FMO DATABASE

FMODB ID: N1YKQ

Calculation Name: 3VEA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VEA

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZG78

Base Structure: X-ray

Registration Date: 2023-06-20

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1222622.654028
FMO2-HF: Nuclear repulsion	1160579.680504
FMO2-HF: Total energy	-62042.973524
FMO2-MP2: Total energy	-62224.398445

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:14:MET)

Summations of interaction energy for fragment #1(B:14: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.
-8.019	-4.38	0.285	-1.473	-2.45	0.002

Interaction energy analysis for fragmet #1(B:14:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.004

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	16	TYR	0	-0.015	-0.016	3.831	-1.806	0.358	-0.027	-0.988	-1.149	0.000
4	B	17	GLN	0	0.068	0.047	3.523	-0.371	0.134	0.018	-0.171	-0.352	-0.001
5	B	18	GLN	0	0.007	-0.019	2.981	-2.474	-1.504	0.294	-0.314	-0.949	0.003
6	B	19	LEU	0	0.004	0.013	7.359	-0.091	-0.091	0.000	0.000	0.000	0.000
7	B	20	GLU	-1	-0.859	-0.930	10.918	0.123	0.123	0.000	0.000	0.000	0.000
8	B	21	ASN	0	0.047	0.017	12.213	-0.050	-0.050	0.000	0.000	0.000	0.000
9	B	22	LEU	0	-0.029	-0.005	12.836	-0.020	-0.020	0.000	0.000	0.000	0.000
10	B	23	GLU	-1	-0.828	-0.929	8.527	0.780	0.780	0.000	0.000	0.000	0.000
11	B	24	SER	0	0.051	0.036	13.230	-0.018	-0.018	0.000	0.000	0.000	0.000
12	B	25	GLY	0	0.100	0.050	15.470	-0.017	-0.017	0.000	0.000	0.000	0.000
13	B	26	TRP	0	-0.071	-0.033	11.346	0.022	0.022	0.000	0.000	0.000	0.000
14	B	27	LYS	1	0.909	0.947	10.687	-0.222	-0.222	0.000	0.000	0.000	0.000
15	B	28	TRP	0	0.060	0.044	16.742	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	29	ALA	0	0.023	0.000	20.204	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	30	TYR	0	-0.101	-0.060	18.788	0.005	0.005	0.000	0.000	0.000	0.000
18	B	31	LEU	0	0.042	0.012	19.174	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	32	VAL	0	0.064	0.042	22.332	-0.008	-0.008	0.000	0.000	0.000	0.000
20	B	33	LYS	1	0.892	0.962	22.934	-0.183	-0.183	0.000	0.000	0.000	0.000
21	B	34	LYS	1	0.860	0.924	22.253	-0.166	-0.166	0.000	0.000	0.000	0.000
22	B	35	HIS	0	0.031	-0.003	25.448	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	36	ARG	1	0.925	0.970	27.931	-0.094	-0.094	0.000	0.000	0.000	0.000
24	B	37	GLU	-1	-0.925	-0.964	27.135	0.137	0.137	0.000	0.000	0.000	0.000
25	B	38	GLY	0	-0.017	0.023	30.280	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	39	GLU	-1	-0.817	-0.917	24.739	0.139	0.139	0.000	0.000	0.000	0.000
27	B	40	ALA	0	-0.026	-0.011	27.606	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	41	ILE	0	-0.008	-0.004	23.614	0.003	0.003	0.000	0.000	0.000	0.000
29	B	42	THR	0	0.022	0.016	23.898	0.002	0.002	0.000	0.000	0.000	0.000
30	B	43	ARG	1	0.832	0.933	20.554	-0.012	-0.012	0.000	0.000	0.000	0.000
31	B	44	HIS	0	-0.019	-0.009	26.366	-0.006	-0.006	0.000	0.000	0.000	0.000
