FMO DATABASE

FMODB ID: JL279

Calculation Name: 4EMZ-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMZ

Chain ID: C

ChEMBL ID:

UniProt ID: P35585

Base Structure: X-ray

Registration Date: 2023-06-22

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1361544.313031
FMO2-HF: Nuclear repulsion	1302998.816053
FMO2-HF: Total energy	-58545.496978
FMO2-MP2: Total energy	-58718.328736

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(C:7:LYS)

Summations of interaction energy for fragment #1(C:7:LYS)

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.
37.534	38.233	10.954	-6.037	-5.614	-0.012

Interaction energy analysis for fragmet #1(C:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.033 / q_NPA : 0.984

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	C	9	SER	0	0.048	0.039	2.844	-2.892	0.005	0.091	-1.369	-1.619	-0.003
4	C	10	VAL	0	0.016	0.029	2.019	4.396	1.018	10.825	-4.374	-3.072	-0.008
5	C	11	ILE	0	-0.079	-0.058	3.547	-0.523	0.164	0.023	-0.187	-0.523	0.000
6	C	12	GLY	0	0.070	0.037	6.738	3.399	3.399	0.000	0.000	0.000	0.000
7	C	13	TRP	0	0.021	0.000	8.544	2.044	2.044	0.000	0.000	0.000	0.000
8	C	14	PRO	0	-0.017	-0.017	10.021	1.882	1.882	0.000	0.000	0.000	0.000
9	C	15	ALA	0	0.082	0.056	12.956	1.447	1.447	0.000	0.000	0.000	0.000
10	C	16	VAL	0	-0.009	0.001	11.464	1.360	1.360	0.000	0.000	0.000	0.000
11	C	17	ARG	1	0.866	0.938	12.194	24.736	24.736	0.000	0.000	0.000	0.000
12	C	18	GLU	-1	-0.973	-0.990	15.459	-14.032	-14.032	0.000	0.000	0.000	0.000
13	C	19	ARG	1	0.964	0.983	16.661	16.576	16.576	0.000	0.000	0.000	0.000
14	C	20	MET	0	-0.026	-0.010	15.115	0.716	0.716	0.000	0.000	0.000	0.000
15	C	21	ARG	1	0.905	0.917	18.150	16.346	16.346	0.000	0.000	0.000	0.000
16	C	22	ARG	1	0.964	0.978	21.473	11.960	11.960	0.000	0.000	0.000	0.000
17	C	23	ALA	0	0.073	0.054	23.576	0.133	0.133	0.000	0.000	0.000	0.000
18	C	55	CYS	0	-0.024	-0.025	48.470	0.014	0.014	0.000	0.000	0.000	0.000
19	C	56	ALA	0	0.006	-0.005	44.134	-0.029	-0.029	0.000	0.000	0.000	0.000
20	C	57	TRP	0	-0.009	-0.003	38.128	-0.043	-0.043	0.000	0.000	0.000	0.000
21	C	58	LEU	0	-0.016	-0.010	39.493	0.022	0.022	0.000	0.000	0.000	0.000
22	C	59	GLU	-1	-0.946	-0.962	33.184	-9.103	-9.103	0.000	0.000	0.000	0.000
23	C	60	ALA	0	-0.047	-0.027	33.330	0.211	0.211	0.000	0.000	0.000	0.000
24	C	61	GLN	0	-0.002	-0.004	33.088	-0.437	-0.437	0.000	0.000	0.000	0.000
25	C	62	GLU	-1	-0.958	-0.978	28.306	-10.151	-10.151	0.000	0.000	0.000	0.000
26	C	63	GLU	-1	-0.990	-0.987	31.648	-7.964	-7.964	0.000	0.000	0.000	0.000
27	C	64	GLU	-1	-1.007	-0.989	29.932	-8.937	-8.937	0.000	0.000	0.000	0.000
28	C	65	GLU	-1	-0.934	-0.967	27.429	-9.587	-9.587	0.000	0.000	0.000	0.000
29	C	66	VAL	0	0.004	-0.009	28.664	-0.221	-0.221	0.000	0.000	0.000	0.000
