FMO DATABASE

FMODB ID: GNMZ1

Calculation Name: 2EJ8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EJ8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UKG1

Base Structure: X-ray

Registration Date: 2023-06-21

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1267943.735572
FMO2-HF: Nuclear repulsion	1211605.089952
FMO2-HF: Total energy	-56338.645621
FMO2-MP2: Total energy	-56499.37475

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:8:GLU)

Summations of interaction energy for fragment #1(A:8:GLU)

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.
5.51	22.536	10.043	-12.691	-14.378	0.003

Interaction energy analysis for fragmet #1(A:8:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.946 / q_NPA : -0.995

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	10	GLU	-1	-0.881	-0.919	2.175	19.254	26.304	4.911	-6.290	-5.671	-0.056
4	A	11	ASP	-1	-0.938	-0.968	5.360	21.308	21.486	-0.001	-0.005	-0.172	0.000
5	A	12	SER	0	-0.011	0.000	5.901	-1.981	-1.981	0.000	0.000	0.000	0.000
6	A	13	ILE	0	-0.002	-0.009	7.927	1.298	1.298	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.037	-0.008	9.270	0.557	0.557	0.000	0.000	0.000	0.000
8	A	15	HIS	0	0.081	0.019	2.798	-6.058	-3.398	0.346	-1.431	-1.576	0.018
9	A	16	GLN	0	-0.043	-0.006	6.638	-1.098	-1.098	0.000	0.000	0.000	0.000
10	A	17	LEU	0	0.055	0.026	4.300	-0.406	-0.230	-0.001	-0.021	-0.154	0.000
11	A	18	PHE	0	-0.020	-0.012	8.251	-4.073	-4.073	0.000	0.000	0.000	0.000
12	A	19	ILE	0	0.013	0.025	10.792	1.485	1.485	0.000	0.000	0.000	0.000
13	A	20	VAL	0	-0.037	-0.020	12.199	-1.758	-1.758	0.000	0.000	0.000	0.000
14	A	21	ARG	1	0.811	0.888	14.705	-16.187	-16.187	0.000	0.000	0.000	0.000
15	A	22	PHE	0	-0.002	0.000	16.296	-0.568	-0.568	0.000	0.000	0.000	0.000
16	A	23	LEU	0	-0.044	-0.026	18.037	-0.739	-0.739	0.000	0.000	0.000	0.000
17	A	24	GLY	0	0.041	0.018	20.806	-0.796	-0.796	0.000	0.000	0.000	0.000
18	A	25	SER	0	-0.015	-0.008	19.946	0.358	0.358	0.000	0.000	0.000	0.000
19	A	26	MET	0	-0.011	0.003	22.073	-0.481	-0.481	0.000	0.000	0.000	0.000
20	A	27	GLU	-1	-0.931	-0.951	24.072	11.756	11.756	0.000	0.000	0.000	0.000
21	A	28	VAL	0	-0.053	-0.025	24.053	-0.373	-0.373	0.000	0.000	0.000	0.000
22	A	29	LYS	1	0.952	0.981	26.723	-9.412	-9.412	0.000	0.000	0.000	0.000
23	A	30	SER	0	0.000	0.000	25.754	0.481	0.481	0.000	0.000	0.000	0.000
24	A	31	ASP	-1	-0.854	-0.930	26.638	9.537	9.537	0.000	0.000	0.000	0.000
25	A	32	ASP	-1	-0.830	-0.909	25.143	11.906	11.906	0.000	0.000	0.000	0.000
26	A	33	HIS	0	0.032	0.021	26.659	0.046	0.046	0.000	0.000	0.000	0.000
27	A	34	PRO	0	0.049	0.019	25.337	0.246	0.246	0.000	0.000	0.000	0.000
28	A	35	ASP	-1	-0.917	-0.964	26.382	10.285	10.285	0.000	0.000	0.000	0.000
