FMO DATABASE

FMODB ID: 5JGJZ

Calculation Name: 4EM8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EM8

Chain ID: A

ChEMBL ID:

UniProt ID: Q2GK74

Base Structure: X-ray

Registration Date: 2023-09-23

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1350376.087918
FMO2-HF: Nuclear repulsion	1292542.285343
FMO2-HF: Total energy	-57833.802576
FMO2-MP2: Total energy	-57997.040837

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:-2:GLY)

Summations of interaction energy for fragment #1(A:-2:GLY)

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.
-5.352	-1.536	0.968	-2.142	-2.645	-0.002

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.022

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	0	MET	0	-0.032	-0.015	3.826	-0.471	0.920	-0.007	-0.742	-0.643	0.004
4	A	1	VAL	0	-0.055	-0.025	6.409	0.612	0.612	0.000	0.000	0.000	0.000
5	A	2	VAL	0	0.030	0.030	8.572	0.323	0.323	0.000	0.000	0.000	0.000
6	A	3	LYS	1	0.861	0.934	10.161	1.357	1.357	0.000	0.000	0.000	0.000
7	A	4	ARG	1	0.891	0.958	12.929	0.635	0.635	0.000	0.000	0.000	0.000
8	A	5	VAL	0	-0.021	-0.017	13.416	-0.029	-0.029	0.000	0.000	0.000	0.000
9	A	6	PHE	0	0.047	0.029	16.528	0.037	0.037	0.000	0.000	0.000	0.000
10	A	7	LEU	0	-0.026	-0.018	16.862	0.000	0.000	0.000	0.000	0.000	0.000
11	A	8	SER	0	-0.011	-0.031	20.726	0.018	0.018	0.000	0.000	0.000	0.000
12	A	9	SER	0	-0.039	-0.035	23.365	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	10	ASP	-1	-0.740	-0.866	25.838	-0.117	-0.117	0.000	0.000	0.000	0.000
14	A	11	HIS	0	0.076	0.041	28.410	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	12	ALA	0	-0.067	-0.034	28.784	0.002	0.002	0.000	0.000	0.000	0.000
16	A	13	GLY	0	0.002	0.003	25.239	0.004	0.004	0.000	0.000	0.000	0.000
17	A	14	VAL	0	0.023	0.030	24.269	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	15	GLU	-1	-0.908	-0.955	24.610	-0.129	-0.129	0.000	0.000	0.000	0.000
19	A	16	LEU	0	0.025	0.004	18.704	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	17	ARG	1	0.809	0.885	20.071	0.194	0.194	0.000	0.000	0.000	0.000
21	A	18	LEU	0	-0.012	0.004	20.405	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	19	PHE	0	-0.003	0.000	16.595	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	20	LEU	0	0.015	-0.005	14.716	-0.045	-0.045	0.000	0.000	0.000	0.000
24	A	21	SER	0	-0.023	-0.017	15.734	-0.093	-0.093	0.000	0.000	0.000	0.000
25	A	22	ALA	0	-0.046	-0.026	17.262	-0.055	-0.055	0.000	0.000	0.000	0.000
26	A	23	TYR	0	0.052	0.034	9.192	-0.130	-0.130	0.000	0.000	0.000	0.000
27	A	24	LEU	0	0.033	0.000	11.353	-0.120	-0.120	0.000	0.000	0.000	0.000
28	A	25	ARG	1	0.938	0.962	13.430	0.325	0.325	0.000	0.000	0.000	0.000
29	A	26	ASP	-1	-0.935	-0.948	14.013	-0.608	-0.608	0.000	0.000	0.000	0.000
30	A	27	LEU	0	-0.016	-0.007	8.315	-0.116	-0.116	0.000	0.000	0.000	0.000
31	A	28	GLY	0	-0.014	-0.021	10.881	-0.276	-0.276	0.000	0.000	0.000	0.000
32	A	29	CYS	0	-0.133	-0.059	11.573	-0.113	-0.113	0.000	0.000	0.000	0.000
