FMO DATABASE

FMODB ID: 4327N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-641612.752585
FMO2-HF: Nuclear repulsion	605281.935211
FMO2-HF: Total energy	-36330.817375
FMO2-MP2: Total energy	-36436.03668

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.
-3.889	1.002	1.246	-2.5	-3.637	-0.005

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 : 0.005 / 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

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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	J	19	TRP	0	0.023	0.006	3.080	-3.634	-1.183	0.121	-1.277	-1.296	-0.005
4	J	20	GLY	0	0.050	0.006	5.902	0.489	0.489	0.000	0.000	0.000	0.000
5	J	21	CYS	0	-0.107	-0.016	9.416	-0.061	-0.061	0.000	0.000	0.000	0.000
6	J	22	GLU	-1	-0.802	-0.896	12.681	-0.199	-0.199	0.000	0.000	0.000	0.000
7	J	23	LEU	0	-0.022	0.012	16.238	-0.005	-0.005	0.000	0.000	0.000	0.000
8	J	24	ASN	0	0.002	-0.030	19.635	0.027	0.027	0.000	0.000	0.000	0.000
9	J	25	GLU	-1	-0.830	-0.923	22.866	-0.092	-0.092	0.000	0.000	0.000	0.000
10	J	26	GLN	0	-0.028	0.006	24.410	0.014	0.014	0.000	0.000	0.000	0.000
11	J	27	ASN	0	0.008	0.007	19.118	0.016	0.016	0.000	0.000	0.000	0.000
12	J	28	LYS	1	0.919	0.947	21.460	0.102	0.102	0.000	0.000	0.000	0.000
13	J	29	THR	0	-0.033	-0.031	20.653	0.020	0.020	0.000	0.000	0.000	0.000
14	J	30	PHE	0	0.017	0.011	11.876	-0.025	-0.025	0.000	0.000	0.000	0.000
15	J	31	GLU	-1	-0.899	-0.947	16.112	-0.220	-0.220	0.000	0.000	0.000	0.000
16	J	32	PHE	0	-0.046	-0.024	7.084	-0.107	-0.107	0.000	0.000	0.000	0.000
17	J	33	LYS	1	0.948	0.975	7.039	1.202	1.202	0.000	0.000	0.000	0.000
18	J	43	HIS	0	-0.061	-0.041	4.857	-0.081	-0.081	0.000	0.000	0.000	0.000
19	J	44	GLN	0	0.000	-0.007	8.397	-0.102	-0.102	0.000	0.000	0.000	0.000
20	J	45	LEU	0	-0.043	-0.015	7.406	0.114	0.114	0.000	0.000	0.000	0.000
21	J	46	ALA	0	0.007	-0.005	7.744	0.051	0.051	0.000	0.000	0.000	0.000
22	J	47	LEU	0	0.004	0.005	9.113	-0.019	-0.019	0.000	0.000	0.000	0.000
23	J	48	ARG	1	0.759	0.867	9.138	-0.750	-0.750	0.000	0.000	0.000	0.000
24	J	49	THR	0	-0.040	-0.015	12.427	0.002	0.002	0.000	0.000	0.000	0.000
25	J	50	VAL	0	0.041	0.028	14.397	-0.064	-0.064	0.000	0.000	0.000	0.000
26	J	51	CYS	0	-0.032	-0.016	15.926	0.027	0.027	0.000	0.000	0.000	0.000
27	J	52	LEU	0	0.039	0.024	18.797	-0.027	-0.027	0.000	0.000	0.000	0.000
28	J	53	GLY	0	0.028	0.021	20.536	0.004	0.004	0.000	0.000	0.000	0.000
29	J	54	ASP	-1	-0.853	-0.919	21.200	-0.090	-0.090	0.000	0.000	0.000	0.000
30	J	55	LYS	1	0.776	0.859	24.207	0.090	0.090	0.000	0.000	0.000	0.000
