FMO DATABASE

FMODB ID: VQVY1

Calculation Name: 2VXQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VXQ

Chain ID: A

ChEMBL ID:

UniProt ID: P01857

Base Structure: X-ray

Registration Date: 2023-09-22

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-663640.262026
FMO2-HF: Nuclear repulsion	627183.994853
FMO2-HF: Total energy	-36456.267172
FMO2-MP2: Total energy	-36562.489566

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-144.124	-135.305	2.876	-4.946	-6.751	-0.045

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.902 / q_NPA : 0.946

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	5	THR	0	-0.045	-0.014	3.828	4.310	6.312	-0.023	-0.978	-1.002	-0.002
4	A	6	PHE	0	0.069	0.015	6.412	-0.878	-0.878	0.000	0.000	0.000	0.000
5	A	7	THR	0	0.019	0.027	10.217	1.019	1.019	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.002	0.020	12.562	0.196	0.196	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.837	-0.922	16.155	-15.795	-15.795	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.954	0.961	18.540	11.550	11.550	0.000	0.000	0.000	0.000
9	A	11	GLY	0	-0.028	-0.015	22.193	-0.102	-0.102	0.000	0.000	0.000	0.000
10	A	12	SER	0	0.007	0.008	20.369	0.131	0.131	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.104	-0.069	22.956	0.511	0.511	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.851	-0.939	25.132	-9.955	-9.955	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.879	0.950	26.849	9.319	9.319	0.000	0.000	0.000	0.000
14	A	16	HIS	0	-0.056	-0.034	23.498	-0.454	-0.454	0.000	0.000	0.000	0.000
15	A	17	LEU	0	0.007	0.025	17.580	-0.075	-0.075	0.000	0.000	0.000	0.000
16	A	18	ALA	0	0.046	0.024	19.350	-0.254	-0.254	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.016	-0.017	13.803	-0.159	-0.159	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.003	0.017	11.741	-0.487	-0.487	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.020	-0.002	8.797	-1.283	-1.283	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.835	0.906	6.460	37.748	37.748	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.043	-0.001	2.484	-24.928	-21.916	2.280	-1.966	-3.327	-0.025
22	A	24	GLU	-1	-0.883	-0.928	2.682	-41.081	-39.423	0.518	-0.736	-1.441	-0.004
23	A	25	GLY	0	-0.007	-0.007	2.911	-16.846	-14.699	0.101	-1.266	-0.981	-0.014
24	A	26	ASP	-1	-0.832	-0.906	5.233	-37.125	-37.125	0.000	0.000	0.000	0.000
25	A	27	THR	0	0.013	0.015	6.986	0.516	0.516	0.000	0.000	0.000	0.000
26	A	28	MET	0	-0.025	-0.001	7.020	-1.004	-1.004	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.005	0.005	11.157	1.768	1.768	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.927	-0.976	13.424	-16.526	-16.526	0.000	0.000	0.000	0.000
29	A	31	VAL	0	-0.022	-0.018	11.701	-2.380	-2.380	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.794	-0.876	14.166	-15.043	-15.043	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.013	-0.004	14.876	-1.327	-1.327	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.908	0.957	17.056	15.293	15.293	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.800	-0.895	18.475	-12.587	-12.587	0.000	0.000	0.000	0.000
34	A	36	HIS	0	-0.086	-0.046	19.565	0.677	0.677	0.000	0.000	0.000	0.000
35	A	37	GLY	0	-0.015	-0.016	21.382	0.143	0.143	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.028	0.005	23.005	0.468	0.468	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.913	-0.967	23.205	-11.425	-11.425	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.962	-0.973	23.791	-11.523	-11.523	0.000	0.000	0.000	0.000
