FMO DATABASE

FMODB ID: J35N9

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1221585.875346
FMO2-HF: Nuclear repulsion	1159540.978115
FMO2-HF: Total energy	-62044.897231
FMO2-MP2: Total energy	-62226.074182

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.
-9.133	-5.898	1.998	-2.042	-3.19	0.005

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 : 0.007 / q_NPA : -0.005

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	0.001	-0.008	3.831	-1.866	0.362	-0.025	-1.025	-1.177	0.000
4	B	17	GLN	0	0.054	0.044	3.415	-0.437	0.173	0.028	-0.222	-0.417	-0.001
5	B	18	GLN	0	0.003	-0.028	2.906	-3.670	-3.273	1.995	-0.795	-1.596	0.006
6	B	19	LEU	0	0.023	0.023	7.150	-0.140	-0.140	0.000	0.000	0.000	0.000
7	B	20	GLU	-1	-0.866	-0.932	10.506	0.253	0.253	0.000	0.000	0.000	0.000
8	B	21	ASN	0	0.030	0.004	11.958	-0.079	-0.079	0.000	0.000	0.000	0.000
9	B	22	LEU	0	-0.011	0.004	13.231	-0.033	-0.033	0.000	0.000	0.000	0.000
10	B	23	GLU	-1	-0.834	-0.929	8.585	1.197	1.197	0.000	0.000	0.000	0.000
11	B	24	SER	0	0.040	0.029	13.180	-0.034	-0.034	0.000	0.000	0.000	0.000
12	B	25	GLY	0	0.094	0.047	15.581	-0.032	-0.032	0.000	0.000	0.000	0.000
13	B	26	TRP	0	-0.072	-0.038	11.152	0.012	0.012	0.000	0.000	0.000	0.000
14	B	27	LYS	1	0.890	0.930	10.752	-0.383	-0.383	0.000	0.000	0.000	0.000
15	B	28	TRP	0	0.007	0.023	16.787	-0.015	-0.015	0.000	0.000	0.000	0.000
16	B	29	ALA	0	0.022	-0.003	20.264	-0.015	-0.015	0.000	0.000	0.000	0.000
17	B	30	TYR	0	-0.091	-0.053	18.791	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	31	LEU	0	0.038	0.009	19.557	-0.008	-0.008	0.000	0.000	0.000	0.000
19	B	32	VAL	0	0.087	0.044	22.339	-0.012	-0.012	0.000	0.000	0.000	0.000
20	B	33	LYS	1	0.879	0.959	23.414	-0.184	-0.184	0.000	0.000	0.000	0.000
21	B	34	LYS	1	0.856	0.920	22.343	-0.166	-0.166	0.000	0.000	0.000	0.000
22	B	35	HIS	0	0.007	0.004	25.422	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	36	ARG	1	0.932	0.964	27.917	-0.111	-0.111	0.000	0.000	0.000	0.000
24	B	37	GLU	-1	-0.905	-0.951	26.626	0.145	0.145	0.000	0.000	0.000	0.000
25	B	38	GLY	0	-0.004	0.026	30.251	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	39	GLU	-1	-0.775	-0.877	24.830	0.131	0.131	0.000	0.000	0.000	0.000
27	B	40	ALA	0	-0.025	-0.009	27.454	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	41	ILE	0	0.005	-0.006	23.216	0.003	0.003	0.000	0.000	0.000	0.000
29	B	42	THR	0	0.015	0.011	23.853	0.002	0.002	0.000	0.000	0.000	0.000
30	B	43	ARG	1	0.775	0.894	20.500	-0.026	-0.026	0.000	0.000	0.000	0.000
31	B	44	HIS	0	-0.009	-0.005	26.301	-0.008	-0.008	0.000	0.000	0.000	0.000
32	B	45	ILE	0	0.014	0.001	29.876	0.003	0.003	0.000	0.000	0.000	0.000
33	B	46	GLU	-1	-0.849	-0.920	32.644	0.031	0.031	0.000	0.000	0.000	0.000
34	B	47	ASN	0	0.031	-0.004	33.734	0.004	0.004	0.000	0.000	0.000	0.000
35	B	48	SER	0	0.015	0.018	35.424	0.002	0.002	0.000	0.000	0.000	0.000
