Nuclear repulsion	1837932.766236
FMO2-HF: Total energy	-69814.468759
FMO2-MP2: Total energy	-70017.983986

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:6:ACE )

Summations of interaction energy for fragment #1(A:6:ACE )

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.
-1.093	0.498	0.648	-0.909	-1.328	-0.001

Interaction energy analysis for fragmet #1(A:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.013

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	8	GLU	-1	-0.921	-0.945	3.879	-0.440	0.813	-0.003	-0.510	-0.740	-0.001
4	A	9	ASP	-1	-0.859	-0.930	5.670	-0.793	-0.793	0.000	0.000	0.000	0.000
5	A	112	CYS	0	-0.167	-0.085	7.110	0.188	0.188	0.000	0.000	0.000	0.000
6	A	11	PHE	0	-0.054	-0.028	6.157	0.164	0.164	0.000	0.000	0.000	0.000
7	A	12	ARG	1	0.919	0.947	10.336	0.229	0.229	0.000	0.000	0.000	0.000
8	A	13	HIS	0	-0.029	-0.005	13.741	0.029	0.029	0.000	0.000	0.000	0.000
9	A	14	GLU	-1	-0.959	-0.967	13.785	-0.091	-0.091	0.000	0.000	0.000	0.000
10	A	15	SER	0	-0.072	-0.070	14.130	0.016	0.016	0.000	0.000	0.000	0.000
11	A	16	LEU	0	0.037	0.016	16.004	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	17	VAL	0	-0.070	-0.042	16.525	0.006	0.006	0.000	0.000	0.000	0.000
13	A	18	PRO	0	0.027	0.016	14.818	0.028	0.028	0.000	0.000	0.000	0.000
14	A	19	ASN	0	-0.052	-0.035	14.950	0.029	0.029	0.000	0.000	0.000	0.000
15	A	20	LEU	0	-0.040	-0.005	14.592	0.001	0.001	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.844	-0.930	16.814	0.155	0.155	0.000	0.000	0.000	0.000
17	A	22	TYR	0	0.014	-0.025	15.508	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	23	GLU	-1	-0.918	-0.970	17.611	0.148	0.148	0.000	0.000	0.000	0.000
19	A	24	ARG	1	0.847	0.923	21.053	-0.097	-0.097	0.000	0.000	0.000	0.000
20	A	25	PHE	0	-0.010	-0.006	15.371	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	26	ARG	1	0.836	0.940	19.267	-0.183	-0.183	0.000	0.000	0.000	0.000
22	A	27	GLY	0	0.009	0.010	20.197	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	28	SER	0	-0.073	-0.042	20.817	0.014	0.014	0.000	0.000	0.000	0.000
24	A	29	TRP	0	-0.005	0.030	19.602	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.022	-0.008	21.595	0.007	0.007	0.000	0.000	0.000	0.000
26	A	31	ILE	0	0.009	-0.001	17.538	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	32	ALA	0	-0.009	-0.011	21.650	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	33	ALA	0	0.007	0.018	22.694	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	34	GLY	0	0.050	0.019	20.007	0.008	0.008	0.000	0.000	0.000	0.000
30	A	35	THR	0	0.063	0.038	18.254	0.001	0.001	0.000	0.000	0.000	0.000
31	A	36	SER	0	-0.028	0.010	17.596	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	37	GLU	-1	-0.855	-0.941	19.733	-0.030	-0.030	0.000	0.000	0.000	0.000
33	A	38	ALA	0	0.000	0.022	19.093	0.008	0.008	0.000	0.000	0.000	0.000
34	A	39	LEU	0	0.024	-0.011	16.049	0.013	0.013	0.000	0.000	0.000	0.000
35	A	40	THR	0	-0.024	-0.009	20.077	0.012	0.012	0.000	0.000	0.000	0.000
36	A	41	GLN	0	-0.079	-0.037	21.560	0.003	0.003	0.000	0.000	0.000	0.000
37	A	42	TYR	0	-0.061	-0.020	19.198	0.005	0.005	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.896	0.967	22.930	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	175	CYS	0	-0.170	-0.089	25.023	0.015	0.015	0.000	0.000	0.000	0.000
