FMO DATABASE

FMODB ID: Q1RQY

Calculation Name: 2VTX-J-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VTX

Chain ID: J

ChEMBL ID:

UniProt ID: P05221

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:

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-639544.802926
FMO2-HF: Nuclear repulsion	603215.623506
FMO2-HF: Total energy	-36329.179419
FMO2-MP2: Total energy	-36434.452921

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(J:17:LEU)

Summations of interaction energy for fragment #1(J:17:LEU)

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.
-0.897	2.577	0.169	-1.338	-2.307	-0.001

Interaction energy analysis for fragmet #1(J:17:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.007

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	J	19	TRP	0	0.017	0.008	3.861	-2.029	-0.222	-0.012	-0.848	-0.947	-0.001
4	J	20	GLY	0	0.027	-0.002	6.002	0.495	0.495	0.000	0.000	0.000	0.000
5	J	21	CYS	0	-0.070	-0.005	9.653	-0.030	-0.030	0.000	0.000	0.000	0.000
6	J	22	GLU	-1	-0.841	-0.925	12.908	-0.201	-0.201	0.000	0.000	0.000	0.000
7	J	23	LEU	0	0.000	0.012	16.126	-0.005	-0.005	0.000	0.000	0.000	0.000
8	J	24	ASN	0	-0.032	-0.048	19.419	0.021	0.021	0.000	0.000	0.000	0.000
9	J	25	GLU	-1	-0.954	-0.974	22.798	-0.107	-0.107	0.000	0.000	0.000	0.000
10	J	26	GLN	0	-0.034	-0.020	24.045	0.011	0.011	0.000	0.000	0.000	0.000
11	J	27	ASN	0	-0.009	-0.003	19.504	0.019	0.019	0.000	0.000	0.000	0.000
12	J	28	LYS	1	0.976	0.984	21.314	0.112	0.112	0.000	0.000	0.000	0.000
13	J	29	THR	0	0.014	0.014	20.502	0.009	0.009	0.000	0.000	0.000	0.000
14	J	30	PHE	0	0.002	-0.006	11.864	-0.019	-0.019	0.000	0.000	0.000	0.000
15	J	31	GLU	-1	-0.914	-0.978	16.780	-0.282	-0.282	0.000	0.000	0.000	0.000
16	J	32	PHE	0	-0.052	-0.034	8.021	-0.132	-0.132	0.000	0.000	0.000	0.000
17	J	33	LYS	1	0.975	1.003	7.669	1.279	1.279	0.000	0.000	0.000	0.000
18	J	43	HIS	0	-0.044	-0.036	5.096	0.039	0.039	0.000	0.000	0.000	0.000
19	J	44	GLN	0	-0.004	0.011	8.918	-0.031	-0.031	0.000	0.000	0.000	0.000
20	J	45	LEU	0	-0.048	-0.038	7.141	-0.097	-0.097	0.000	0.000	0.000	0.000
21	J	46	ALA	0	0.029	0.026	7.959	0.114	0.114	0.000	0.000	0.000	0.000
22	J	47	LEU	0	0.004	0.000	9.007	-0.092	-0.092	0.000	0.000	0.000	0.000
23	J	48	ARG	1	0.841	0.927	8.066	-0.685	-0.685	0.000	0.000	0.000	0.000
24	J	49	THR	0	-0.014	0.006	12.188	0.015	0.015	0.000	0.000	0.000	0.000
25	J	50	VAL	0	0.095	0.055	14.641	-0.062	-0.062	0.000	0.000	0.000	0.000
26	J	51	CYS	0	-0.100	-0.058	17.347	0.025	0.025	0.000	0.000	0.000	0.000