36	B	49	ALA	0	0.056	0.019	31.515	0.002	0.002	0.000	0.000	0.000	0.000
37	B	50	ALA	0	-0.069	-0.025	30.016	0.004	0.004	0.000	0.000	0.000	0.000
38	B	51	GLN	0	-0.016	-0.035	30.450	0.008	0.008	0.000	0.000	0.000	0.000
39	B	52	ASP	-1	-0.883	-0.939	31.958	0.040	0.040	0.000	0.000	0.000	0.000
40	B	53	ALA	0	-0.049	-0.018	26.900	0.003	0.003	0.000	0.000	0.000	0.000
41	B	54	VAL	0	-0.014	-0.016	28.016	0.008	0.008	0.000	0.000	0.000	0.000
42	B	55	GLU	-1	-0.823	-0.895	29.047	0.059	0.059	0.000	0.000	0.000	0.000
43	B	56	GLN	0	-0.070	-0.036	27.612	0.004	0.004	0.000	0.000	0.000	0.000
44	B	57	LEU	0	-0.004	0.000	21.953	0.008	0.008	0.000	0.000	0.000	0.000
45	B	58	MET	0	-0.011	-0.005	25.680	0.015	0.015	0.000	0.000	0.000	0.000
46	B	59	LYS	1	0.952	0.982	28.053	-0.058	-0.058	0.000	0.000	0.000	0.000
47	B	60	LEU	0	-0.077	-0.021	22.587	0.001	0.001	0.000	0.000	0.000	0.000
48	B	61	GLU	-1	-0.916	-0.973	23.265	0.153	0.153	0.000	0.000	0.000	0.000
49	B	62	ASN	0	-0.035	-0.019	22.548	0.009	0.009	0.000	0.000	0.000	0.000
50	B	63	GLU	-1	-0.810	-0.888	22.312	0.086	0.086	0.000	0.000	0.000	0.000
51	B	64	PRO	0	0.012	0.003	16.689	-0.006	-0.006	0.000	0.000	0.000	0.000
52	B	65	VAL	0	0.010	-0.007	17.495	0.004	0.004	0.000	0.000	0.000	0.000
53	B	66	LYS	1	0.896	0.939	18.653	-0.085	-0.085	0.000	0.000	0.000	0.000
54	B	67	VAL	0	-0.071	-0.027	17.721	-0.006	-0.006	0.000	0.000	0.000	0.000
55	B	68	GLN	0	-0.003	-0.016	13.137	0.055	0.055	0.000	0.000	0.000	0.000
56	B	69	GLU	-1	-0.836	-0.915	16.740	0.039	0.039	0.000	0.000	0.000	0.000
57	B	70	TRP	0	-0.016	0.004	19.456	-0.010	-0.010	0.000	0.000	0.000	0.000
58	B	71	ILE	0	-0.060	-0.034	15.760	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	72	ASP	-1	-0.878	-0.939	15.694	0.007	0.007	0.000	0.000	0.000	0.000
60	B	73	ALA	0	-0.027	-0.002	18.304	-0.015	-0.015	0.000	0.000	0.000	0.000
61	B	74	HIS	0	0.047	-0.002	22.134	0.000	0.000	0.000	0.000	0.000	0.000
62	B	75	MET	0	-0.037	0.008	17.622	0.006	0.006	0.000	0.000	0.000	0.000
63	B	76	ASN	0	-0.045	-0.027	21.565	-0.011	-0.011	0.000	0.000	0.000	0.000
64	B	77	VAL	0	0.081	0.019	20.251	0.012	0.012	0.000	0.000	0.000	0.000
65	B	78	ASN	0	0.016	-0.001	19.444	0.019	0.019	0.000	0.000	0.000	0.000
66	B	79	LEU	0	0.034	0.019	19.718	0.021	0.021	0.000	0.000	0.000	0.000
67	B	80	ALA	0	0.052	0.041	16.264	0.030	0.030	0.000	0.000	0.000	0.000
68	B	81	THR	0	-0.022	-0.024	14.854	0.025	0.025	0.000	0.000	0.000	0.000
69	B	82	ARG	1	0.809	0.889	14.848	-0.099	-0.099	0.000	0.000	0.000	0.000
70	B	83	MET	0	0.028	0.040	14.487	0.052	0.052	0.000	0.000	0.000	0.000
71	B	84	LYS	1	0.942	0.967	9.840	-0.051	-0.051	0.000	0.000	0.000	0.000
72	B	85	GLN	0	-0.043	-0.024	11.036	0.119	0.119	0.000	0.000	0.000	0.000
73	B	86	THR	0	-0.041	-0.025	12.919	0.056	0.056	0.000	0.000	0.000	0.000
74	B	87	ILE	0	0.029	0.013	9.902	0.030	0.030	0.000	0.000	0.000	0.000