40	A	45	TRP	0	0.026	-0.005	16.350	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	46	ILE	0	-0.035	-0.021	21.983	0.000	0.000	0.000	0.000	0.000	0.000
42	A	47	ASP	-1	-0.766	-0.846	15.911	0.213	0.213	0.000	0.000	0.000	0.000
43	A	48	ARG	1	0.904	0.941	19.112	-0.145	-0.145	0.000	0.000	0.000	0.000
44	A	49	PHE	0	0.070	0.039	13.179	0.009	0.009	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.065	-0.053	18.235	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	51	TYR	0	0.021	-0.005	19.052	0.016	0.016	0.000	0.000	0.000	0.000
47	A	52	ASP	-1	-0.823	-0.897	17.796	0.223	0.223	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.938	-0.952	13.754	0.403	0.403	0.000	0.000	0.000	0.000
49	A	54	ALA	0	0.011	0.021	14.752	0.034	0.034	0.000	0.000	0.000	0.000
50	A	55	LEU	0	0.029	0.018	13.354	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	56	VAL	0	-0.110	-0.049	16.627	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	57	SER	0	0.042	0.023	16.676	0.004	0.004	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.841	0.886	19.082	-0.117	-0.117	0.000	0.000	0.000	0.000
54	A	59	TYR	0	0.076	0.061	19.568	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	60	THR	0	-0.067	-0.041	23.734	0.002	0.002	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.814	-0.899	25.862	0.030	0.030	0.000	0.000	0.000	0.000
57	A	62	SER	0	0.013	-0.034	28.242	0.001	0.001	0.000	0.000	0.000	0.000
58	A	63	GLN	0	0.002	0.000	29.917	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	64	GLY	0	-0.018	-0.010	31.148	0.000	0.000	0.000	0.000	0.000	0.000
60	A	65	LYN	0	0.054	0.048	31.715	0.005	0.005	0.000	0.000	0.000	0.000
61	A	66	ASN	0	0.039	0.002	26.957	0.001	0.001	0.000	0.000	0.000	0.000
62	A	67	ARG	1	0.925	0.968	27.239	-0.059	-0.059	0.000	0.000	0.000	0.000
63	A	68	THR	0	0.003	0.019	21.831	0.001	0.001	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.100	-0.046	21.688	0.002	0.002	0.000	0.000	0.000	0.000
65	A	70	ILE	0	-0.029	-0.002	15.746	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.942	0.954	17.640	-0.150	-0.150	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.079	0.044	13.590	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	73	ARG	1	0.868	0.954	10.154	-0.669	-0.669	0.000	0.000	0.000	0.000
69	A	74	THR	0	-0.039	-0.013	10.226	0.080	0.080	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.993	0.991	7.832	-0.709	-0.709	0.000	0.000	0.000	0.000
71	A	76	PHE	0	0.017	0.003	8.521	0.164	0.164	0.000	0.000	0.000	0.000
72	A	77	GLU	-1	-0.982	-0.994	6.671	0.746	0.746	0.000	0.000	0.000	0.000
73	A	78	GLY	0	0.049	0.035	10.210	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	79	ASN	0	-0.025	-0.025	11.277	0.037	0.037	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.962	0.989	6.852	0.122	0.122	0.000	0.000	0.000	0.000
76	A	81	PHE	0	0.025	0.009	8.027	0.041	0.041	0.000	0.000	0.000	0.000
77	A	82	THR	0	-0.001	0.009	3.391	-0.216	-0.073	0.036	-0.078	-0.101	0.000
78	A	83	ILE	0	0.011	0.004	6.143	-0.266	-0.266	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.906	-0.942	7.880	0.706	0.706	0.000	0.000	0.000	0.000
80	A	85	TYR	0	-0.045	-0.085	9.516	-0.084	-0.084	0.000	0.000	0.000	0.000
81	A	86	ASN	0	0.002	-0.008	12.862	0.017	0.017	0.000	0.000	0.000	0.000
82	A	87	ASP	-1	-0.899	-0.958	15.608	0.110	0.110	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.881	0.974	16.487	-0.131	-0.131	0.000	0.000	0.000	0.000