30	C	67	GLY	0	-0.039	-0.017	28.322	-0.061	-0.061	0.000	0.000	0.000	0.000
31	C	68	PHE	0	-0.016	-0.020	24.157	-0.241	-0.241	0.000	0.000	0.000	0.000
32	C	69	PRO	0	-0.004	0.003	21.637	-0.024	-0.024	0.000	0.000	0.000	0.000
33	C	70	VAL	0	0.038	0.020	19.539	-0.436	-0.436	0.000	0.000	0.000	0.000
34	C	71	THR	0	-0.069	-0.029	15.199	0.419	0.419	0.000	0.000	0.000	0.000
35	C	72	PRO	0	0.066	0.007	18.207	-0.317	-0.317	0.000	0.000	0.000	0.000
36	C	73	GLN	0	-0.001	-0.007	17.790	-0.119	-0.119	0.000	0.000	0.000	0.000
37	C	74	VAL	0	-0.033	0.008	13.188	-0.335	-0.335	0.000	0.000	0.000	0.000
38	C	75	PRO	0	-0.011	0.006	13.749	0.416	0.416	0.000	0.000	0.000	0.000
39	C	76	LEU	0	-0.009	0.005	14.701	-0.978	-0.978	0.000	0.000	0.000	0.000
40	C	77	ARG	1	0.841	0.929	10.901	21.343	21.343	0.000	0.000	0.000	0.000
41	C	78	PRO	0	0.087	0.029	16.908	-0.541	-0.541	0.000	0.000	0.000	0.000
42	C	79	MET	0	-0.009	0.019	12.039	-1.118	-1.118	0.000	0.000	0.000	0.000
43	C	80	THR	0	0.016	0.005	13.626	0.410	0.410	0.000	0.000	0.000	0.000
44	C	81	TYR	0	0.013	0.012	14.244	-1.618	-1.618	0.000	0.000	0.000	0.000
45	C	82	LYS	1	0.907	0.943	8.924	29.303	29.303	0.000	0.000	0.000	0.000
46	C	83	ALA	0	0.029	0.028	9.783	-2.446	-2.446	0.000	0.000	0.000	0.000
47	C	84	ALA	0	0.022	0.015	9.798	-2.519	-2.519	0.000	0.000	0.000	0.000
48	C	85	VAL	0	0.062	0.023	10.067	-0.599	-0.599	0.000	0.000	0.000	0.000
49	C	86	ASP	-1	-0.893	-0.950	6.030	-38.895	-38.895	0.000	0.000	0.000	0.000
50	C	87	LEU	0	-0.032	-0.022	6.603	-4.820	-4.820	0.000	0.000	0.000	0.000
51	C	88	SER	0	-0.002	-0.003	8.239	-0.014	-0.014	0.000	0.000	0.000	0.000
52	C	89	HIS	0	-0.046	-0.022	7.524	2.347	2.347	0.000	0.000	0.000	0.000
53	C	90	PHE	0	-0.024	-0.010	3.199	-3.320	-2.827	0.015	-0.107	-0.400	-0.001
54	C	91	LEU	0	0.025	-0.007	6.157	1.899	1.899	0.000	0.000	0.000	0.000
55	C	92	LYS	1	0.892	0.976	9.514	23.519	23.519	0.000	0.000	0.000	0.000
56	C	93	GLU	-1	-0.975	-0.970	6.379	-41.506	-41.506	0.000	0.000	0.000	0.000
57	C	94	LYS	1	0.877	0.939	5.015	51.502	51.502	0.000	0.000	0.000	0.000
58	C	95	GLY	0	0.060	0.040	9.520	2.523	2.523	0.000	0.000	0.000	0.000
59	C	96	GLY	0	-0.034	-0.047	12.744	-0.749	-0.749	0.000	0.000	0.000	0.000
60	C	97	LEU	0	0.023	0.008	13.855	0.922	0.922	0.000	0.000	0.000	0.000
61	C	98	GLU	-1	-0.911	-0.976	15.858	-16.154	-16.154	0.000	0.000	0.000	0.000
62	C	99	GLY	0	0.010	0.008	17.680	0.243	0.243	0.000	0.000	0.000	0.000
63	C	100	LEU	0	-0.043	-0.002	18.530	0.659	0.659	0.000	0.000	0.000	0.000
64	C	101	ILE	0	0.020	-0.002	21.141	0.038	0.038	0.000	0.000	0.000	0.000
65	C	102	HIS	0	-0.054	-0.025	22.059	0.242	0.242	0.000	0.000	0.000	0.000
66	C	103	SER	0	0.011	-0.006	24.006	0.468	0.468	0.000	0.000	0.000	0.000
67	C	104	GLN	0	0.040	0.016	23.866	-0.169	-0.169	0.000	0.000	0.000	0.000
68	C	105	ARG	1	1.010	1.009	23.585	10.584	10.584	0.000	0.000	0.000	0.000