27	J	52	LEU	0	0.052	0.043	19.054	-0.029	-0.029	0.000	0.000	0.000	0.000
28	J	53	GLY	0	0.016	0.010	20.687	0.005	0.005	0.000	0.000	0.000	0.000
29	J	54	ASP	-1	-0.907	-0.961	21.411	-0.080	-0.080	0.000	0.000	0.000	0.000
30	J	55	LYS	1	0.856	0.927	24.150	0.082	0.082	0.000	0.000	0.000	0.000
31	J	56	ALA	0	0.015	0.039	24.263	-0.001	-0.001	0.000	0.000	0.000	0.000
32	J	57	LYS	1	0.967	0.976	26.080	0.086	0.086	0.000	0.000	0.000	0.000
33	J	58	ASP	-1	-0.836	-0.924	29.166	-0.039	-0.039	0.000	0.000	0.000	0.000
34	J	59	GLU	-1	-0.864	-0.941	29.345	-0.079	-0.079	0.000	0.000	0.000	0.000
35	J	60	PHE	0	-0.033	-0.034	29.704	-0.001	-0.001	0.000	0.000	0.000	0.000
36	J	61	HIS	0	-0.004	0.011	24.407	-0.013	-0.013	0.000	0.000	0.000	0.000
37	J	62	ILE	0	-0.012	-0.017	25.409	0.009	0.009	0.000	0.000	0.000	0.000
38	J	63	VAL	0	0.004	0.019	18.994	-0.011	-0.011	0.000	0.000	0.000	0.000
39	J	64	GLU	-1	-0.830	-0.930	22.444	-0.087	-0.087	0.000	0.000	0.000	0.000
40	J	65	ILE	0	-0.011	-0.009	17.339	-0.025	-0.025	0.000	0.000	0.000	0.000
41	J	66	VAL	0	-0.045	-0.041	20.727	0.024	0.024	0.000	0.000	0.000	0.000
42	J	67	ASP	-1	-0.880	-0.934	20.645	-0.138	-0.138	0.000	0.000	0.000	0.000
43	J	68	GLN	0	-0.053	-0.017	22.689	0.021	0.021	0.000	0.000	0.000	0.000
44	J	69	GLU	-1	-0.846	-0.914	24.413	-0.051	-0.051	0.000	0.000	0.000	0.000
45	J	70	GLU	-1	-0.829	-0.934	26.710	-0.048	-0.048	0.000	0.000	0.000	0.000
46	J	71	GLY	0	-0.083	-0.038	28.539	-0.008	-0.008	0.000	0.000	0.000	0.000
47	J	72	ALA	0	-0.045	-0.025	30.151	0.002	0.002	0.000	0.000	0.000	0.000
48	J	73	GLU	-1	-0.942	-0.971	26.557	-0.126	-0.126	0.000	0.000	0.000	0.000
49	J	74	LYS	1	0.784	0.903	25.938	0.069	0.069	0.000	0.000	0.000	0.000
50	J	75	VAL	0	-0.001	0.001	25.189	-0.010	-0.010	0.000	0.000	0.000	0.000
51	J	76	VAL	0	0.024	-0.001	23.267	0.014	0.014	0.000	0.000	0.000	0.000
52	J	77	PRO	0	-0.061	-0.036	23.134	-0.012	-0.012	0.000	0.000	0.000	0.000
53	J	78	ILE	0	0.009	-0.004	18.047	0.011	0.011	0.000	0.000	0.000	0.000
54	J	79	ALA	0	0.018	0.018	20.892	0.014	0.014	0.000	0.000	0.000	0.000
55	J	80	THR	0	-0.032	-0.018	23.019	-0.012	-0.012	0.000	0.000	0.000	0.000
56	J	81	LEU	0	-0.028	-0.009	21.435	0.009	0.009	0.000	0.000	0.000	0.000
57	J	82	LYS	1	0.935	0.972	26.010	0.031	0.031	0.000	0.000	0.000	0.000
58	J	83	PRO	0	0.040	0.029	26.901	0.009	0.009	0.000	0.000	0.000	0.000
59	J	84	SER	0	-0.079	-0.044	28.071	0.008	0.008	0.000	0.000	0.000	0.000
60	J	85	ILE	0	-0.087	-0.029	30.066	0.005	0.005	0.000	0.000	0.000	0.000