84	A	89	GLY	0	0.057	-0.005	15.912	0.016	0.016	0.000	0.000	0.000	0.000
85	A	90	LYS	1	0.999	1.009	12.014	-0.062	-0.062	0.000	0.000	0.000	0.000
86	A	91	ALA	0	-0.039	-0.013	11.648	0.010	0.010	0.000	0.000	0.000	0.000
87	A	92	PHE	0	0.036	0.001	12.125	-0.038	-0.038	0.000	0.000	0.000	0.000
88	A	93	SER	0	0.013	0.033	8.327	0.020	0.020	0.000	0.000	0.000	0.000
89	A	94	ALA	0	-0.004	0.005	5.566	-0.124	-0.124	0.000	0.000	0.000	0.000
90	A	95	PRO	0	-0.008	0.005	2.458	0.132	0.343	0.615	-0.314	-0.511	0.000
91	A	96	TYR	0	-0.010	-0.032	4.756	-0.429	-0.445	0.000	-0.007	0.024	0.000
92	A	97	SER	0	0.018	0.011	8.283	0.116	0.116	0.000	0.000	0.000	0.000
93	A	98	VAL	0	0.010	0.008	10.756	-0.044	-0.044	0.000	0.000	0.000	0.000
94	A	99	LEU	0	0.001	0.025	14.175	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.067	0.037	16.409	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	101	THR	0	0.004	-0.021	19.354	0.016	0.016	0.000	0.000	0.000	0.000
97	A	102	ASP	-1	-0.727	-0.828	21.537	0.056	0.056	0.000	0.000	0.000	0.000
98	A	103	TYR	0	-0.033	0.010	19.700	0.004	0.004	0.000	0.000	0.000	0.000
99	A	104	GLU	-1	-0.891	-0.970	23.532	0.084	0.084	0.000	0.000	0.000	0.000
100	A	105	ASN	0	-0.107	-0.070	26.168	0.001	0.001	0.000	0.000	0.000	0.000
101	A	106	TYR	0	-0.040	-0.056	23.022	0.005	0.005	0.000	0.000	0.000	0.000
102	A	107	ALA	0	0.019	0.020	18.538	0.006	0.006	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.003	0.017	18.114	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	109	VAL	0	-0.021	-0.009	12.757	0.008	0.008	0.000	0.000	0.000	0.000
105	A	110	GLU	-1	-0.709	-0.828	11.175	-0.190	-0.190	0.000	0.000	0.000	0.000
106	A	111	GLY	0	0.010	-0.005	9.268	0.078	0.078	0.000	0.000	0.000	0.000
107	A	113	PRO	0	0.002	0.027	8.895	-0.041	-0.041	0.000	0.000	0.000	0.000
108	A	114	ALA	0	0.063	0.014	10.475	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	115	ALA	0	-0.022	-0.016	12.699	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	116	ALA	0	-0.053	-0.019	14.121	0.005	0.005	0.000	0.000	0.000	0.000
111	A	117	ASN	0	-0.033	-0.028	15.748	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	118	GLY	0	-0.001	-0.004	11.702	-0.025	-0.025	0.000	0.000	0.000	0.000
113	A	119	HIS	0	-0.091	-0.041	11.384	-0.034	-0.034	0.000	0.000	0.000	0.000
114	A	120	VAL	0	-0.038	-0.016	13.191	0.030	0.030	0.000	0.000	0.000	0.000
115	A	121	ILE	0	0.059	0.038	14.067	0.003	0.003	0.000	0.000	0.000	0.000
116	A	122	TYR	0	-0.029	-0.031	13.595	0.003	0.003	0.000	0.000	0.000	0.000
117	A	123	VAL	0	0.034	0.023	18.473	0.007	0.007	0.000	0.000	0.000	0.000
118	A	124	GLN	0	-0.022	-0.006	17.620	0.005	0.005	0.000	0.000	0.000	0.000
119	A	125	LEU	0	0.031	-0.002	21.549	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	126	ARG	1	0.790	0.908	22.500	-0.107	-0.107	0.000	0.000	0.000	0.000
121	A	127	MET	0	-0.028	0.001	24.946	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	128	THR	0	-0.015	-0.024	26.749	0.005	0.005	0.000	0.000	0.000	0.000
123	A	129	LEU	0	0.064	0.018	29.473	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	130	ARG	1	0.921	0.973	30.010	-0.070	-0.070	0.000	0.000	0.000	0.000
125	A	131	ARG	1	0.868	0.930	28.927	-0.061	-0.061	0.000	0.000	0.000	0.000
126	A	132	PHE	0	-0.029	-0.004	31.807	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	133	HIS	0	0.049	0.021	33.914	0.004	0.004	0.000	0.000	0.000	0.000
