FMO DATABASE

FMODB ID: MV9JZ

Calculation Name: 4EMZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMZ

Chain ID: B

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	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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1340530.712953
FMO2-HF: Nuclear repulsion	1283766.327846
FMO2-HF: Total energy	-56764.385108
FMO2-MP2: Total energy	-56932.918245

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(B:5:TRP)

Summations of interaction energy for fragment #1(B:5:TRP)

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.
-15.684	-9.912	1.9	-2.651	-5.022	0.02

Interaction energy analysis for fragmet #1(B:5:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.012

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	B	7	LYS	1	0.962	0.982	3.828	-3.967	-1.759	0.014	-1.020	-1.202	0.007
4	B	8	SER	0	0.036	0.020	6.226	0.175	0.175	0.000	0.000	0.000	0.000
5	B	9	SER	0	0.037	0.015	4.012	-0.304	0.032	0.001	-0.073	-0.265	0.000
6	B	10	VAL	0	-0.030	-0.040	3.882	-0.916	-0.563	0.005	-0.122	-0.236	0.001
7	B	11	ILE	0	0.019	-0.006	6.412	-0.464	-0.464	0.000	0.000	0.000	0.000
8	B	12	GLY	0	0.011	0.017	9.290	-0.311	-0.311	0.000	0.000	0.000	0.000
9	B	13	TRP	0	0.019	-0.005	8.277	-0.259	-0.259	0.000	0.000	0.000	0.000
10	B	14	PRO	0	-0.016	-0.003	10.335	-0.205	-0.205	0.000	0.000	0.000	0.000
11	B	15	ALA	0	0.062	0.023	13.189	-0.136	-0.136	0.000	0.000	0.000	0.000
12	B	16	VAL	0	-0.007	0.002	12.458	-0.120	-0.120	0.000	0.000	0.000	0.000
13	B	17	ARG	1	0.872	0.945	11.949	-1.118	-1.118	0.000	0.000	0.000	0.000
14	B	18	GLU	-1	-0.844	-0.919	15.127	0.350	0.350	0.000	0.000	0.000	0.000
15	B	19	ARG	1	0.946	0.976	16.316	-0.336	-0.336	0.000	0.000	0.000	0.000
16	B	20	MET	0	-0.042	-0.008	15.304	-0.030	-0.030	0.000	0.000	0.000	0.000
17	B	21	ARG	1	0.848	0.907	18.022	-0.513	-0.513	0.000	0.000	0.000	0.000
18	B	22	ARG	1	0.937	0.978	20.630	-0.281	-0.281	0.000	0.000	0.000	0.000
19	B	23	ALA	0	-0.008	0.008	23.587	-0.008	-0.008	0.000	0.000	0.000	0.000
20	B	59	GLU	-1	-0.916	-0.969	25.063	0.154	0.154	0.000	0.000	0.000	0.000
21	B	60	ALA	0	-0.023	-0.025	26.194	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	61	GLN	0	-0.060	-0.043	28.111	-0.015	-0.015	0.000	0.000	0.000	0.000
23	B	62	GLU	-1	-0.937	-0.956	25.048	0.112	0.112	0.000	0.000	0.000	0.000
24	B	63	GLU	-1	-1.012	-1.005	24.075	0.062	0.062	0.000	0.000	0.000	0.000
25	B	64	GLU	-1	-1.060	-1.027	26.383	0.023	0.023	0.000	0.000	0.000	0.000
26	B	65	GLU	-1	-0.910	-0.932	28.026	0.042	0.042	0.000	0.000	0.000	0.000
27	B	66	VAL	0	-0.054	-0.025	28.120	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	67	GLY	0	0.003	-0.007	27.085	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	68	PHE	0	-0.013	-0.014	22.312	0.005	0.005	0.000	0.000	0.000	0.000