61	J	86	LEU	0	0.017	-0.011	25.169	0.009	0.009	0.000	0.000	0.000	0.000
62	J	87	PRO	0	0.048	0.035	24.033	-0.008	-0.008	0.000	0.000	0.000	0.000
63	J	88	MET	0	-0.023	-0.024	17.589	-0.016	-0.016	0.000	0.000	0.000	0.000
64	J	89	ALA	0	0.010	0.014	19.845	0.015	0.015	0.000	0.000	0.000	0.000
65	J	90	THR	0	-0.045	-0.032	16.207	-0.022	-0.022	0.000	0.000	0.000	0.000
66	J	91	MET	0	-0.020	-0.008	14.801	-0.015	-0.015	0.000	0.000	0.000	0.000
67	J	92	VAL	0	-0.001	-0.011	15.319	0.047	0.047	0.000	0.000	0.000	0.000
68	J	93	GLY	0	0.014	0.007	15.405	-0.029	-0.029	0.000	0.000	0.000	0.000
69	J	94	ILE	0	-0.003	0.010	15.062	-0.024	-0.024	0.000	0.000	0.000	0.000
70	J	95	GLU	-1	-0.964	-0.999	11.380	0.312	0.312	0.000	0.000	0.000	0.000
71	J	96	LEU	0	0.014	0.007	12.287	-0.005	-0.005	0.000	0.000	0.000	0.000
72	J	97	ASP	-1	-0.797	-0.904	12.056	-0.187	-0.187	0.000	0.000	0.000	0.000
73	J	98	PRO	0	-0.128	-0.037	11.240	-0.023	-0.023	0.000	0.000	0.000	0.000
74	J	99	PRO	0	0.004	0.009	14.212	0.025	0.025	0.000	0.000	0.000	0.000
75	J	100	VAL	0	0.062	0.021	13.833	0.033	0.033	0.000	0.000	0.000	0.000
76	J	101	THR	0	0.009	0.025	16.018	-0.049	-0.049	0.000	0.000	0.000	0.000
77	J	102	PHE	0	-0.001	0.009	13.173	0.031	0.031	0.000	0.000	0.000	0.000
78	J	103	ARG	1	0.877	0.936	18.680	0.120	0.120	0.000	0.000	0.000	0.000
79	J	104	LEU	0	-0.033	-0.027	22.211	0.013	0.013	0.000	0.000	0.000	0.000
80	J	105	LYS	1	0.940	0.997	23.750	0.082	0.082	0.000	0.000	0.000	0.000
81	J	106	ALA	0	-0.050	-0.037	26.778	0.011	0.011	0.000	0.000	0.000	0.000
82	J	107	GLY	0	0.016	0.019	26.833	-0.006	-0.006	0.000	0.000	0.000	0.000
83	J	108	SER	0	-0.044	-0.021	26.990	-0.009	-0.009	0.000	0.000	0.000	0.000
84	J	109	GLY	0	0.008	0.010	22.916	-0.013	-0.013	0.000	0.000	0.000	0.000
85	J	110	PRO	0	0.030	0.004	19.950	0.013	0.013	0.000	0.000	0.000	0.000
86	J	111	LEU	0	-0.021	-0.004	18.425	0.025	0.025	0.000	0.000	0.000	0.000
87	J	112	TYR	0	-0.027	-0.024	14.563	-0.020	-0.020	0.000	0.000	0.000	0.000
88	J	113	ILE	0	0.008	0.019	13.200	0.053	0.053	0.000	0.000	0.000	0.000
89	J	114	SER	0	0.000	-0.010	10.214	-0.087	-0.087	0.000	0.000	0.000	0.000
90	J	115	GLY	0	0.094	0.008	8.656	0.147	0.147	0.000	0.000	0.000	0.000
91	J	116	GLN	0	-0.043	-0.017	4.211	-1.236	-0.934	-0.001	-0.057	-0.245	0.000
92	J	117	HIS	0	0.008	0.017	2.694	0.352	1.547	0.183	-0.419	-0.959	0.000
93	J	118	VAL	0	0.000	0.018	4.289	1.568	1.738	-0.001	-0.014	-0.156	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(J:17:LEU)