FMO DATABASE

FMODB ID: N3RVQ

Calculation Name: 3EBM-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EBM

Chain ID: A

ChEMBL ID:

UniProt ID: P13693

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	150
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1494632.678866
FMO2-HF: Nuclear repulsion	1432125.921014
FMO2-HF: Total energy	-62506.757851
FMO2-MP2: Total energy	-62682.403669

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:1:MET )

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

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.
-16.793	-4.917	4.739	-6.812	-9.801	-0.06

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / 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	3	ILE	0	-0.035	-0.024	2.856	-0.786	1.475	0.085	-0.768	-1.579	0.000
4	A	4	TYR	0	0.006	-0.014	4.925	0.097	0.138	0.000	-0.006	-0.034	0.000
5	A	5	ARG	1	0.976	0.990	8.665	0.463	0.463	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.750	-0.863	11.347	-0.063	-0.063	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.041	-0.018	15.125	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.101	-0.048	16.937	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.034	-0.024	17.679	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	10	HIS	1	0.847	0.927	14.887	0.125	0.125	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.771	-0.870	13.553	-0.075	-0.075	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.028	-0.030	8.079	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.029	-0.008	10.759	0.051	0.051	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.008	-0.008	9.080	0.041	0.041	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.019	0.018	3.905	-0.190	0.159	0.039	-0.089	-0.299	0.000
16	A	16	ASP	-1	-0.798	-0.901	2.428	-9.535	-4.203	2.182	-3.658	-3.856	-0.045
17	A	17	ILE	0	-0.030	0.003	3.883	-0.563	-0.043	0.093	-0.095	-0.518	0.000
18	A	18	TYR	0	-0.056	-0.025	6.208	-0.167	-0.167	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.897	0.948	9.371	-0.120	-0.120	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.021	0.017	8.404	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.905	0.956	12.459	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.896	-0.935	15.995	0.002	0.002	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.012	-0.011	17.541	0.010	0.010	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.028	-0.025	21.087	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.939	-0.969	24.039	0.020	0.020	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.043	0.024	19.926	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.099	-0.019	20.299	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.026	-0.016	19.353	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.020	-0.009	12.571	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.791	-0.899	16.307	0.019	0.019	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.014	0.008	11.770	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.929	-0.974	14.238	0.051	0.051	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.006	-0.006	13.953	0.023	0.023	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.898	0.929	13.415	-0.108	-0.108	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.022	0.023	17.186	0.008	0.008	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.035	-0.013	15.582	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.053	0.009	18.908	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	38	NME	0	-0.037	0.000	20.169	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	66	ACE	0	-0.006	-0.013	21.706	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	67	ILE	0	-0.038	-0.030	21.582	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	68	THR	0	-0.040	-0.011	21.090	0.006	0.006	0.000	0.000	0.000	0.000
42	A	69	GLY	0	0.076	0.040	20.436	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	70	VAL	0	0.008	0.005	16.374	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	71	ASP	-1	-0.787	-0.895	12.786	0.123	0.123	0.000	0.000	0.000	0.000