75	B	88	ARG	1	0.974	0.994	7.324	-0.612	-0.612	0.000	0.000	0.000	0.000
76	B	89	ALA	0	-0.037	-0.005	9.261	0.085	0.085	0.000	0.000	0.000	0.000
77	B	90	ARG	1	0.941	0.964	12.185	-0.359	-0.359	0.000	0.000	0.000	0.000
78	B	91	ARG	1	0.877	0.926	5.007	-1.549	-1.549	0.000	0.000	0.000	0.000
79	B	92	LYS	1	0.877	0.940	8.548	-0.870	-0.870	0.000	0.000	0.000	0.000
80	B	93	ARG	1	0.902	0.936	9.983	-0.496	-0.496	0.000	0.000	0.000	0.000
81	B	94	HIS	0	0.021	0.016	12.271	-0.042	-0.042	0.000	0.000	0.000	0.000
82	B	95	PHE	0	0.063	0.022	8.812	-0.030	-0.030	0.000	0.000	0.000	0.000
83	B	96	ASN	0	-0.032	-0.010	11.879	0.048	0.048	0.000	0.000	0.000	0.000
84	B	97	ALA	0	-0.086	-0.041	14.003	-0.034	-0.034	0.000	0.000	0.000	0.000
85	B	98	GLU	-1	-0.837	-0.907	13.636	0.195	0.195	0.000	0.000	0.000	0.000
86	B	99	HIS	0	-0.006	-0.009	15.702	-0.045	-0.045	0.000	0.000	0.000	0.000
87	B	100	GLN	0	0.057	0.010	18.292	0.022	0.022	0.000	0.000	0.000	0.000
88	B	101	HIS	0	0.058	0.041	17.855	0.040	0.040	0.000	0.000	0.000	0.000
89	B	102	THR	0	0.009	0.018	14.130	0.033	0.033	0.000	0.000	0.000	0.000
90	B	103	ARG	1	0.935	0.996	15.486	-0.157	-0.157	0.000	0.000	0.000	0.000
91	B	104	LYS	1	0.833	0.896	14.604	-0.338	-0.338	0.000	0.000	0.000	0.000
92	B	105	LYS	1	0.943	0.963	19.424	-0.158	-0.158	0.000	0.000	0.000	0.000
93	B	106	SER	0	0.004	0.006	23.051	0.011	0.011	0.000	0.000	0.000	0.000
94	B	107	ILE	0	-0.006	0.000	24.482	-0.011	-0.011	0.000	0.000	0.000	0.000
95	B	108	ASP	-1	-0.871	-0.921	27.417	0.149	0.149	0.000	0.000	0.000	0.000
96	B	109	LEU	0	-0.043	-0.022	29.303	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	110	GLU	-1	-0.873	-0.933	31.843	0.082	0.082	0.000	0.000	0.000	0.000
98	B	111	PHE	0	0.021	-0.009	32.271	0.003	0.003	0.000	0.000	0.000	0.000
99	B	112	LEU	0	0.078	0.021	33.782	0.004	0.004	0.000	0.000	0.000	0.000
100	B	113	VAL	0	0.013	0.015	33.331	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	114	TRP	0	0.018	0.013	26.439	0.000	0.000	0.000	0.000	0.000	0.000
102	B	115	GLN	0	-0.004	0.001	30.432	0.003	0.003	0.000	0.000	0.000	0.000
103	B	116	ARG	1	0.958	0.974	32.188	-0.073	-0.073	0.000	0.000	0.000	0.000
104	B	117	LEU	0	-0.001	0.010	27.585	0.000	0.000	0.000	0.000	0.000	0.000
105	B	118	ALA	0	0.023	-0.004	27.590	0.006	0.006	0.000	0.000	0.000	0.000
106	B	119	VAL	0	-0.091	-0.041	28.468	0.002	0.002	0.000	0.000	0.000	0.000
107	B	120	LEU	0	0.002	-0.007	30.073	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	121	ALA	0	0.033	0.034	24.840	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	122	ARG	1	0.944	0.957	25.445	-0.118	-0.118	0.000	0.000	0.000	0.000
110	B	123	ARG	1	0.900	0.967	26.498	-0.082	-0.082	0.000	0.000	0.000	0.000
111	B	124	ARG	1	0.899	0.943	26.896	-0.105	-0.105	0.000	0.000	0.000	0.000
112	B	125	GLY	0	0.014	0.033	23.555	0.000	0.000	0.000	0.000	0.000	0.000