33	A	30	GLU	-1	-0.837	-0.912	14.010	-0.449	-0.449	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.058	-0.036	16.096	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	32	PHE	0	-0.019	-0.004	18.579	0.052	0.052	0.000	0.000	0.000	0.000
36	A	33	ASP	-1	-0.858	-0.905	21.770	-0.266	-0.266	0.000	0.000	0.000	0.000
37	A	34	CYS	0	-0.018	-0.013	23.736	0.011	0.011	0.000	0.000	0.000	0.000
38	A	35	GLY	0	0.014	0.031	26.071	0.021	0.021	0.000	0.000	0.000	0.000
39	A	36	CYS	0	-0.028	-0.018	26.532	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.773	-0.883	29.137	-0.153	-0.153	0.000	0.000	0.000	0.000
41	A	38	PRO	0	0.042	-0.001	28.598	0.008	0.008	0.000	0.000	0.000	0.000
42	A	39	LYS	1	0.828	0.904	31.112	0.137	0.137	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.949	-0.955	33.513	-0.098	-0.098	0.000	0.000	0.000	0.000
44	A	41	HIS	0	-0.060	-0.048	33.698	0.002	0.002	0.000	0.000	0.000	0.000
45	A	42	SER	0	-0.039	-0.040	35.398	0.006	0.006	0.000	0.000	0.000	0.000
46	A	43	VAL	0	-0.016	0.009	32.031	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	44	ASP	-1	-0.853	-0.926	34.193	-0.082	-0.082	0.000	0.000	0.000	0.000
48	A	45	TYR	0	-0.030	-0.030	28.750	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	46	PRO	0	-0.020	-0.023	29.794	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	47	ASP	-1	-0.893	-0.938	31.395	-0.119	-0.119	0.000	0.000	0.000	0.000
51	A	48	TYR	0	0.006	-0.003	27.973	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	49	VAL	0	-0.022	0.011	25.885	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	50	HIS	0	-0.030	-0.016	26.529	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.797	-0.899	27.708	-0.206	-0.206	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.007	0.019	21.402	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	53	VAL	0	-0.034	-0.032	23.319	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	54	ARG	1	0.841	0.898	24.560	0.186	0.186	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.904	-0.947	22.788	-0.318	-0.318	0.000	0.000	0.000	0.000
59	A	56	VAL	0	-0.090	-0.028	18.855	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	57	SER	0	-0.061	-0.042	18.960	0.025	0.025	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.945	-0.975	16.756	-0.486	-0.486	0.000	0.000	0.000	0.000
62	A	59	THR	0	0.012	-0.008	15.338	-0.093	-0.093	0.000	0.000	0.000	0.000
63	A	60	SER	0	-0.015	0.007	16.269	-0.082	-0.082	0.000	0.000	0.000	0.000
64	A	61	PHE	0	0.039	0.024	10.845	0.051	0.051	0.000	0.000	0.000	0.000
65	A	62	GLY	0	0.043	0.020	16.149	0.016	0.016	0.000	0.000	0.000	0.000
66	A	63	VAL	0	-0.045	-0.026	15.541	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	64	LEU	0	0.028	0.009	18.330	0.024	0.024	0.000	0.000	0.000	0.000
68	A	65	ILE	0	-0.023	-0.013	19.724	0.016	0.016	0.000	0.000	0.000	0.000
69	A	66	CYS	0	0.005	0.035	23.173	0.008	0.008	0.000	0.000	0.000	0.000