30	B	69	PRO	0	0.013	0.011	21.327	-0.020	-0.020	0.000	0.000	0.000	0.000
31	B	70	VAL	0	-0.004	-0.004	18.133	-0.023	-0.023	0.000	0.000	0.000	0.000
32	B	71	THR	0	-0.011	-0.008	14.977	0.017	0.017	0.000	0.000	0.000	0.000
33	B	72	PRO	0	0.031	0.012	17.661	-0.039	-0.039	0.000	0.000	0.000	0.000
34	B	73	GLN	0	0.017	-0.007	16.801	-0.030	-0.030	0.000	0.000	0.000	0.000
35	B	74	VAL	0	-0.065	-0.008	11.740	-0.050	-0.050	0.000	0.000	0.000	0.000
36	B	75	PRO	0	0.025	0.014	12.061	0.015	0.015	0.000	0.000	0.000	0.000
37	B	76	LEU	0	0.013	0.036	12.216	-0.139	-0.139	0.000	0.000	0.000	0.000
38	B	77	ARG	1	0.777	0.876	7.254	1.675	1.675	0.000	0.000	0.000	0.000
39	B	78	PRO	0	0.081	0.038	12.969	-0.044	-0.044	0.000	0.000	0.000	0.000
40	B	79	MET	0	-0.014	0.013	7.499	-0.169	-0.169	0.000	0.000	0.000	0.000
41	B	80	THR	0	-0.007	-0.004	8.802	0.103	0.103	0.000	0.000	0.000	0.000
42	B	81	TYR	0	0.005	-0.006	9.897	-0.083	-0.083	0.000	0.000	0.000	0.000
43	B	82	LYS	1	0.979	0.972	7.536	1.221	1.221	0.000	0.000	0.000	0.000
44	B	83	ALA	0	0.059	0.042	5.525	0.164	0.164	0.000	0.000	0.000	0.000
45	B	84	ALA	0	0.012	0.006	6.324	-0.076	-0.076	0.000	0.000	0.000	0.000
46	B	85	VAL	0	0.062	0.053	8.500	0.233	0.233	0.000	0.000	0.000	0.000
47	B	86	ASP	-1	-0.921	-0.948	3.777	-0.409	0.265	0.013	-0.102	-0.585	0.000
48	B	87	LEU	0	-0.058	-0.028	4.682	0.128	0.432	-0.001	-0.016	-0.287	0.000
49	B	88	SER	0	-0.019	-0.035	5.734	0.617	0.617	0.000	0.000	0.000	0.000
50	B	89	HIS	0	-0.002	-0.008	5.953	0.160	0.160	0.000	0.000	0.000	0.000
51	B	90	PHE	0	0.004	0.019	2.589	-2.229	-0.686	1.870	-1.212	-2.201	0.012
52	B	91	LEU	0	-0.013	-0.024	4.825	0.154	0.184	-0.001	-0.010	-0.019	0.000
53	B	92	LYS	1	0.836	0.952	8.334	-0.538	-0.538	0.000	0.000	0.000	0.000
54	B	93	GLU	-1	-0.874	-0.941	5.964	0.594	0.594	0.000	0.000	0.000	0.000
55	B	94	LYS	1	0.846	0.934	4.125	-5.504	-5.404	-0.001	-0.023	-0.076	0.000
56	B	95	GLY	0	0.109	0.066	9.056	-0.236	-0.236	0.000	0.000	0.000	0.000
57	B	96	GLY	0	-0.044	-0.031	11.858	0.104	0.104	0.000	0.000	0.000	0.000
58	B	97	LEU	0	0.002	-0.005	12.820	-0.062	-0.062	0.000	0.000	0.000	0.000
59	B	98	GLU	-1	-0.768	-0.863	14.829	0.172	0.172	0.000	0.000	0.000	0.000
60	B	99	GLY	0	-0.030	0.003	16.560	0.016	0.016	0.000	0.000	0.000	0.000
61	B	100	LEU	0	-0.023	-0.012	18.301	-0.031	-0.031	0.000	0.000	0.000	0.000
62	B	101	ILE	0	0.047	0.012	20.512	-0.022	-0.022	0.000	0.000	0.000	0.000
63	B	102	HIS	1	0.879	0.951	19.414	-0.047	-0.047	0.000	0.000	0.000	0.000
64	B	103	SER	0	0.003	-0.003	22.140	-0.016	-0.016	0.000	0.000	0.000	0.000
65	B	104	GLN	0	-0.005	-0.020	20.870	0.015	0.015	0.000	0.000	0.000	0.000
66	B	105	ARG	1	1.029	1.021	21.533	-0.098	-0.098	0.000	0.000	0.000	0.000