39	A	41	TRP	0	-0.092	-0.059	15.229	-0.607	-0.607	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.037	0.025	20.106	0.459	0.459	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.020	0.011	19.292	-0.893	-0.893	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.068	-0.017	16.679	0.109	0.109	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.012	-0.012	19.196	-0.129	-0.129	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.806	0.923	15.258	19.431	19.431	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.044	0.019	18.619	0.945	0.945	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.936	-0.981	19.094	-15.224	-15.224	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.031	-0.020	16.841	-0.320	-0.320	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.004	-0.006	13.621	-0.643	-0.643	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.014	-0.002	13.998	-1.022	-1.022	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.011	-0.006	13.336	0.460	0.460	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.016	-0.006	17.166	-0.093	-0.093	0.000	0.000	0.000	0.000
52	A	54	PHE	0	0.005	-0.001	20.323	-0.213	-0.213	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.856	-0.905	22.264	-11.808	-11.808	0.000	0.000	0.000	0.000
54	A	56	SER	0	-0.034	-0.034	25.610	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.910	-0.949	27.378	-9.394	-9.394	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.897	-0.960	29.966	-8.673	-8.673	0.000	0.000	0.000	0.000
57	A	59	PRO	0	-0.076	-0.026	28.673	-0.363	-0.363	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.017	0.012	22.498	-0.172	-0.172	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.120	-0.075	24.645	0.312	0.312	0.000	0.000	0.000	0.000
60	A	62	GLY	0	-0.013	0.007	20.623	-0.279	-0.279	0.000	0.000	0.000	0.000
61	A	63	PRO	0	-0.047	-0.059	17.748	0.585	0.585	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.014	0.010	16.270	0.318	0.318	0.000	0.000	0.000	0.000
63	A	65	ASN	0	0.002	0.023	14.167	-1.360	-1.360	0.000	0.000	0.000	0.000
64	A	66	PHE	0	0.025	0.002	11.172	0.451	0.451	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.798	0.895	11.613	15.865	15.865	0.000	0.000	0.000	0.000
66	A	68	PHE	0	0.029	0.007	5.517	-0.605	-0.605	0.000	0.000	0.000	0.000
67	A	69	LEU	0	0.010	0.013	11.271	-1.255	-1.255	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.060	-0.048	6.321	1.719	1.719	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.831	-0.940	9.722	-19.456	-19.456	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.816	0.910	7.396	37.675	37.675	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.012	0.019	10.338	0.828	0.828	0.000	0.000	0.000	0.000
72	A	74	MET	0	-0.081	-0.035	5.359	2.568	2.568	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.946	0.970	8.554	23.959	23.959	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.076	-0.041	6.438	-6.057	-6.057	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.042	0.014	9.746	1.135	1.135	0.000	0.000	0.000	0.000
76	A	78	PHE	0	-0.077	-0.042	4.986	-2.267	-2.267	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.821	-0.930	10.138	-17.107	-17.107	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.890	-0.950	12.694	-15.815	-15.815	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.046	-0.008	9.543	-0.399	-0.399	0.000	0.000	0.000	0.000
80	A	82	VAL	0	-0.027	-0.008	12.222	0.053	0.053	0.000	0.000	0.000	0.000
81	A	83	PRO	0	0.013	0.011	15.069	0.560	0.560	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.776	-0.874	18.221	-10.944	-10.944	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.816	0.896	21.736	10.952	10.952	0.000	0.000	0.000	0.000
84	A	86	TYR	0	-0.007	0.019	18.042	-0.190	-0.190	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.028	-0.026	18.440	0.795	0.795	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.011	-0.011	18.095	-0.637	-0.637	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.017	-0.011	17.301	0.492	0.492	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.044	-0.008	15.163	-0.474	-0.474	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.018	-0.030	8.652	-0.110	-0.110	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.014	0.006	10.596	0.812	0.812	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.015	0.001	5.560	-1.979	-1.979	0.000	0.000	0.000	0.000
92	A	94	PRO	0	-0.004	0.019	5.092	1.515	1.515	0.000	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)