FMO DATABASE

FMODB ID: JQ3N9

Calculation Name: 1VR4-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VR4

Chain ID: B

ChEMBL ID:

UniProt ID: Q81H14

Base Structure: X-ray

Registration Date: 2023-09-21

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-479485.168325
FMO2-HF: Nuclear repulsion	447480.530156
FMO2-HF: Total energy	-32004.638169
FMO2-MP2: Total energy	-32093.941311

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:1:MET)

Summations of interaction energy for fragment #1(B:1: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.
-35.868	-33.015	33.019	-14.341	-21.531	0.035

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.070

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	B	3	VAL	0	0.021	0.011	2.699	-2.825	0.133	0.280	-1.292	-1.946	0.002
4	B	4	THR	0	-0.034	-0.005	4.772	0.663	0.741	-0.001	-0.011	-0.065	0.000
5	B	5	THR	0	0.071	0.041	8.468	-0.048	-0.048	0.000	0.000	0.000	0.000
6	B	6	THR	0	-0.033	-0.014	11.493	0.138	0.138	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.045	0.007	11.675	-0.153	-0.153	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.021	0.005	11.935	0.121	0.121	0.000	0.000	0.000	0.000
9	B	9	ILE	0	-0.023	0.001	7.759	-0.133	-0.133	0.000	0.000	0.000	0.000
10	B	10	GLN	0	0.014	0.008	11.350	0.214	0.214	0.000	0.000	0.000	0.000
11	B	11	GLY	0	-0.008	-0.004	13.170	0.006	0.006	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.874	0.915	9.236	1.162	1.162	0.000	0.000	0.000	0.000
13	B	13	GLU	-1	-0.885	-0.925	11.921	-0.716	-0.716	0.000	0.000	0.000	0.000
14	B	14	ILE	0	-0.030	-0.009	9.915	-0.107	-0.107	0.000	0.000	0.000	0.000
15	B	15	ILE	0	-0.030	-0.013	11.118	0.156	0.156	0.000	0.000	0.000	0.000
16	B	16	GLU	-1	-0.872	-0.925	10.064	-0.588	-0.588	0.000	0.000	0.000	0.000
17	B	17	TYR	0	-0.008	-0.019	9.710	-0.312	-0.312	0.000	0.000	0.000	0.000
18	B	18	ILE	0	-0.049	-0.009	6.267	0.106	0.106	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.779	-0.876	8.777	-0.372	-0.372	0.000	0.000	0.000	0.000
20	B	20	ILE	0	-0.040	-0.011	8.661	-0.335	-0.335	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.069	-0.038	5.560	0.084	0.084	0.000	0.000	0.000	0.000
22	B	22	ASN	0	0.028	-0.025	8.981	-0.085	-0.085	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.011	0.023	10.815	0.138	0.138	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.908	-0.960	12.268	-0.044	-0.044	0.000	0.000	0.000	0.000
25	B	25	ALA	0	-0.014	0.018	15.857	0.076	0.076	0.000	0.000	0.000	0.000
26	B	26	ILE	0	0.024	-0.004	17.975	-0.055	-0.055	0.000	0.000	0.000	0.000
27	B	27	MET	0	-0.082	-0.017	21.747	0.023	0.023	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.065	0.027	24.210	-0.019	-0.019	0.000	0.000	0.000	0.000
29	B	29	ALA	0	-0.037	-0.013	27.955	0.005	0.005	0.000	0.000	0.000	0.000
30	B	51	GLU	-1	-0.923	-0.970	24.284	-0.055	-0.055	0.000	0.000	0.000	0.000
31	B	52	SER	0	0.010	-0.013	22.676	-0.010	-0.010	0.000	0.000	0.000	0.000
32	B	53	LYS	1	0.842	0.898	21.598	-0.141	-0.141	0.000	0.000	0.000	0.000
33	B	54	LEU	0	0.021	0.013	20.038	0.019	0.019	0.000	0.000	0.000	0.000
34	B	55	LYS	1	0.787	0.862	14.871	-0.089	-0.089	0.000	0.000	0.000	0.000
35	B	56	GLU	-1	-0.789	-0.871	16.825	0.196	0.196	0.000	0.000	0.000	0.000
36	B	57	ALA	0	0.029	0.020	16.745	0.063	0.063	0.000	0.000	0.000	0.000
37	B	58	ARG	1	0.961	0.970	14.160	0.167	0.167	0.000	0.000	0.000	0.000