67	B	106	ARG	1	0.843	0.919	18.961	-0.198	-0.198	0.000	0.000	0.000	0.000
68	B	107	GLN	0	0.023	-0.009	16.885	0.059	0.059	0.000	0.000	0.000	0.000
69	B	108	ASP	-1	-0.809	-0.890	16.373	-0.023	-0.023	0.000	0.000	0.000	0.000
70	B	109	ILE	0	-0.035	-0.008	15.929	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	110	LEU	0	-0.035	-0.020	10.466	0.028	0.028	0.000	0.000	0.000	0.000
72	B	111	ASP	-1	-0.782	-0.900	12.337	-0.192	-0.192	0.000	0.000	0.000	0.000
73	B	112	LEU	0	0.036	0.021	13.457	-0.091	-0.091	0.000	0.000	0.000	0.000
74	B	113	TRP	0	-0.023	0.000	7.165	0.003	0.003	0.000	0.000	0.000	0.000
75	B	114	ILE	0	-0.028	-0.009	7.344	-0.006	-0.006	0.000	0.000	0.000	0.000
76	B	115	TYR	0	0.033	0.021	9.710	-0.245	-0.245	0.000	0.000	0.000	0.000
77	B	116	HIS	0	0.014	0.011	12.358	-0.082	-0.082	0.000	0.000	0.000	0.000
78	B	117	THR	0	-0.093	-0.067	8.537	-0.009	-0.009	0.000	0.000	0.000	0.000
79	B	118	GLN	0	-0.057	-0.039	3.901	-2.130	-1.906	0.000	-0.073	-0.151	0.000
80	B	119	GLY	0	0.064	0.049	7.703	-0.314	-0.314	0.000	0.000	0.000	0.000
81	B	120	TYR	0	-0.028	-0.027	5.326	0.210	0.210	0.000	0.000	0.000	0.000
82	B	121	PHE	0	0.043	0.023	11.192	0.109	0.109	0.000	0.000	0.000	0.000
83	B	122	PRO	0	-0.002	-0.006	14.520	-0.049	-0.049	0.000	0.000	0.000	0.000
84	B	123	ASP	-1	-0.904	-0.951	15.921	-0.325	-0.325	0.000	0.000	0.000	0.000
85	B	124	TRP	0	0.007	-0.008	10.923	-0.026	-0.026	0.000	0.000	0.000	0.000
86	B	125	GLN	0	-0.033	0.006	14.188	0.085	0.085	0.000	0.000	0.000	0.000
87	B	126	ASN	0	0.050	0.024	16.192	0.049	0.049	0.000	0.000	0.000	0.000
88	B	127	TYR	0	-0.035	-0.040	16.669	-0.007	-0.007	0.000	0.000	0.000	0.000
89	B	128	THR	0	0.012	0.014	21.915	-0.002	-0.002	0.000	0.000	0.000	0.000
90	B	129	PRO	0	-0.018	-0.011	25.279	0.013	0.013	0.000	0.000	0.000	0.000
91	B	130	GLY	0	-0.045	-0.002	28.409	0.002	0.002	0.000	0.000	0.000	0.000
92	B	131	PRO	0	-0.009	-0.010	29.859	-0.006	-0.006	0.000	0.000	0.000	0.000
93	B	132	GLY	0	0.064	0.023	29.997	-0.006	-0.006	0.000	0.000	0.000	0.000
94	B	133	VAL	0	-0.032	-0.035	24.574	0.005	0.005	0.000	0.000	0.000	0.000
95	B	134	ARG	1	0.768	0.898	23.116	-0.012	-0.012	0.000	0.000	0.000	0.000
96	B	135	TYR	0	0.059	0.002	21.598	0.013	0.013	0.000	0.000	0.000	0.000
97	B	136	PRO	0	0.034	0.020	16.826	-0.006	-0.006	0.000	0.000	0.000	0.000
98	B	137	LEU	0	0.003	-0.002	18.966	-0.002	-0.002	0.000	0.000	0.000	0.000
99	B	138	THR	0	-0.034	-0.018	13.514	-0.039	-0.039	0.000	0.000	0.000	0.000
100	B	139	PHE	0	-0.006	-0.016	16.080	0.015	0.015	0.000	0.000	0.000	0.000
101	B	140	GLY	0	0.078	0.013	12.962	-0.077	-0.077	0.000	0.000	0.000	0.000
102	B	141	TRP	0	-0.035	-0.016	9.622	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	142	CYS	0	-0.051	-0.038	11.990	0.030	0.030	0.000	0.000	0.000	0.000