45	A	72	ILE	0	0.001	0.006	11.964	0.028	0.028	0.000	0.000	0.000	0.000
46	A	73	VAL	0	0.005	-0.007	12.947	0.015	0.015	0.000	0.000	0.000	0.000
47	A	74	MET	0	-0.040	-0.021	15.340	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	75	ASN	0	-0.034	-0.024	9.847	0.052	0.052	0.000	0.000	0.000	0.000
49	A	76	HIS	0	-0.015	0.000	6.773	0.096	0.096	0.000	0.000	0.000	0.000
50	A	77	HIS	0	0.008	0.021	11.692	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	78	LEU	0	-0.016	0.002	14.292	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	79	GLN	0	-0.015	-0.016	16.948	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	80	GLU	-1	-0.917	-0.955	20.716	0.004	0.004	0.000	0.000	0.000	0.000
54	A	81	THR	0	-0.026	-0.008	23.310	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	82	SER	0	-0.015	-0.009	26.172	0.002	0.002	0.000	0.000	0.000	0.000
56	A	83	PHE	0	0.041	0.011	26.151	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	84	THR	0	0.027	0.020	31.379	0.001	0.001	0.000	0.000	0.000	0.000
58	A	85	LYS	1	0.998	0.982	33.564	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	86	GLU	-1	-0.912	-0.974	34.849	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	87	ALA	0	-0.014	-0.003	33.225	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	88	TYR	0	0.093	0.054	26.362	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	89	LYS	1	0.878	0.948	30.717	0.002	0.002	0.000	0.000	0.000	0.000
63	A	90	LYS	1	0.921	0.958	32.980	0.011	0.011	0.000	0.000	0.000	0.000
64	A	91	TYR	0	0.015	-0.013	23.416	0.001	0.001	0.000	0.000	0.000	0.000
65	A	92	ILE	0	0.024	0.021	25.720	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	93	LYS	1	0.914	0.953	28.854	0.006	0.006	0.000	0.000	0.000	0.000
67	A	94	ASP	-1	-0.892	-0.949	29.682	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	95	TYR	0	0.044	0.022	19.864	0.000	0.000	0.000	0.000	0.000	0.000
69	A	96	MET	0	-0.029	-0.021	25.640	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	97	LYS	1	0.931	0.963	27.308	0.016	0.016	0.000	0.000	0.000	0.000
71	A	98	SER	0	-0.011	-0.001	25.262	0.000	0.000	0.000	0.000	0.000	0.000
72	A	99	ILE	0	0.017	0.023	20.774	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	100	LYS	1	0.926	0.958	24.073	0.009	0.009	0.000	0.000	0.000	0.000
74	A	101	GLY	0	0.002	-0.002	26.983	0.002	0.002	0.000	0.000	0.000	0.000
75	A	102	LYS	1	0.967	0.989	21.327	0.057	0.057	0.000	0.000	0.000	0.000
76	A	103	LEU	0	-0.034	-0.020	21.156	0.000	0.000	0.000	0.000	0.000	0.000
77	A	104	GLU	-1	-0.963	-0.989	23.891	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	105	GLU	-1	-0.980	-0.968	24.509	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	106	GLN	0	0.005	0.008	17.948	0.002	0.002	0.000	0.000	0.000	0.000
80	A	107	ARG	1	0.878	0.940	17.891	0.050	0.050	0.000	0.000	0.000	0.000
81	A	108	PRO	0	0.089	0.044	22.785	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	109	GLU	-1	-0.903	-0.959	22.322	0.015	0.015	0.000	0.000	0.000	0.000
83	A	110	ARG	1	0.832	0.889	21.175	0.004	0.004	0.000	0.000	0.000	0.000
84	A	111	VAL	0	0.005	0.018	24.640	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	112	LYS	1	0.939	0.963	27.634	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	113	PRO	0	0.038	0.017	25.368	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	114	PHE	0	0.053	0.034	23.319	0.000	0.000	0.000	0.000	0.000	0.000
88	A	115	MET	0	-0.046	-0.027	26.063	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	116	THR	0	-0.060	-0.022	29.441	0.000	0.000	0.000	0.000	0.000	0.000
90	A	117	GLY	0	0.060	0.030	27.249	0.001	0.001	0.000	0.000	0.000	0.000
91	A	118	ALA	0	0.037	0.010	26.160	0.000	0.000	0.000	0.000	0.000	0.000
92	A	119	ALA	0	-0.040	-0.012	27.648	0.000	0.000	0.000	0.000	0.000	0.000
93	A	120	GLU	-1	-0.933	-0.968	30.365	0.005	0.005	0.000	0.000	0.000	0.000
94	A	121	GLN	0	0.032	0.012	24.949	0.002	0.002	0.000	0.000	0.000	0.000
95	A	122	ILE	0	-0.044	-0.031	27.908	0.000	0.000	0.000	0.000	0.000	0.000
96	A	123	LYS	1	0.930	0.962	30.280	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	124	HIS	0	0.058	0.042	27.869	0.000	0.000	0.000	0.000	0.000	0.000
98	A	125	ILE	0	-0.004	0.002	25.764	0.000	0.000	0.000	0.000	0.000	0.000