29	A	36	VAL	0	0.060	0.027	25.524	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	37	VAL	0	0.000	0.004	22.350	0.153	0.153	0.000	0.000	0.000	0.000
31	A	38	TYR	0	-0.013	-0.006	24.978	-0.057	-0.057	0.000	0.000	0.000	0.000
32	A	39	GLU	-1	-0.728	-0.806	27.907	9.578	9.578	0.000	0.000	0.000	0.000
33	A	40	THR	0	0.000	-0.023	24.647	-0.048	-0.048	0.000	0.000	0.000	0.000
34	A	41	MET	0	-0.040	-0.005	22.795	-0.089	-0.089	0.000	0.000	0.000	0.000
35	A	42	ARG	1	0.811	0.878	26.673	-9.544	-9.544	0.000	0.000	0.000	0.000
36	A	43	GLN	0	-0.058	-0.050	29.546	-0.176	-0.176	0.000	0.000	0.000	0.000
37	A	44	ILE	0	0.032	0.013	24.216	-0.148	-0.148	0.000	0.000	0.000	0.000
38	A	45	LEU	0	-0.032	-0.020	25.940	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	46	ALA	0	0.002	0.008	28.871	-0.207	-0.207	0.000	0.000	0.000	0.000
40	A	47	ALA	0	0.004	0.007	29.712	-0.233	-0.233	0.000	0.000	0.000	0.000
41	A	48	ARG	1	0.846	0.903	23.375	-13.330	-13.330	0.000	0.000	0.000	0.000
42	A	49	ALA	0	-0.005	0.008	29.697	-0.115	-0.115	0.000	0.000	0.000	0.000
43	A	50	ILE	0	-0.039	-0.014	32.489	-0.225	-0.225	0.000	0.000	0.000	0.000
44	A	51	HIS	0	-0.020	-0.009	31.983	-0.326	-0.326	0.000	0.000	0.000	0.000
45	A	52	ASN	0	-0.032	-0.005	33.005	0.122	0.122	0.000	0.000	0.000	0.000
46	A	53	ILE	0	-0.034	-0.014	26.509	0.245	0.245	0.000	0.000	0.000	0.000
47	A	54	PHE	0	0.036	0.007	27.838	0.233	0.233	0.000	0.000	0.000	0.000
48	A	55	ARG	1	0.930	0.966	21.882	-13.679	-13.679	0.000	0.000	0.000	0.000
49	A	56	MET	0	0.013	0.019	20.628	0.342	0.342	0.000	0.000	0.000	0.000
50	A	57	THR	0	-0.021	-0.014	16.449	-0.507	-0.507	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.875	-0.940	13.443	22.330	22.330	0.000	0.000	0.000	0.000
52	A	59	SER	0	-0.076	-0.042	11.094	0.552	0.552	0.000	0.000	0.000	0.000
53	A	60	HIS	0	-0.012	0.002	7.483	1.107	1.107	0.000	0.000	0.000	0.000
54	A	61	LEU	0	-0.014	-0.010	8.226	1.978	1.978	0.000	0.000	0.000	0.000
55	A	62	LEU	0	0.003	0.011	2.564	-6.246	-3.934	1.806	-1.524	-2.594	0.018
56	A	63	VAL	0	-0.019	-0.009	6.669	-2.180	-2.180	0.000	0.000	0.000	0.000
57	A	64	THR	0	0.022	0.013	3.175	0.318	0.644	0.044	-0.100	-0.270	0.000
58	A	65	CYS	0	-0.051	-0.040	6.686	-2.658	-2.658	0.000	0.000	0.000	0.000
59	A	66	ASP	-1	-0.850	-0.905	6.223	23.385	23.385	0.000	0.000	0.000	0.000
60	A	67	CYS	0	-0.146	-0.078	5.192	0.741	0.826	-0.001	-0.011	-0.072	0.000
61	A	68	LEU	0	0.026	0.030	6.943	1.390	1.390	0.000	0.000	0.000	0.000
62	A	69	LYS	1	0.953	0.975	2.258	-58.638	-56.453	2.657	-2.326	-2.516	0.015
63	A	70	LEU	0	-0.025	-0.006	6.709	-0.481	-0.481	0.000	0.000	0.000	0.000
64	A	71	ILE	0	0.022	0.006	3.133	-4.823	-3.059	0.284	-0.967	-1.081	0.008
65	A	72	ASP	-1	-0.802	-0.877	7.457	21.685	21.685	0.000	0.000	0.000	0.000
66	A	73	PRO	0	0.031	0.012	9.219	2.645	2.645	0.000	0.000	0.000	0.000