69	C	106	ARG	1	0.842	0.936	21.026	13.215	13.215	0.000	0.000	0.000	0.000
70	C	107	GLN	0	-0.022	-0.030	19.526	-0.298	-0.298	0.000	0.000	0.000	0.000
71	C	108	ASP	-1	-0.786	-0.893	18.579	-14.203	-14.203	0.000	0.000	0.000	0.000
72	C	109	ILE	0	-0.087	0.015	17.604	-0.511	-0.511	0.000	0.000	0.000	0.000
73	C	110	LEU	0	-0.022	-0.015	12.881	-1.243	-1.243	0.000	0.000	0.000	0.000
74	C	111	ASP	-1	-0.795	-0.891	14.013	-17.897	-17.897	0.000	0.000	0.000	0.000
75	C	112	LEU	0	0.023	0.008	15.007	-0.643	-0.643	0.000	0.000	0.000	0.000
76	C	113	TRP	0	-0.003	0.018	7.461	-1.105	-1.105	0.000	0.000	0.000	0.000
77	C	114	ILE	0	-0.017	-0.005	9.403	-1.280	-1.280	0.000	0.000	0.000	0.000
78	C	115	TYR	0	-0.003	-0.004	11.406	-0.368	-0.368	0.000	0.000	0.000	0.000
79	C	116	HIS	0	0.027	0.003	12.652	-0.192	-0.192	0.000	0.000	0.000	0.000
80	C	117	THR	0	-0.097	-0.058	7.036	-1.099	-1.099	0.000	0.000	0.000	0.000
81	C	118	GLN	0	-0.048	-0.030	6.761	-1.461	-1.461	0.000	0.000	0.000	0.000
82	C	119	GLY	0	0.082	0.052	9.063	0.374	0.374	0.000	0.000	0.000	0.000
83	C	120	TYR	0	-0.089	-0.058	9.928	0.982	0.982	0.000	0.000	0.000	0.000
84	C	121	PHE	0	0.051	0.023	14.578	-0.076	-0.076	0.000	0.000	0.000	0.000
85	C	122	PRO	0	0.014	0.006	17.804	-0.556	-0.556	0.000	0.000	0.000	0.000
86	C	123	ASP	-1	-0.883	-0.937	18.753	-13.657	-13.657	0.000	0.000	0.000	0.000
87	C	124	TRP	0	0.001	-0.003	14.291	0.189	0.189	0.000	0.000	0.000	0.000
88	C	125	GLN	0	0.011	0.035	17.478	0.120	0.120	0.000	0.000	0.000	0.000
89	C	126	ASN	0	0.004	0.005	19.906	0.673	0.673	0.000	0.000	0.000	0.000
90	C	127	TYR	0	-0.012	-0.048	19.552	-0.532	-0.532	0.000	0.000	0.000	0.000
91	C	128	THR	0	0.005	0.015	25.061	0.293	0.293	0.000	0.000	0.000	0.000
92	C	129	PRO	0	-0.009	-0.009	28.236	-0.142	-0.142	0.000	0.000	0.000	0.000
93	C	130	GLY	0	-0.053	0.007	31.234	-0.028	-0.028	0.000	0.000	0.000	0.000
94	C	131	PRO	0	0.002	-0.029	32.877	0.137	0.137	0.000	0.000	0.000	0.000
95	C	132	GLY	0	0.050	0.022	32.137	0.089	0.089	0.000	0.000	0.000	0.000
96	C	133	VAL	0	-0.018	-0.010	25.895	-0.188	-0.188	0.000	0.000	0.000	0.000
97	C	134	ARG	1	0.785	0.914	25.625	10.933	10.933	0.000	0.000	0.000	0.000
98	C	135	TYR	0	0.060	-0.001	23.956	-0.716	-0.716	0.000	0.000	0.000	0.000
99	C	136	PRO	0	0.025	0.030	19.724	0.393	0.393	0.000	0.000	0.000	0.000
100	C	137	LEU	0	0.035	0.012	21.923	0.350	0.350	0.000	0.000	0.000	0.000
101	C	138	THR	0	-0.038	-0.040	17.512	0.296	0.296	0.000	0.000	0.000	0.000
102	C	139	PHE	0	-0.022	-0.003	18.765	-0.771	-0.771	0.000	0.000	0.000	0.000
103	C	140	GLY	0	0.064	0.014	15.686	-0.430	-0.430	0.000	0.000	0.000	0.000
104	C	141	TRP	0	-0.035	-0.016	11.956	-2.404	-2.404	0.000	0.000	0.000	0.000
105	C	142	CYS	0	-0.038	-0.024	13.978	1.315	1.315	0.000	0.000	0.000	0.000