38	B	59	ASP	-1	-0.802	-0.878	12.523	0.162	0.162	0.000	0.000	0.000	0.000
39	B	60	ILE	0	0.025	0.012	12.047	0.172	0.172	0.000	0.000	0.000	0.000
40	B	61	ALA	0	0.030	0.032	12.382	0.131	0.131	0.000	0.000	0.000	0.000
41	B	62	MET	0	0.010	-0.005	8.980	0.005	0.005	0.000	0.000	0.000	0.000
42	B	63	ASP	-1	-0.904	-0.948	7.766	1.950	1.950	0.000	0.000	0.000	0.000
43	B	64	GLU	-1	-0.898	-0.938	8.047	1.171	1.171	0.000	0.000	0.000	0.000
44	B	65	MET	0	-0.028	0.005	6.440	-0.067	-0.067	0.000	0.000	0.000	0.000
45	B	66	LYS	1	0.769	0.851	3.653	-2.934	-1.937	0.257	-0.228	-1.027	0.000
46	B	67	GLU	-1	-0.948	-0.960	3.769	1.305	2.611	0.063	-0.667	-0.702	-0.006
47	B	68	LEU	0	0.010	0.007	5.956	-0.408	-0.408	0.000	0.000	0.000	0.000
48	B	69	ALA	0	-0.001	-0.009	2.334	-0.750	-1.458	2.785	-0.673	-1.404	-0.001
49	B	70	LYS	1	0.813	0.868	2.147	-26.713	-33.883	21.934	-8.313	-6.451	0.094
50	B	71	GLN	0	-0.029	-0.008	3.452	-0.234	-0.224	0.023	0.088	-0.121	0.000
51	B	72	LYS	1	0.822	0.903	5.724	0.540	0.540	0.000	0.000	0.000	0.000
52	B	73	GLY	0	0.009	0.020	5.942	-0.083	-0.083	0.000	0.000	0.000	0.000
53	B	74	ALA	0	-0.019	-0.008	2.477	-0.462	-0.013	0.782	-0.350	-0.881	-0.002
54	B	75	ASN	0	-0.067	-0.042	2.380	-1.476	-0.519	2.681	-1.095	-2.544	-0.015
55	B	76	ALA	0	-0.021	-0.021	2.632	-3.737	-1.167	2.999	-1.770	-3.799	-0.031
56	B	77	ILE	0	0.018	0.018	2.310	-1.588	-0.449	1.220	0.002	-2.361	-0.006
57	B	78	VAL	0	-0.034	-0.016	4.505	0.286	0.341	-0.001	-0.017	-0.037	0.000
58	B	79	GLY	0	0.016	0.003	8.294	0.134	0.134	0.000	0.000	0.000	0.000
59	B	80	VAL	0	-0.075	-0.042	7.558	0.088	0.088	0.000	0.000	0.000	0.000
60	B	81	ASP	-1	-0.851	-0.932	10.764	-0.483	-0.483	0.000	0.000	0.000	0.000
61	B	82	VAL	0	-0.121	-0.064	13.624	0.047	0.047	0.000	0.000	0.000	0.000
62	B	83	ASP	-1	-0.849	-0.903	15.620	-0.295	-0.295	0.000	0.000	0.000	0.000
63	B	84	TYR	0	-0.071	-0.059	18.008	0.055	0.055	0.000	0.000	0.000	0.000
64	B	85	GLU	-1	-0.852	-0.928	21.575	-0.109	-0.109	0.000	0.000	0.000	0.000
65	B	86	VAL	0	-0.055	-0.018	24.201	0.025	0.025	0.000	0.000	0.000	0.000
66	B	87	VAL	0	0.019	0.019	24.440	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	88	ARG	1	0.874	0.927	27.474	-0.024	-0.024	0.000	0.000	0.000	0.000
68	B	89	ASP	-1	-0.827	-0.907	30.862	-0.025	-0.025	0.000	0.000	0.000	0.000
69	B	90	GLY	0	-0.053	-0.027	31.224	0.008	0.008	0.000	0.000	0.000	0.000
70	B	91	MET	0	-0.080	-0.031	25.651	0.008	0.008	0.000	0.000	0.000	0.000
71	B	92	LEU	0	0.005	-0.001	23.160	-0.015	-0.015	0.000	0.000	0.000	0.000
72	B	93	MET	0	-0.006	-0.012	20.008	0.036	0.036	0.000	0.000	0.000	0.000
73	B	94	VAL	0	-0.058	-0.029	16.502	-0.031	-0.031	0.000	0.000	0.000	0.000
74	B	95	ALA	0	0.045	0.022	15.726	0.060	0.060	0.000	0.000	0.000	0.000
75	B	96	VAL	0	-0.026	-0.016	10.648	-0.051	-0.051	0.000	0.000	0.000	0.000
76	B	97	SER	0	0.044	0.030	11.048	0.036	0.036	0.000	0.000	0.000	0.000
77	B	98	GLY	0	0.059	0.011	8.132	-0.065	-0.065	0.000	0.000	0.000	0.000
78	B	99	THR	0	-0.033	-0.009	8.185	0.174	0.174	0.000	0.000	0.000	0.000
79	B	100	ALA	0	0.006	0.014	4.328	-0.763	-0.695	-0.001	-0.009	-0.057	0.000
80	B	101	VAL	0	0.006	-0.004	4.630	0.801	0.884	-0.001	-0.003	-0.079	0.000
81	B	102	ARG	1	0.895	0.942	4.966	-0.414	-0.353	-0.001	-0.003	-0.057	0.000
82	B	103	ILE	0	0.005	-0.008	5.449	0.416	0.416	0.000	0.000	0.000	0.000

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