67	A	74	GLN	0	-0.090	-0.037	10.461	-1.395	-1.395	0.000	0.000	0.000	0.000
68	A	75	THR	0	-0.037	-0.058	10.751	0.647	0.647	0.000	0.000	0.000	0.000
69	A	76	GLN	0	-0.007	0.003	5.420	3.076	3.076	0.000	0.000	0.000	0.000
70	A	77	VAL	0	0.018	0.025	5.500	7.472	7.563	-0.001	0.000	-0.090	0.000
71	A	78	THR	0	0.004	-0.007	4.241	0.868	1.067	-0.001	-0.016	-0.182	0.000
72	A	79	ARG	1	0.831	0.905	6.580	-29.678	-29.678	0.000	0.000	0.000	0.000
73	A	80	LEU	0	-0.012	-0.002	8.872	-2.950	-2.950	0.000	0.000	0.000	0.000
74	A	81	THR	0	0.037	0.008	6.988	5.820	5.820	0.000	0.000	0.000	0.000
75	A	82	PHE	0	-0.005	-0.005	8.764	-2.708	-2.708	0.000	0.000	0.000	0.000
76	A	83	PRO	0	0.039	0.020	9.844	1.046	1.046	0.000	0.000	0.000	0.000
77	A	84	LEU	0	0.092	0.035	10.431	-1.463	-1.463	0.000	0.000	0.000	0.000
78	A	85	PRO	0	-0.025	-0.019	12.030	-1.071	-1.071	0.000	0.000	0.000	0.000
79	A	86	CYS	0	-0.002	0.012	14.536	-0.835	-0.835	0.000	0.000	0.000	0.000
80	A	87	VAL	0	-0.016	0.010	12.735	-0.535	-0.535	0.000	0.000	0.000	0.000
81	A	88	VAL	0	-0.029	-0.013	15.800	-0.214	-0.214	0.000	0.000	0.000	0.000
82	A	89	LEU	0	-0.005	0.008	19.257	-0.541	-0.541	0.000	0.000	0.000	0.000
83	A	90	TYR	0	0.027	-0.005	17.336	0.930	0.930	0.000	0.000	0.000	0.000
84	A	91	ALA	0	-0.016	0.003	19.440	-0.613	-0.613	0.000	0.000	0.000	0.000
85	A	92	THR	0	0.026	-0.004	21.324	0.406	0.406	0.000	0.000	0.000	0.000
86	A	93	HIS	0	0.004	0.000	23.180	-0.299	-0.299	0.000	0.000	0.000	0.000
87	A	94	GLN	0	0.034	0.004	26.762	0.347	0.347	0.000	0.000	0.000	0.000
88	A	95	GLU	-1	-0.931	-0.973	29.422	9.407	9.407	0.000	0.000	0.000	0.000
89	A	96	ASN	0	-0.002	-0.016	26.261	0.155	0.155	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.869	0.942	24.144	-11.396	-11.396	0.000	0.000	0.000	0.000
91	A	98	ARG	1	0.801	0.881	22.012	-13.000	-13.000	0.000	0.000	0.000	0.000
92	A	99	LEU	0	-0.026	0.008	20.880	0.813	0.813	0.000	0.000	0.000	0.000
93	A	100	PHE	0	0.055	0.023	14.840	-0.088	-0.088	0.000	0.000	0.000	0.000
94	A	101	GLY	0	0.010	0.003	19.340	0.137	0.137	0.000	0.000	0.000	0.000
95	A	102	PHE	0	-0.010	-0.004	13.822	-0.028	-0.028	0.000	0.000	0.000	0.000
96	A	103	VAL	0	0.037	0.015	18.437	-0.138	-0.138	0.000	0.000	0.000	0.000
97	A	104	LEU	0	-0.039	-0.015	14.331	0.566	0.566	0.000	0.000	0.000	0.000
98	A	105	ARG	1	0.810	0.895	17.759	-12.828	-12.828	0.000	0.000	0.000	0.000
99	A	106	THR	0	0.006	-0.008	18.842	0.807	0.807	0.000	0.000	0.000	0.000
100	A	107	SER	0	0.005	-0.006	20.113	-0.563	-0.563	0.000	0.000	0.000	0.000
101	A	108	SER	0	0.019	0.004	21.283	0.367	0.367	0.000	0.000	0.000	0.000
102	A	109	GLY	0	0.020	0.018	22.252	0.395	0.395	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.788	0.851	23.173	-11.017	-11.017	0.000	0.000	0.000	0.000