106	C	143	TYR	0	0.010	0.004	12.316	0.244	0.244	0.000	0.000	0.000	0.000
107	C	144	LYS	1	0.935	0.969	17.777	13.847	13.847	0.000	0.000	0.000	0.000
108	C	145	LEU	0	-0.002	-0.001	21.545	-0.232	-0.232	0.000	0.000	0.000	0.000
109	C	146	VAL	0	-0.031	-0.013	24.156	0.486	0.486	0.000	0.000	0.000	0.000
110	C	147	PRO	0	0.029	-0.007	26.537	-0.203	-0.203	0.000	0.000	0.000	0.000
111	C	148	VAL	0	-0.001	0.010	28.090	-0.033	-0.033	0.000	0.000	0.000	0.000
112	C	149	GLU	-1	-0.953	-0.983	30.705	-8.734	-8.734	0.000	0.000	0.000	0.000
113	C	150	PRO	0	-0.007	0.006	32.139	0.142	0.142	0.000	0.000	0.000	0.000
114	C	151	ASP	-1	-0.879	-0.948	29.593	-10.512	-10.512	0.000	0.000	0.000	0.000
115	C	152	LYS	1	0.842	0.947	32.638	9.675	9.675	0.000	0.000	0.000	0.000
116	C	178	ARG	1	1.002	0.989	33.322	9.346	9.346	0.000	0.000	0.000	0.000
117	C	179	GLU	-1	-0.855	-0.947	32.002	-9.798	-9.798	0.000	0.000	0.000	0.000
118	C	180	VAL	0	0.018	0.018	28.969	-0.153	-0.153	0.000	0.000	0.000	0.000
119	C	181	LEU	0	-0.022	-0.011	26.356	0.064	0.064	0.000	0.000	0.000	0.000
120	C	182	GLU	-1	-0.789	-0.872	22.838	-12.814	-12.814	0.000	0.000	0.000	0.000
121	C	183	TRP	0	-0.020	-0.007	18.260	0.131	0.131	0.000	0.000	0.000	0.000
122	C	184	ARG	1	0.825	0.926	19.461	13.672	13.672	0.000	0.000	0.000	0.000
123	C	185	PHE	0	0.001	-0.010	12.445	0.024	0.024	0.000	0.000	0.000	0.000
124	C	186	ASP	-1	-0.865	-0.955	17.331	-13.880	-13.880	0.000	0.000	0.000	0.000
125	C	187	SER	0	0.059	0.021	15.770	-0.012	-0.012	0.000	0.000	0.000	0.000
126	C	188	ARG	1	0.936	0.978	17.123	12.695	12.695	0.000	0.000	0.000	0.000
127	C	189	LEU	0	-0.033	-0.023	18.430	0.614	0.614	0.000	0.000	0.000	0.000
128	C	190	ALA	0	-0.016	-0.007	16.018	0.060	0.060	0.000	0.000	0.000	0.000
129	C	191	PHE	0	-0.026	-0.015	16.666	-0.026	-0.026	0.000	0.000	0.000	0.000
130	C	192	HIS	0	-0.013	-0.003	20.774	0.316	0.316	0.000	0.000	0.000	0.000
131	C	193	HIS	0	-0.021	0.001	23.070	-0.333	-0.333	0.000	0.000	0.000	0.000
132	C	194	VAL	0	0.013	0.003	24.079	0.481	0.481	0.000	0.000	0.000	0.000
133	C	195	ALA	0	0.046	0.017	25.048	0.533	0.533	0.000	0.000	0.000	0.000
134	C	196	ARG	1	0.924	0.958	26.526	11.601	11.601	0.000	0.000	0.000	0.000
135	C	197	GLU	-1	-0.863	-0.936	28.228	-10.480	-10.480	0.000	0.000	0.000	0.000
136	C	198	LEU	0	-0.054	-0.026	28.274	0.333	0.333	0.000	0.000	0.000	0.000
137	C	199	HIS	1	0.881	0.934	30.530	10.171	10.171	0.000	0.000	0.000	0.000
138	C	200	PRO	0	0.006	0.024	31.396	-0.216	-0.216	0.000	0.000	0.000	0.000
139	C	201	GLU	-1	-0.856	-0.927	32.459	-9.480	-9.480	0.000	0.000	0.000	0.000
140	C	202	TYR	0	-0.040	-0.020	29.138	-0.034	-0.034	0.000	0.000	0.000	0.000
141	C	203	PHE	0	-0.069	-0.015	24.948	-0.401	-0.401	0.000	0.000	0.000	0.000
142	C	204	LYS	1	0.975	0.992	28.099	9.700	9.700	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:7:LYS)