104	B	143	TYR	0	-0.008	-0.001	11.070	0.082	0.082	0.000	0.000	0.000	0.000
105	B	144	LYS	1	0.904	0.937	15.873	-0.085	-0.085	0.000	0.000	0.000	0.000
106	B	145	LEU	0	-0.038	-0.008	19.455	0.034	0.034	0.000	0.000	0.000	0.000
107	B	146	VAL	0	-0.004	-0.018	22.016	-0.021	-0.021	0.000	0.000	0.000	0.000
108	B	147	PRO	0	0.000	0.014	24.938	0.011	0.011	0.000	0.000	0.000	0.000
109	B	148	VAL	0	-0.020	-0.008	26.473	0.004	0.004	0.000	0.000	0.000	0.000
110	B	149	GLU	-1	-0.938	-0.965	29.320	0.063	0.063	0.000	0.000	0.000	0.000
111	B	150	PRO	0	-0.022	0.006	31.607	-0.001	-0.001	0.000	0.000	0.000	0.000
112	B	178	ARG	1	0.964	0.982	31.695	-0.022	-0.022	0.000	0.000	0.000	0.000
113	B	179	GLU	-1	-0.777	-0.881	30.584	0.024	0.024	0.000	0.000	0.000	0.000
114	B	180	VAL	0	0.007	-0.005	27.596	-0.004	-0.004	0.000	0.000	0.000	0.000
115	B	181	LEU	0	-0.019	-0.012	24.945	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	182	GLU	-1	-0.833	-0.911	22.439	0.152	0.152	0.000	0.000	0.000	0.000
117	B	183	TRP	0	-0.002	0.004	16.242	-0.008	-0.008	0.000	0.000	0.000	0.000
118	B	184	ARG	1	0.801	0.865	18.572	-0.155	-0.155	0.000	0.000	0.000	0.000
119	B	185	PHE	0	0.008	-0.003	10.839	-0.035	-0.035	0.000	0.000	0.000	0.000
120	B	186	ASP	-1	-0.770	-0.864	15.917	0.017	0.017	0.000	0.000	0.000	0.000
121	B	187	SER	0	0.072	0.024	13.893	-0.018	-0.018	0.000	0.000	0.000	0.000
122	B	188	ARG	1	0.871	0.915	15.728	-0.043	-0.043	0.000	0.000	0.000	0.000
123	B	189	LEU	0	0.009	0.031	16.481	-0.022	-0.022	0.000	0.000	0.000	0.000
124	B	190	ALA	0	-0.022	-0.010	13.911	-0.035	-0.035	0.000	0.000	0.000	0.000
125	B	191	PHE	0	-0.038	-0.024	15.506	-0.037	-0.037	0.000	0.000	0.000	0.000
126	B	192	HIS	0	-0.080	-0.042	18.944	0.003	0.003	0.000	0.000	0.000	0.000
127	B	193	HIS	0	-0.009	0.007	20.524	0.021	0.021	0.000	0.000	0.000	0.000
128	B	194	VAL	0	0.054	0.027	21.931	0.002	0.002	0.000	0.000	0.000	0.000
129	B	195	ALA	0	0.026	0.010	22.238	0.006	0.006	0.000	0.000	0.000	0.000
130	B	196	ARG	1	0.872	0.949	23.390	0.182	0.182	0.000	0.000	0.000	0.000
131	B	197	GLU	-1	-0.863	-0.916	25.328	-0.092	-0.092	0.000	0.000	0.000	0.000
132	B	198	LEU	0	-0.023	-0.023	26.926	0.006	0.006	0.000	0.000	0.000	0.000
133	B	199	HIS	1	0.825	0.889	27.388	0.087	0.087	0.000	0.000	0.000	0.000
134	B	200	PRO	0	0.024	0.027	27.731	-0.015	-0.015	0.000	0.000	0.000	0.000
135	B	201	GLU	-1	-0.821	-0.904	28.973	-0.105	-0.105	0.000	0.000	0.000	0.000
136	B	202	TYR	0	-0.027	-0.029	25.363	-0.001	-0.001	0.000	0.000	0.000	0.000
137	B	203	PHE	0	-0.039	-0.007	21.115	-0.017	-0.017	0.000	0.000	0.000	0.000
138	B	204	LYS	1	0.971	1.002	25.999	0.126	0.126	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:5:TRP)