32	B	45	ILE	0	0.012	0.002	29.933	0.003	0.003	0.000	0.000	0.000	0.000
33	B	46	GLU	-1	-0.892	-0.943	32.718	0.026	0.026	0.000	0.000	0.000	0.000
34	B	47	ASN	0	0.021	-0.012	33.777	0.002	0.002	0.000	0.000	0.000	0.000
35	B	48	SER	0	-0.001	0.014	35.446	0.002	0.002	0.000	0.000	0.000	0.000
36	B	49	ALA	0	0.126	0.057	31.495	0.001	0.001	0.000	0.000	0.000	0.000
37	B	50	ALA	0	-0.069	-0.032	30.045	0.002	0.002	0.000	0.000	0.000	0.000
38	B	51	GLN	0	0.004	-0.004	30.458	0.006	0.006	0.000	0.000	0.000	0.000
39	B	52	ASP	-1	-0.877	-0.925	32.185	0.028	0.028	0.000	0.000	0.000	0.000
40	B	53	ALA	0	-0.039	-0.024	26.901	0.001	0.001	0.000	0.000	0.000	0.000
41	B	54	VAL	0	-0.037	-0.023	27.987	0.005	0.005	0.000	0.000	0.000	0.000
42	B	55	GLU	-1	-0.840	-0.921	29.012	0.045	0.045	0.000	0.000	0.000	0.000
43	B	56	GLN	0	-0.053	-0.040	27.396	0.002	0.002	0.000	0.000	0.000	0.000
44	B	57	LEU	0	-0.015	-0.010	21.912	0.004	0.004	0.000	0.000	0.000	0.000
45	B	58	MET	0	-0.008	-0.009	25.618	0.011	0.011	0.000	0.000	0.000	0.000
46	B	59	LYS	1	0.930	0.986	28.010	-0.037	-0.037	0.000	0.000	0.000	0.000
47	B	60	LEU	0	-0.095	-0.039	22.680	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	61	GLU	-1	-0.923	-0.976	23.250	0.111	0.111	0.000	0.000	0.000	0.000
49	B	62	ASN	0	0.034	0.024	22.547	0.010	0.010	0.000	0.000	0.000	0.000
50	B	63	GLU	-1	-0.926	-0.972	22.554	0.047	0.047	0.000	0.000	0.000	0.000
51	B	64	PRO	0	0.007	0.000	17.009	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	65	VAL	0	0.014	-0.010	17.766	0.000	0.000	0.000	0.000	0.000	0.000
53	B	66	LYS	1	0.989	1.012	18.900	-0.045	-0.045	0.000	0.000	0.000	0.000
54	B	67	VAL	0	-0.069	-0.024	17.797	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	68	GLN	0	-0.017	-0.037	12.755	0.030	0.030	0.000	0.000	0.000	0.000
56	B	69	GLU	-1	-0.835	-0.910	16.986	0.006	0.006	0.000	0.000	0.000	0.000
57	B	70	TRP	0	-0.013	0.008	19.701	-0.003	-0.003	0.000	0.000	0.000	0.000
58	B	71	ILE	0	-0.075	-0.044	15.769	0.002	0.002	0.000	0.000	0.000	0.000
59	B	72	ASP	-1	-0.920	-0.959	15.906	-0.048	-0.048	0.000	0.000	0.000	0.000
60	B	73	ALA	0	-0.044	-0.022	18.528	-0.007	-0.007	0.000	0.000	0.000	0.000
61	B	74	HIS	0	0.046	0.003	22.359	0.001	0.001	0.000	0.000	0.000	0.000
62	B	75	MET	0	-0.037	0.002	17.278	0.011	0.011	0.000	0.000	0.000	0.000
63	B	76	ASN	0	-0.049	-0.029	21.604	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	77	VAL	0	0.083	0.017	20.466	0.012	0.012	0.000	0.000	0.000	0.000
65	B	78	ASN	0	0.026	0.007	19.557	0.028	0.028	0.000	0.000	0.000	0.000
66	B	79	LEU	0	0.039	0.016	19.837	0.025	0.025	0.000	0.000	0.000	0.000
67	B	80	ALA	0	0.031	0.032	16.322	0.029	0.029	0.000	0.000	0.000	0.000
68	B	81	THR	0	-0.020	-0.021	14.996	0.022	0.022	0.000	0.000	0.000	0.000
69	B	82	ARG	1	0.859	0.929	14.978	-0.104	-0.104	0.000	0.000	0.000	0.000
70	B	83	MET	0	0.001	0.025	14.756	0.052	0.052	0.000	0.000	0.000	0.000
71	B	84	LYS	1	0.982	0.986	10.011	-0.059	-0.059	0.000	0.000	0.000	0.000