113	B	126	ASN	0	-0.013	0.009	21.493	0.010	0.010	0.000	0.000	0.000	0.000
114	B	127	THR	0	-0.006	-0.043	17.925	0.003	0.003	0.000	0.000	0.000	0.000
115	B	128	LEU	0	0.058	0.018	21.249	-0.021	-0.021	0.000	0.000	0.000	0.000
116	B	129	SER	0	-0.003	-0.007	20.450	-0.020	-0.020	0.000	0.000	0.000	0.000
117	B	130	ASP	-1	-0.827	-0.873	20.115	0.216	0.216	0.000	0.000	0.000	0.000
118	B	131	THR	0	-0.006	-0.016	23.211	-0.021	-0.021	0.000	0.000	0.000	0.000
119	B	132	VAL	0	-0.051	-0.032	26.110	-0.014	-0.014	0.000	0.000	0.000	0.000
120	B	133	VAL	0	0.007	0.004	24.429	-0.010	-0.010	0.000	0.000	0.000	0.000
121	B	134	GLN	0	0.056	0.027	26.189	-0.006	-0.006	0.000	0.000	0.000	0.000
122	B	135	LEU	0	-0.029	-0.004	29.093	-0.009	-0.009	0.000	0.000	0.000	0.000
123	B	136	ILE	0	-0.009	-0.003	29.474	-0.007	-0.007	0.000	0.000	0.000	0.000
124	B	137	GLU	-1	-0.922	-0.955	28.888	0.075	0.075	0.000	0.000	0.000	0.000
125	B	138	ASP	-1	-0.926	-0.986	32.663	0.067	0.067	0.000	0.000	0.000	0.000
126	B	139	ALA	0	-0.066	-0.034	34.801	-0.006	-0.006	0.000	0.000	0.000	0.000
127	B	140	GLU	-1	-0.772	-0.882	35.582	0.049	0.049	0.000	0.000	0.000	0.000
128	B	141	ARG	1	0.846	0.927	36.324	-0.042	-0.042	0.000	0.000	0.000	0.000
129	B	142	LYS	1	0.840	0.909	38.574	-0.055	-0.055	0.000	0.000	0.000	0.000
130	B	143	GLU	-1	-0.859	-0.922	40.548	0.051	0.051	0.000	0.000	0.000	0.000
131	B	144	LYS	1	0.827	0.899	38.172	-0.046	-0.046	0.000	0.000	0.000	0.000
132	B	145	TYR	0	0.021	0.007	40.601	-0.002	-0.002	0.000	0.000	0.000	0.000
133	B	146	ALA	0	0.021	0.012	44.940	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	147	SER	0	-0.007	0.014	45.739	-0.002	-0.002	0.000	0.000	0.000	0.000
135	B	148	GLN	0	0.070	0.028	44.100	0.000	0.000	0.000	0.000	0.000	0.000
136	B	149	MET	0	-0.016	-0.003	48.350	-0.001	-0.001	0.000	0.000	0.000	0.000
137	B	150	SER	0	-0.026	-0.019	50.582	-0.001	-0.001	0.000	0.000	0.000	0.000
138	B	151	SER	0	-0.040	-0.023	50.101	-0.001	-0.001	0.000	0.000	0.000	0.000
139	B	152	LEU	0	0.055	0.040	52.377	-0.001	-0.001	0.000	0.000	0.000	0.000
140	B	153	LYS	1	0.913	0.946	54.120	-0.024	-0.024	0.000	0.000	0.000	0.000
141	B	154	GLN	0	-0.059	-0.034	55.671	0.000	0.000	0.000	0.000	0.000	0.000
142	B	155	ASP	-1	-0.875	-0.937	53.890	0.018	0.018	0.000	0.000	0.000	0.000
143	B	156	LEU	0	-0.076	-0.050	57.261	-0.001	-0.001	0.000	0.000	0.000	0.000
144	B	157	LYS	1	0.775	0.863	59.728	-0.016	-0.016	0.000	0.000	0.000	0.000
145	B	158	ASP	-1	-0.781	-0.882	59.988	0.017	0.017	0.000	0.000	0.000	0.000
146	B	159	ILE	0	-0.090	-0.048	61.086	-0.001	-0.001	0.000	0.000	0.000	0.000
147	B	160	LEU	0	-0.057	-0.027	63.778	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	161	ASP	-1	-0.813	-0.854	65.812	0.015	0.015	0.000	0.000	0.000	0.000
149	B	162	LYS	1	0.901	0.958	64.633	-0.012	-0.012	0.000	0.000	0.000	0.000

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