128	A	134	PRO	0	-0.040	-0.016	35.326	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	135	LYS	1	0.929	0.985	36.648	-0.037	-0.037	0.000	0.000	0.000	0.000
130	A	136	LEU	0	0.007	-0.011	40.666	0.000	0.000	0.000	0.000	0.000	0.000
131	A	137	GLY	0	-0.007	0.005	40.647	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	138	ASP	-1	-0.902	-0.950	37.893	0.040	0.040	0.000	0.000	0.000	0.000
133	A	139	LYS	1	0.849	0.925	34.162	-0.033	-0.033	0.000	0.000	0.000	0.000
134	A	140	GLU	-1	-0.792	-0.876	34.603	0.034	0.034	0.000	0.000	0.000	0.000
135	A	141	MET	0	-0.093	-0.057	33.570	0.000	0.000	0.000	0.000	0.000	0.000
136	A	142	LEU	0	0.034	-0.004	27.580	0.000	0.000	0.000	0.000	0.000	0.000
137	A	143	GLN	0	0.078	0.033	30.871	0.004	0.004	0.000	0.000	0.000	0.000
138	A	144	HIS	0	-0.018	-0.003	31.939	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	145	TYR	0	-0.025	-0.036	28.303	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	146	THR	0	0.010	-0.017	27.070	0.002	0.002	0.000	0.000	0.000	0.000
141	A	147	LEU	0	0.024	0.025	29.739	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	148	ASP	-1	-0.893	-0.950	32.152	0.026	0.026	0.000	0.000	0.000	0.000
143	A	149	GLN	0	-0.022	-0.012	29.209	0.001	0.001	0.000	0.000	0.000	0.000
144	A	150	VAL	0	0.013	0.021	27.460	0.000	0.000	0.000	0.000	0.000	0.000
145	A	151	ASN	0	-0.008	-0.022	29.811	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	152	GLN	0	-0.082	-0.042	32.865	0.000	0.000	0.000	0.000	0.000	0.000
147	A	153	ASN	0	-0.049	-0.031	28.832	0.000	0.000	0.000	0.000	0.000	0.000
148	A	154	LYS	1	0.921	0.992	29.605	-0.012	-0.012	0.000	0.000	0.000	0.000
149	A	155	LYS	1	0.959	0.962	30.281	-0.012	-0.012	0.000	0.000	0.000	0.000
150	A	156	ALA	0	0.026	0.023	28.111	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	157	ILE	0	0.016	0.021	24.873	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	158	GLU	-1	-0.843	-0.949	25.883	-0.006	-0.006	0.000	0.000	0.000	0.000
153	A	159	GLU	-1	-0.963	-0.973	27.802	-0.012	-0.012	0.000	0.000	0.000	0.000
154	A	160	ASP	-1	-0.781	-0.872	22.800	0.018	0.018	0.000	0.000	0.000	0.000
155	A	161	LEU	0	-0.041	-0.039	21.907	-0.006	-0.006	0.000	0.000	0.000	0.000
156	A	162	LYS	1	0.940	0.990	24.074	0.008	0.008	0.000	0.000	0.000	0.000
157	A	163	HIS	0	-0.043	-0.011	21.591	-0.005	-0.005	0.000	0.000	0.000	0.000
158	A	164	PHE	0	-0.060	-0.029	18.564	-0.006	-0.006	0.000	0.000	0.000	0.000
159	A	165	ASN	0	-0.067	-0.033	21.841	-0.001	-0.001	0.000	0.000	0.000	0.000
160	A	166	LEU	0	-0.018	-0.009	20.219	-0.003	-0.003	0.000	0.000	0.000	0.000
161	A	167	LYS	1	0.999	0.994	24.732	0.032	0.032	0.000	0.000	0.000	0.000
162	A	168	TYR	0	0.024	-0.008	25.528	-0.001	-0.001	0.000	0.000	0.000	0.000
163	A	169	GLU	-1	-1.010	-1.011	27.354	-0.013	-0.013	0.000	0.000	0.000	0.000
164	A	170	ASP	-1	-0.895	-0.939	26.568	-0.029	-0.029	0.000	0.000	0.000	0.000
165	A	171	LEU	0	-0.120	-0.046	21.962	-0.004	-0.004	0.000	0.000	0.000	0.000
166	A	172	HIS	0	0.031	0.018	23.023	0.007	0.007	0.000	0.000	0.000	0.000
167	A	173	SER	0	0.047	0.010	24.597	0.007	0.007	0.000	0.000	0.000	0.000
168	A	174	THR	0	-0.007	-0.025	21.955	-0.004	-0.004	0.000	0.000	0.000	0.000
169	A	176	HIS	-1	-0.888	-0.933	27.556	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ACE )