72	B	85	GLN	0	-0.050	-0.034	11.120	0.142	0.142	0.000	0.000	0.000	0.000
73	B	86	THR	0	-0.046	-0.013	13.000	0.064	0.064	0.000	0.000	0.000	0.000
74	B	87	ILE	0	0.020	0.009	10.083	0.027	0.027	0.000	0.000	0.000	0.000
75	B	88	ARG	1	0.979	1.000	7.635	-0.810	-0.810	0.000	0.000	0.000	0.000
76	B	89	ALA	0	-0.049	-0.005	9.450	0.099	0.099	0.000	0.000	0.000	0.000
77	B	90	ARG	1	0.923	0.954	12.189	-0.335	-0.335	0.000	0.000	0.000	0.000
78	B	91	ARG	1	0.897	0.921	5.899	-1.104	-1.104	0.000	0.000	0.000	0.000
79	B	92	LYS	1	0.877	0.942	8.518	-0.907	-0.907	0.000	0.000	0.000	0.000
80	B	93	ARG	1	0.897	0.935	9.986	-0.513	-0.513	0.000	0.000	0.000	0.000
81	B	94	HIS	0	0.022	0.017	12.221	-0.035	-0.035	0.000	0.000	0.000	0.000
82	B	95	PHE	0	0.087	0.035	8.365	-0.038	-0.038	0.000	0.000	0.000	0.000
83	B	96	ASN	0	-0.048	-0.017	11.778	0.060	0.060	0.000	0.000	0.000	0.000
84	B	97	ALA	0	-0.059	-0.019	14.012	-0.024	-0.024	0.000	0.000	0.000	0.000
85	B	98	GLU	-1	-0.872	-0.927	13.998	0.121	0.121	0.000	0.000	0.000	0.000
86	B	99	HIS	0	0.037	0.017	15.202	-0.039	-0.039	0.000	0.000	0.000	0.000
87	B	100	GLN	0	0.043	0.022	18.307	0.028	0.028	0.000	0.000	0.000	0.000
88	B	101	HIS	0	0.057	0.044	17.602	0.041	0.041	0.000	0.000	0.000	0.000
89	B	102	THR	0	-0.034	-0.028	14.247	0.023	0.023	0.000	0.000	0.000	0.000
90	B	103	ARG	1	0.875	0.943	15.512	-0.137	-0.137	0.000	0.000	0.000	0.000
91	B	104	LYS	1	0.921	0.952	14.163	-0.422	-0.422	0.000	0.000	0.000	0.000
92	B	105	LYS	1	0.934	0.959	19.452	-0.163	-0.163	0.000	0.000	0.000	0.000
93	B	106	SER	0	0.019	0.014	23.079	0.016	0.016	0.000	0.000	0.000	0.000
94	B	107	ILE	0	-0.026	-0.013	24.509	-0.013	-0.013	0.000	0.000	0.000	0.000
95	B	108	ASP	-1	-0.861	-0.912	27.449	0.160	0.160	0.000	0.000	0.000	0.000
96	B	109	LEU	0	-0.047	-0.030	29.554	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	110	GLU	-1	-0.876	-0.933	31.882	0.091	0.091	0.000	0.000	0.000	0.000
98	B	111	PHE	0	0.031	-0.004	32.847	0.004	0.004	0.000	0.000	0.000	0.000
99	B	112	LEU	0	0.082	0.021	33.826	0.005	0.005	0.000	0.000	0.000	0.000
100	B	113	VAL	0	0.010	0.017	33.198	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	114	TRP	0	0.015	0.014	26.662	0.000	0.000	0.000	0.000	0.000	0.000
102	B	115	GLN	0	0.002	0.001	30.481	0.002	0.002	0.000	0.000	0.000	0.000
103	B	116	ARG	1	0.940	0.964	32.239	-0.083	-0.083	0.000	0.000	0.000	0.000
104	B	117	LEU	0	-0.001	0.013	27.507	0.001	0.001	0.000	0.000	0.000	0.000
105	B	118	ALA	0	0.015	-0.006	27.633	0.008	0.008	0.000	0.000	0.000	0.000
106	B	119	VAL	0	-0.083	-0.039	28.468	0.003	0.003	0.000	0.000	0.000	0.000
107	B	120	LEU	0	0.011	-0.006	30.073	0.000	0.000	0.000	0.000	0.000	0.000
108	B	121	ALA	0	0.018	0.032	24.764	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	122	ARG	1	0.947	0.956	25.449	-0.142	-0.142	0.000	0.000	0.000	0.000
110	B	123	ARG	1	0.902	0.961	26.498	-0.101	-0.101	0.000	0.000	0.000	0.000