70	A	67	GLY	0	0.040	0.018	25.573	0.003	0.003	0.000	0.000	0.000	0.000
71	A	68	THR	0	0.015	-0.007	26.622	0.002	0.002	0.000	0.000	0.000	0.000
72	A	69	GLY	0	0.069	0.030	23.625	0.007	0.007	0.000	0.000	0.000	0.000
73	A	70	ILE	0	-0.001	-0.009	24.518	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	71	GLY	0	0.014	0.002	26.973	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	72	MET	0	0.052	0.022	24.227	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	73	SER	0	0.012	-0.001	22.999	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	74	ILE	0	-0.059	-0.029	24.686	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	75	ALA	0	-0.006	-0.008	28.217	0.000	0.000	0.000	0.000	0.000	0.000
79	A	76	ALA	0	0.036	0.012	23.484	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	77	ASN	0	-0.003	-0.007	23.238	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	78	ARG	1	0.878	0.955	26.103	0.101	0.101	0.000	0.000	0.000	0.000
82	A	79	HIS	0	0.001	0.019	26.496	0.007	0.007	0.000	0.000	0.000	0.000
83	A	80	LYS	1	0.916	0.935	26.048	0.092	0.092	0.000	0.000	0.000	0.000
84	A	81	ASN	0	-0.006	0.008	23.569	0.023	0.023	0.000	0.000	0.000	0.000
85	A	82	ILE	0	-0.047	-0.002	21.578	-0.034	-0.034	0.000	0.000	0.000	0.000
86	A	83	ARG	1	0.835	0.914	17.170	0.290	0.290	0.000	0.000	0.000	0.000
87	A	84	ALA	0	0.007	-0.005	18.654	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	85	ALA	0	0.006	-0.004	17.330	0.039	0.039	0.000	0.000	0.000	0.000
89	A	86	LEU	0	-0.012	0.017	18.502	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	87	CYS	0	-0.071	-0.015	15.663	0.034	0.034	0.000	0.000	0.000	0.000
91	A	88	SER	0	0.036	0.002	17.685	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.021	0.005	15.888	0.029	0.029	0.000	0.000	0.000	0.000
93	A	90	THR	0	0.089	0.038	10.591	-0.081	-0.081	0.000	0.000	0.000	0.000
94	A	91	MET	0	0.000	0.010	11.993	0.015	0.015	0.000	0.000	0.000	0.000
95	A	92	LEU	0	0.022	0.003	14.072	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.064	0.034	11.332	-0.036	-0.036	0.000	0.000	0.000	0.000
97	A	94	LYS	1	0.859	0.918	8.900	-0.761	-0.761	0.000	0.000	0.000	0.000
98	A	95	LEU	0	-0.024	-0.011	10.930	-0.048	-0.048	0.000	0.000	0.000	0.000
99	A	96	SER	0	-0.004	-0.002	13.868	-0.065	-0.065	0.000	0.000	0.000	0.000
100	A	97	ARG	1	0.791	0.892	9.574	0.611	0.611	0.000	0.000	0.000	0.000
101	A	98	GLU	-1	-0.801	-0.903	10.299	0.574	0.574	0.000	0.000	0.000	0.000
102	A	99	HIS	0	-0.043	-0.048	12.328	-0.039	-0.039	0.000	0.000	0.000	0.000
103	A	100	ASN	0	-0.013	-0.022	15.843	0.003	0.003	0.000	0.000	0.000	0.000
104	A	101	ASP	-1	-0.809	-0.888	13.814	-0.446	-0.446	0.000	0.000	0.000	0.000
105	A	102	ALA	0	0.002	0.009	14.692	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	103	ASN	0	0.064	0.033	14.227	-0.060	-0.060	0.000	0.000	0.000	0.000
107	A	104	VAL	0	0.013	0.013	16.311	-0.039	-0.039	0.000	0.000	0.000	0.000
108	A	105	LEU	0	-0.002	0.018	13.106	0.051	0.051	0.000	0.000	0.000	0.000
