FMO DATABASE

FMODB ID: 89V8Y

Calculation Name: 1VJK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VJK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U3C7

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-635221.215732
FMO2-HF: Nuclear repulsion	600777.814114
FMO2-HF: Total energy	-34443.401618
FMO2-MP2: Total energy	-34546.792856

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:1:SER)

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

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.
-26.534	-24.988	15.92	-9.65	-7.816	-0.07

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.049

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

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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	3	LYS	1	0.836	0.904	3.876	2.296	4.163	-0.008	-0.866	-0.993	0.003
4	A	4	VAL	0	0.022	0.024	5.123	-0.760	-0.715	-0.001	-0.006	-0.037	0.000
5	A	5	LYS	1	0.842	0.902	8.715	0.229	0.229	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.031	0.028	11.660	-0.008	-0.008	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.830	0.888	13.986	0.046	0.046	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.041	0.006	15.120	0.014	0.014	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.014	-0.011	20.271	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.034	0.007	24.022	0.010	0.010	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.802	0.856	25.933	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.044	0.031	21.992	0.004	0.004	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.774	0.883	21.958	0.036	0.036	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.018	0.005	22.662	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.047	-0.002	22.658	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.009	0.009	18.227	0.012	0.012	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.046	-0.026	19.371	0.005	0.005	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.036	-0.018	16.488	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.794	-0.902	19.935	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.845	-0.909	15.824	-0.150	-0.150	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.785	-0.838	11.651	0.152	0.152	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.844	-0.899	7.980	-0.659	-0.659	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.051	-0.030	7.665	-0.075	-0.075	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.872	-0.908	1.720	-23.308	-26.318	14.817	-7.204	-4.603	-0.061
25	A	25	LEU	0	-0.026	-0.008	3.495	-1.710	-1.140	0.013	-0.198	-0.386	0.001
26	A	26	PRO	0	0.011	-0.011	2.608	0.749	2.240	1.089	-1.224	-1.355	-0.012
27	A	27	GLU	-1	-0.920	-0.962	3.330	-2.369	-1.913	0.012	-0.131	-0.337	-0.001
28	A	28	GLY	0	-0.010	-0.006	4.519	0.516	0.612	-0.001	-0.012	-0.084	0.000
29	A	29	ALA	0	-0.024	0.011	6.860	0.095	0.095	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.804	0.866	8.464	-0.280	-0.280	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.002	0.004	11.911	0.105	0.105	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.863	0.912	14.319	-0.149	-0.149	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.815	-0.905	10.639	0.500	0.500	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.011	-0.003	10.197	0.078	0.078	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.001	0.007	12.199	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.805	-0.897	14.896	0.246	0.246	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.768	-0.851	9.463	0.748	0.748	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.029	-0.014	12.831	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.817	0.900	15.018	-0.258	-0.258	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.790	0.881	11.003	-0.712	-0.712	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.755	0.860	7.729	-0.416	-0.416	0.000	0.000	0.000	0.000
42	A	42	HIS	1	0.778	0.874	14.688	-0.188	-0.188	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.824	-0.912	18.640	0.157	0.157	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.853	0.929	21.237	-0.075	-0.075	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.047	0.003	19.831	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.828	0.911	20.882	-0.197	-0.197	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.928	-0.971	23.013	0.133	0.133	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.800	-0.843	23.577	0.066	0.066	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.014	0.006	24.442	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.020	-0.027	19.078	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.090	0.051	23.543	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.906	-0.947	21.840	0.085	0.085	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.007	-0.004	22.669	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.129	-0.076	24.450	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.839	-0.929	27.299	0.052	0.052	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.895	-0.961	29.106	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.942	-0.960	31.670	0.033	0.033	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.081	-0.026	26.774	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.852	-0.925	26.820	0.058	0.058	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.082	-0.049	21.797	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.034	-0.029	23.682	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.036	0.008	17.875	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.007	-0.010	19.284	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.024	0.019	14.560	0.007	0.007	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.046	-0.049	14.726	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.019	-0.006	18.147	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.797	0.883	18.336	0.121	0.121	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.040	0.028	20.850	0.007	0.007	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.055	-0.025	17.612	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.034	0.016	19.763	0.018	0.018	0.000	0.000	0.000	0.000
71	A	71	TRP	0	-0.028	-0.047	18.020	0.011	0.011	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.830	-0.895	16.281	0.179	0.179	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.841	-0.881	15.800	-0.118	-0.118	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.873	-0.929	11.446	-0.103	-0.103	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.009	0.007	9.024	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.786	0.875	8.796	0.287	0.287	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.849	-0.919	5.190	-1.681	-1.650	-0.001	-0.009	-0.021	0.000
78	A	78	GLY	0	-0.004	-0.004	7.813	0.053	0.053	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.837	-0.895	10.423	-0.211	-0.211	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.031	-0.018	11.837	0.076	0.076	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.006	-0.009	12.769	0.005	0.005	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.036	-0.007	15.444	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.029	0.002	17.170	0.018	0.018	0.000	0.000	0.000	0.000
84	A	84	PHE	0	-0.055	-0.032	20.023	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.022	0.027	23.837	0.007	0.007	0.000	0.000	0.000	0.000
86	A	86	PRO	0	0.042	0.034	27.249	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.043	0.000	27.564	-0.004	-0.004	0.000	0.000	0.000	0.000

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