111	B	124	ARG	1	0.932	0.960	26.825	-0.126	-0.126	0.000	0.000	0.000	0.000
112	B	125	GLY	0	0.018	0.042	23.556	0.000	0.000	0.000	0.000	0.000	0.000
113	B	126	ASN	0	-0.011	0.004	21.493	0.010	0.010	0.000	0.000	0.000	0.000
114	B	127	THR	0	0.008	-0.005	17.941	-0.003	-0.003	0.000	0.000	0.000	0.000
115	B	128	LEU	0	0.050	0.002	21.249	-0.023	-0.023	0.000	0.000	0.000	0.000
116	B	129	SER	0	-0.023	-0.020	20.696	-0.018	-0.018	0.000	0.000	0.000	0.000
117	B	130	ASP	-1	-0.832	-0.906	20.209	0.233	0.233	0.000	0.000	0.000	0.000
118	B	131	THR	0	-0.005	-0.004	23.211	-0.024	-0.024	0.000	0.000	0.000	0.000
119	B	132	VAL	0	-0.051	-0.030	26.156	-0.015	-0.015	0.000	0.000	0.000	0.000
120	B	133	VAL	0	0.020	0.009	24.405	-0.011	-0.011	0.000	0.000	0.000	0.000
121	B	134	GLN	0	0.049	0.026	26.634	-0.001	-0.001	0.000	0.000	0.000	0.000
122	B	135	LEU	0	-0.050	-0.016	29.017	-0.010	-0.010	0.000	0.000	0.000	0.000
123	B	136	ILE	0	-0.006	0.002	29.296	-0.007	-0.007	0.000	0.000	0.000	0.000
124	B	137	GLU	-1	-0.908	-0.946	28.662	0.083	0.083	0.000	0.000	0.000	0.000
125	B	138	ASP	-1	-0.946	-1.001	32.322	0.076	0.076	0.000	0.000	0.000	0.000
126	B	139	ALA	0	-0.074	-0.040	34.680	-0.006	-0.006	0.000	0.000	0.000	0.000
127	B	140	GLU	-1	-0.850	-0.918	34.516	0.062	0.062	0.000	0.000	0.000	0.000
128	B	141	ARG	1	0.815	0.907	35.928	-0.050	-0.050	0.000	0.000	0.000	0.000
129	B	142	LYS	1	0.957	0.973	38.384	-0.056	-0.056	0.000	0.000	0.000	0.000
130	B	143	GLU	-1	-0.935	-0.975	39.740	0.054	0.054	0.000	0.000	0.000	0.000
131	B	144	LYS	1	0.919	0.957	38.251	-0.047	-0.047	0.000	0.000	0.000	0.000
132	B	145	TYR	0	0.029	0.024	40.520	-0.002	-0.002	0.000	0.000	0.000	0.000
133	B	146	ALA	0	0.008	0.003	44.750	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	147	SER	0	0.023	0.021	45.445	-0.002	-0.002	0.000	0.000	0.000	0.000
135	B	148	GLN	0	0.015	-0.012	44.056	0.000	0.000	0.000	0.000	0.000	0.000
136	B	149	MET	0	-0.006	0.001	48.159	-0.001	-0.001	0.000	0.000	0.000	0.000
137	B	150	SER	0	-0.026	-0.020	50.389	-0.001	-0.001	0.000	0.000	0.000	0.000
138	B	151	SER	0	-0.035	-0.006	50.187	-0.001	-0.001	0.000	0.000	0.000	0.000
139	B	152	LEU	0	0.062	0.042	52.010	-0.001	-0.001	0.000	0.000	0.000	0.000
140	B	153	LYS	1	0.894	0.939	53.930	-0.027	-0.027	0.000	0.000	0.000	0.000
141	B	154	GLN	0	-0.068	-0.035	55.503	0.000	0.000	0.000	0.000	0.000	0.000
142	B	155	ASP	-1	-0.847	-0.927	53.744	0.019	0.019	0.000	0.000	0.000	0.000
143	B	156	LEU	0	-0.088	-0.054	57.100	-0.001	-0.001	0.000	0.000	0.000	0.000
144	B	157	LYS	1	0.886	0.937	59.539	-0.019	-0.019	0.000	0.000	0.000	0.000
145	B	158	ASP	-1	-0.772	-0.871	59.572	0.018	0.018	0.000	0.000	0.000	0.000
146	B	159	ILE	0	-0.094	-0.049	60.880	-0.001	-0.001	0.000	0.000	0.000	0.000
147	B	160	LEU	0	-0.075	-0.029	63.588	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	161	ASP	-1	-0.891	-0.928	65.172	0.016	0.016	0.000	0.000	0.000	0.000
149	B	162	LYS	1	0.887	0.949	64.933	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:14:MET)