109	A	106	CYS	0	-0.058	-0.021	16.781	0.001	0.001	0.000	0.000	0.000	0.000
110	A	107	PHE	0	0.075	0.015	14.411	0.026	0.026	0.000	0.000	0.000	0.000
111	A	108	GLY	0	0.023	-0.003	20.407	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	109	SER	0	-0.042	-0.035	23.020	0.017	0.017	0.000	0.000	0.000	0.000
113	A	110	ARG	1	0.926	0.957	24.028	0.075	0.075	0.000	0.000	0.000	0.000
114	A	111	TYR	0	-0.041	-0.023	24.905	0.009	0.009	0.000	0.000	0.000	0.000
115	A	112	ILE	0	-0.050	-0.001	17.329	0.019	0.019	0.000	0.000	0.000	0.000
116	A	113	ASP	-1	-0.791	-0.857	19.601	0.005	0.005	0.000	0.000	0.000	0.000
117	A	114	PRO	0	0.063	0.004	18.901	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	115	ASP	-1	-0.822	-0.906	16.265	-0.108	-0.108	0.000	0.000	0.000	0.000
119	A	116	THR	0	-0.069	-0.063	14.767	0.020	0.020	0.000	0.000	0.000	0.000
120	A	117	ALA	0	-0.037	-0.032	14.339	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	118	GLN	0	0.006	0.009	11.993	-0.120	-0.120	0.000	0.000	0.000	0.000
122	A	119	SER	0	-0.003	0.007	10.060	-0.097	-0.097	0.000	0.000	0.000	0.000
123	A	120	VAL	0	-0.090	-0.041	9.530	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	121	LEU	0	0.056	0.019	10.638	-0.044	-0.044	0.000	0.000	0.000	0.000
125	A	122	TYR	0	0.031	0.028	2.320	-3.188	-2.106	0.605	-0.770	-0.917	-0.002
126	A	123	THR	0	-0.038	-0.026	6.034	-0.508	-0.508	0.000	0.000	0.000	0.000
127	A	124	PHE	0	-0.043	-0.017	7.118	-0.188	-0.188	0.000	0.000	0.000	0.000
128	A	125	MET	0	0.016	0.008	7.420	0.083	0.083	0.000	0.000	0.000	0.000
129	A	126	THR	0	-0.046	-0.013	2.572	-0.443	0.327	0.351	-0.371	-0.751	-0.002
130	A	127	THR	0	-0.064	-0.021	3.501	0.082	0.655	0.019	-0.259	-0.334	-0.002
131	A	128	ALA	0	0.026	0.009	6.158	-0.158	-0.158	0.000	0.000	0.000	0.000
132	A	129	PHE	0	-0.022	-0.002	7.923	0.239	0.239	0.000	0.000	0.000	0.000
133	A	130	LEU	0	-0.019	-0.017	10.933	0.022	0.022	0.000	0.000	0.000	0.000
134	A	131	GLY	0	0.005	0.024	13.127	0.011	0.011	0.000	0.000	0.000	0.000
135	A	132	GLY	0	0.029	0.001	16.359	0.034	0.034	0.000	0.000	0.000	0.000
136	A	133	ARG	1	0.921	0.935	19.009	-0.100	-0.100	0.000	0.000	0.000	0.000
137	A	134	HIS	0	0.025	0.019	16.334	-0.029	-0.029	0.000	0.000	0.000	0.000
138	A	135	ALA	0	0.026	0.028	19.439	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	136	VAL	0	0.029	0.014	20.494	-0.013	-0.013	0.000	0.000	0.000	0.000
140	A	137	ARG	1	0.894	0.946	21.802	-0.051	-0.051	0.000	0.000	0.000	0.000
141	A	138	VAL	0	0.047	0.026	18.209	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	139	GLN	0	-0.057	-0.028	21.635	-0.013	-0.013	0.000	0.000	0.000	0.000
143	A	140	LYS	1	0.955	0.968	24.165	0.028	0.028	0.000	0.000	0.000	0.000
144	A	141	LEU	0	-0.060	-0.020	21.855	0.002	0.002	0.000	0.000	0.000	0.000
145	A	142	GLY	0	0.036	0.036	25.547	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	143	GLU	-1	-0.928	-0.940	26.348	-0.072	-0.072	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)