FMO DATABASE

FMODB ID: YV9R2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-663485.994827
FMO2-HF: Nuclear repulsion	627030.859715
FMO2-HF: Total energy	-36455.135112
FMO2-MP2: Total energy	-36561.343246

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.
-118.983	-114.538	0.457	-1.907	-2.997	-0.007

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 : 0.905 / q_NPA : 0.939

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	-0.043	-0.016	3.673	1.112	3.545	-0.024	-1.205	-1.205	-0.003
4	A	6	PHE	0	0.063	0.012	6.581	-0.308	-0.308	0.000	0.000	0.000	0.000
5	A	7	THR	0	0.022	0.034	10.267	0.597	0.597	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.006	0.027	12.968	0.291	0.291	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.860	-0.932	16.395	-15.034	-15.034	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.967	0.955	19.001	11.006	11.006	0.000	0.000	0.000	0.000
9	A	11	GLY	0	-0.027	-0.018	22.691	-0.057	-0.057	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.015	0.007	20.532	0.080	0.080	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.071	-0.057	23.071	0.304	0.304	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.874	-0.951	24.955	-9.828	-9.828	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.944	0.998	26.662	9.134	9.134	0.000	0.000	0.000	0.000
14	A	16	HIS	0	-0.034	-0.021	23.575	-0.340	-0.340	0.000	0.000	0.000	0.000
15	A	17	LEU	0	0.003	0.025	17.311	-0.111	-0.111	0.000	0.000	0.000	0.000
16	A	18	ALA	0	0.033	0.018	19.148	-0.196	-0.196	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.015	-0.015	13.685	-0.210	-0.210	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.005	0.019	11.888	-0.319	-0.319	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.025	-0.003	8.778	-1.256	-1.256	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.911	0.966	6.094	31.946	31.946	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.026	-0.003	4.368	-8.833	-8.237	0.004	-0.139	-0.462	-0.001
22	A	24	GLU	-1	-0.965	-0.998	2.556	-32.486	-31.436	0.480	-0.547	-0.982	-0.003
23	A	25	GLY	0	-0.011	-0.003	4.355	-5.628	-5.526	-0.001	-0.008	-0.094	0.000
24	A	26	ASP	-1	-0.833	-0.926	7.070	-30.576	-30.576	0.000	0.000	0.000	0.000
25	A	27	THR	0	0.000	0.002	8.696	0.507	0.507	0.000	0.000	0.000	0.000
26	A	28	MET	0	-0.049	-0.016	7.684	-0.821	-0.821	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.023	0.018	11.807	1.336	1.336	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.953	-0.987	13.931	-15.645	-15.645	0.000	0.000	0.000	0.000
29	A	31	VAL	0	-0.017	-0.017	11.656	-2.115	-2.115	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.819	-0.901	13.986	-14.656	-14.656	0.000	0.000	0.000	0.000
31	A	33	LEU	0	0.018	0.005	14.512	-1.390	-1.390	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.905	0.950	16.758	15.692	15.692	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.807	-0.902	18.371	-12.532	-12.532	0.000	0.000	0.000	0.000
34	A	36	HIS	0	-0.041	-0.012	20.331	0.620	0.620	0.000	0.000	0.000	0.000
35	A	37	GLY	0	-0.006	-0.011	21.413	0.124	0.124	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.028	0.002	22.930	0.465	0.465	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.913	-0.968	23.107	-11.628	-11.628	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.949	-0.969	23.528	-11.483	-11.483	0.000	0.000	0.000	0.000
39	A	41	TRP	0	-0.113	-0.064	14.787	-0.654	-0.654	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.044	0.026	19.768	0.474	0.474	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.014	0.008	19.013	-0.840	-0.840	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.063	-0.018	16.196	0.066	0.066	0.000	0.000	0.000	0.000
43	A	45	THR	0	0.004	-0.007	18.919	-0.076	-0.076	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.859	0.939	16.934	16.522	16.522	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.036	0.018	18.621	0.825	0.825	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.947	-0.985	19.143	-13.763	-13.763	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.018	-0.016	16.822	-0.301	-0.301	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.007	-0.004	13.602	-0.538	-0.538	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.001	0.006	13.998	-0.978	-0.978	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.014	-0.008	13.343	0.555	0.555	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.009	-0.013	16.952	0.164	0.164	0.000	0.000	0.000	0.000
52	A	54	PHE	0	0.037	0.008	19.980	-0.222	-0.222	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.849	-0.893	21.852	-11.281	-11.281	0.000	0.000	0.000	0.000
54	A	56	SER	0	-0.054	-0.055	25.342	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.933	-0.970	27.051	-9.290	-9.290	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.934	-0.981	29.674	-8.620	-8.620	0.000	0.000	0.000	0.000
57	A	59	PRO	0	-0.079	-0.018	28.443	-0.364	-0.364	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.011	0.010	22.308	-0.201	-0.201	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.115	-0.065	24.595	0.279	0.279	0.000	0.000	0.000	0.000
60	A	62	GLY	0	-0.029	-0.003	20.479	-0.304	-0.304	0.000	0.000	0.000	0.000
61	A	63	PRO	0	-0.012	-0.043	17.688	0.548	0.548	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.001	0.004	16.153	0.335	0.335	0.000	0.000	0.000	0.000
63	A	65	ASN	0	0.037	0.054	14.145	-1.644	-1.644	0.000	0.000	0.000	0.000
64	A	66	PHE	0	0.015	-0.004	10.925	0.652	0.652	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.808	0.910	11.293	15.336	15.336	0.000	0.000	0.000	0.000
66	A	68	PHE	0	0.019	0.002	5.436	-0.303	-0.303	0.000	0.000	0.000	0.000
67	A	69	LEU	0	0.012	0.011	11.357	-1.357	-1.357	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.033	-0.014	7.686	1.235	1.235	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.855	-0.944	11.085	-17.676	-17.676	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.796	0.909	8.783	32.196	32.196	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.004	0.013	12.239	0.398	0.398	0.000	0.000	0.000	0.000
72	A	74	MET	0	-0.094	-0.038	6.007	0.722	0.722	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.968	0.977	9.760	22.633	22.633	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.073	-0.036	6.670	-5.118	-5.118	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.032	0.006	9.505	1.593	1.593	0.000	0.000	0.000	0.000
76	A	78	PHE	0	-0.087	-0.047	4.708	-3.299	-3.189	-0.001	-0.003	-0.106	0.000
77	A	79	ASP	-1	-0.840	-0.935	10.163	-17.455	-17.455	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.925	-0.979	12.901	-17.034	-17.034	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.061	-0.017	9.367	-0.586	-0.586	0.000	0.000	0.000	0.000
80	A	82	VAL	0	-0.028	-0.008	12.051	0.075	0.075	0.000	0.000	0.000	0.000
81	A	83	PRO	0	0.004	0.009	14.636	0.545	0.545	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.845	-0.925	17.634	-11.280	-11.280	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.883	0.940	21.271	11.126	11.126	0.000	0.000	0.000	0.000
84	A	86	TYR	0	0.011	0.022	17.798	-0.187	-0.187	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.025	-0.025	18.396	0.838	0.838	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.017	-0.015	18.286	-0.598	-0.598	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.030	-0.017	17.933	0.454	0.454	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.043	-0.007	15.479	-0.410	-0.410	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.016	-0.035	9.097	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.017	0.011	10.428	0.661	0.661	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.016	-0.002	5.081	-1.587	-1.587	0.000	0.000	0.000	0.000
92	A	94	PRO	0	-0.011	0.019	4.742	1.057	1.211	-0.001	-0.005	-0.148	0.000

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