104	A	111	SER	0	-0.016	-0.037	26.965	-0.078	-0.078	0.000	0.000	0.000	0.000
105	A	112	GLU	-1	-0.827	-0.863	27.279	10.283	10.283	0.000	0.000	0.000	0.000
106	A	113	SER	0	0.021	0.025	27.377	-0.178	-0.178	0.000	0.000	0.000	0.000
107	A	114	ASN	0	-0.034	-0.022	24.920	0.494	0.494	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.009	0.000	24.123	0.461	0.461	0.000	0.000	0.000	0.000
109	A	116	SER	0	0.028	0.013	23.462	-0.060	-0.060	0.000	0.000	0.000	0.000
110	A	117	SER	0	0.014	-0.004	21.907	0.669	0.669	0.000	0.000	0.000	0.000
111	A	118	VAL	0	0.001	0.015	19.853	-0.364	-0.364	0.000	0.000	0.000	0.000
112	A	119	CYS	0	-0.063	-0.015	20.108	0.735	0.735	0.000	0.000	0.000	0.000
113	A	120	TYR	0	0.013	0.001	17.026	-0.045	-0.045	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.012	-0.009	19.195	0.125	0.125	0.000	0.000	0.000	0.000
115	A	122	PHE	0	0.003	-0.005	14.592	0.555	0.555	0.000	0.000	0.000	0.000
116	A	123	GLU	-1	-0.791	-0.861	18.880	13.567	13.567	0.000	0.000	0.000	0.000
117	A	124	SER	0	0.033	0.006	17.184	1.057	1.057	0.000	0.000	0.000	0.000
118	A	125	ASN	0	0.050	0.018	17.229	-1.531	-1.531	0.000	0.000	0.000	0.000
119	A	126	ASN	0	-0.021	-0.021	19.744	0.012	0.012	0.000	0.000	0.000	0.000
120	A	127	GLU	-1	-0.846	-0.930	15.550	19.969	19.969	0.000	0.000	0.000	0.000
121	A	128	GLY	0	0.040	0.038	18.138	0.650	0.650	0.000	0.000	0.000	0.000
122	A	129	GLU	-1	-0.817	-0.914	19.661	12.686	12.686	0.000	0.000	0.000	0.000
123	A	130	LYS	1	0.970	1.014	13.869	-20.871	-20.871	0.000	0.000	0.000	0.000
124	A	131	ILE	0	-0.009	-0.005	14.092	0.770	0.770	0.000	0.000	0.000	0.000
125	A	132	CYS	0	-0.079	-0.042	15.586	0.417	0.417	0.000	0.000	0.000	0.000
126	A	133	ASP	-1	-0.865	-0.928	17.755	14.835	14.835	0.000	0.000	0.000	0.000
127	A	134	SER	0	-0.026	-0.012	12.129	0.516	0.516	0.000	0.000	0.000	0.000
128	A	135	VAL	0	-0.041	-0.024	12.656	0.602	0.602	0.000	0.000	0.000	0.000
129	A	136	GLY	0	-0.008	0.000	14.141	-0.297	-0.297	0.000	0.000	0.000	0.000
130	A	137	LEU	0	-0.005	0.001	14.840	-0.438	-0.438	0.000	0.000	0.000	0.000
131	A	138	ALA	0	0.044	0.012	11.280	-0.295	-0.295	0.000	0.000	0.000	0.000
132	A	139	LYS	1	0.825	0.901	13.187	-16.991	-16.991	0.000	0.000	0.000	0.000
133	A	140	GLN	0	-0.009	0.003	15.947	-0.356	-0.356	0.000	0.000	0.000	0.000
134	A	141	ILE	0	-0.018	-0.012	13.376	-0.595	-0.595	0.000	0.000	0.000	0.000
135	A	142	ALA	0	0.007	-0.003	14.327	-0.517	-0.517	0.000	0.000	0.000	0.000
136	A	143	LEU	0	-0.032	-0.016	16.121	-0.581	-0.581	0.000	0.000	0.000	0.000
137	A	144	HIS	0	-0.058	-0.025	19.198	-0.593	-0.593	0.000	0.000	0.000	0.000
138	A	145	ALA	0	-0.065	-0.024	16.370	-0.351	-0.351	0.000	0.000	0.000	0.000
139	A	146	GLU	-1	-1.004	-0.982	18.415	11.713	11.713	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:GLU)