99	A	126	LEU	0	-0.078	-0.059	29.728	0.000	0.000	0.000	0.000	0.000	0.000
100	A	127	ALA	0	-0.048	-0.012	33.183	0.000	0.000	0.000	0.000	0.000	0.000
101	A	128	ASN	0	-0.010	-0.004	30.049	0.000	0.000	0.000	0.000	0.000	0.000
102	A	129	PHE	0	-0.035	-0.019	30.465	0.000	0.000	0.000	0.000	0.000	0.000
103	A	130	LYS	1	0.904	0.930	31.101	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	131	ASN	0	0.016	0.018	29.350	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	132	TYR	0	0.001	0.024	25.225	0.000	0.000	0.000	0.000	0.000	0.000
106	A	133	GLN	0	-0.009	0.014	24.420	0.000	0.000	0.000	0.000	0.000	0.000
107	A	134	PHE	0	-0.026	-0.028	23.769	0.000	0.000	0.000	0.000	0.000	0.000
108	A	135	PHE	0	0.058	0.021	19.154	0.003	0.003	0.000	0.000	0.000	0.000
109	A	136	ILE	0	-0.021	0.002	19.580	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	137	GLY	0	0.037	0.011	16.495	0.009	0.009	0.000	0.000	0.000	0.000
111	A	138	GLU	-1	-0.895	-0.947	15.390	0.007	0.007	0.000	0.000	0.000	0.000
112	A	139	ASN	0	-0.040	-0.022	17.911	0.001	0.001	0.000	0.000	0.000	0.000
113	A	140	MET	0	-0.073	-0.034	20.211	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	141	ASN	0	0.011	0.009	21.422	0.004	0.004	0.000	0.000	0.000	0.000
115	A	142	PRO	0	0.005	0.004	22.911	0.000	0.000	0.000	0.000	0.000	0.000
116	A	143	ASP	-1	-0.934	-0.970	24.874	-0.027	-0.027	0.000	0.000	0.000	0.000
117	A	144	GLY	0	-0.047	-0.023	20.710	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	145	MET	0	-0.073	-0.014	16.654	0.010	0.010	0.000	0.000	0.000	0.000
119	A	146	VAL	0	-0.004	0.005	20.251	0.004	0.004	0.000	0.000	0.000	0.000
120	A	147	ALA	0	-0.023	-0.001	17.775	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	148	LEU	0	-0.038	-0.026	19.828	0.003	0.003	0.000	0.000	0.000	0.000
122	A	149	LEU	0	-0.041	-0.007	19.715	0.003	0.003	0.000	0.000	0.000	0.000
123	A	150	ASP	-1	-0.790	-0.897	22.014	0.009	0.009	0.000	0.000	0.000	0.000
124	A	151	TYR	0	-0.004	-0.016	22.700	0.005	0.005	0.000	0.000	0.000	0.000
125	A	152	ARG	1	0.774	0.883	18.411	-0.028	-0.028	0.000	0.000	0.000	0.000
126	A	153	GLU	-1	-0.895	-0.948	25.005	0.014	0.014	0.000	0.000	0.000	0.000
127	A	154	ASP	-1	-0.842	-0.911	25.281	0.020	0.020	0.000	0.000	0.000	0.000
128	A	155	GLY	0	-0.018	-0.001	27.733	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	156	VAL	0	-0.081	-0.045	24.977	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	157	THR	0	-0.054	-0.047	20.176	0.002	0.002	0.000	0.000	0.000	0.000
131	A	158	PRO	0	-0.009	0.025	18.509	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	159	TYR	0	-0.081	-0.076	17.945	0.008	0.008	0.000	0.000	0.000	0.000
133	A	160	MET	0	0.017	0.007	16.360	0.001	0.001	0.000	0.000	0.000	0.000
134	A	161	ILE	0	-0.041	-0.006	17.266	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	162	PHE	0	0.072	0.015	14.751	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	163	PHE	0	0.018	-0.015	17.918	0.004	0.004	0.000	0.000	0.000	0.000
137	A	164	LYS	1	0.978	0.977	15.366	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	165	ASP	-1	-0.834	-0.918	16.576	-0.038	-0.038	0.000	0.000	0.000	0.000
139	A	166	GLY	0	-0.016	-0.010	18.329	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	167	LEU	0	-0.048	-0.012	12.457	-0.007	-0.007	0.000	0.000	0.000	0.000
141	A	168	GLU	-1	-0.924	-0.961	12.386	-0.156	-0.156	0.000	0.000	0.000	0.000
142	A	169	MET	0	-0.064	-0.037	8.644	-0.048	-0.048	0.000	0.000	0.000	0.000
143	A	170	GLU	-1	-0.871	-0.931	6.665	-0.402	-0.402	0.000	0.000	0.000	0.000
144	A	171	LYS	1	0.918	0.959	3.832	-3.901	-3.381	0.007	-0.219	-0.307	0.001
145	A	172	CYS	0	-0.029	0.002	2.476	0.320	1.915	0.272	-0.543	-1.324	0.001
146	A	173	LEU	0	-0.014	-0.031	2.372	-1.750	-0.546	2.061	-1.431	-1.833	-0.017
147	A	174	GLU	-1	-0.908	-0.954	5.153	-0.562	-0.508	0.000	-0.003	-0.051	0.000
148	A	175	HIS	0	-0.012	-0.002	8.393	0.179	0.179	0.000	0.000	0.000	0.000
149	A	176	HIS	0	-0.020	-0.006	11.257	-0.040	-0.040	0.000	0.000	0.000	0.000
150	A	177	NME	0	-0.017	0.003	14.992	0.025	0.025	0.000	0.000	0.000	0.000

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