31	J	56	ALA	0	0.020	0.042	24.030	-0.001	-0.001	0.000	0.000	0.000	0.000
32	J	57	LYS	1	0.868	0.930	25.997	0.092	0.092	0.000	0.000	0.000	0.000
33	J	58	ASP	-1	-0.749	-0.842	28.923	-0.035	-0.035	0.000	0.000	0.000	0.000
34	J	59	GLU	-1	-0.825	-0.902	29.221	-0.069	-0.069	0.000	0.000	0.000	0.000
35	J	60	PHE	0	0.002	-0.019	29.239	-0.002	-0.002	0.000	0.000	0.000	0.000
36	J	61	HIS	0	0.017	0.019	24.149	-0.015	-0.015	0.000	0.000	0.000	0.000
37	J	62	ILE	0	-0.040	-0.026	25.705	0.011	0.011	0.000	0.000	0.000	0.000
38	J	63	VAL	0	-0.009	0.001	19.689	-0.013	-0.013	0.000	0.000	0.000	0.000
39	J	64	GLU	-1	-0.766	-0.871	22.525	-0.053	-0.053	0.000	0.000	0.000	0.000
40	J	65	ILE	0	0.032	0.018	17.719	-0.024	-0.024	0.000	0.000	0.000	0.000
41	J	66	VAL	0	-0.038	-0.024	20.271	0.017	0.017	0.000	0.000	0.000	0.000
42	J	67	ASP	-1	-0.868	-0.928	20.252	-0.077	-0.077	0.000	0.000	0.000	0.000
43	J	68	GLN	0	-0.024	-0.024	22.225	0.011	0.011	0.000	0.000	0.000	0.000
44	J	69	GLU	-1	-0.843	-0.908	24.095	-0.003	-0.003	0.000	0.000	0.000	0.000
45	J	70	GLU	-1	-0.884	-0.937	26.543	-0.025	-0.025	0.000	0.000	0.000	0.000
46	J	71	GLY	0	-0.051	-0.023	29.164	-0.005	-0.005	0.000	0.000	0.000	0.000
47	J	72	ALA	0	-0.040	-0.019	29.801	-0.002	-0.002	0.000	0.000	0.000	0.000
48	J	73	GLU	-1	-0.825	-0.915	26.187	-0.088	-0.088	0.000	0.000	0.000	0.000
49	J	74	LYS	1	0.776	0.892	25.261	0.039	0.039	0.000	0.000	0.000	0.000
50	J	75	VAL	0	-0.011	-0.013	25.050	-0.010	-0.010	0.000	0.000	0.000	0.000
51	J	76	VAL	0	0.026	0.010	22.817	0.011	0.011	0.000	0.000	0.000	0.000
52	J	77	PRO	0	-0.048	-0.032	22.879	-0.007	-0.007	0.000	0.000	0.000	0.000
53	J	78	ILE	0	-0.002	0.007	17.986	0.012	0.012	0.000	0.000	0.000	0.000
54	J	79	ALA	0	0.001	0.001	20.993	0.015	0.015	0.000	0.000	0.000	0.000
55	J	80	THR	0	-0.044	-0.034	22.993	-0.011	-0.011	0.000	0.000	0.000	0.000
56	J	81	LEU	0	-0.033	0.006	21.076	0.009	0.009	0.000	0.000	0.000	0.000
57	J	82	LYS	1	0.825	0.903	25.803	0.027	0.027	0.000	0.000	0.000	0.000
58	J	83	PRO	0	0.015	0.021	26.452	0.009	0.009	0.000	0.000	0.000	0.000
59	J	84	SER	0	-0.082	-0.069	27.770	0.006	0.006	0.000	0.000	0.000	0.000
60	J	85	ILE	0	-0.074	-0.033	29.634	0.005	0.005	0.000	0.000	0.000	0.000
61	J	86	LEU	0	0.007	-0.003	25.075	0.008	0.008	0.000	0.000	0.000	0.000
62	J	87	PRO	0	0.049	0.032	23.301	-0.007	-0.007	0.000	0.000	0.000	0.000
63	J	88	MET	0	-0.005	-0.018	18.102	-0.019	-0.019	0.000	0.000	0.000	0.000
64	J	89	ALA	0	0.025	0.013	19.816	0.013	0.013	0.000	0.000	0.000	0.000
65	J	90	THR	0	-0.006	-0.009	16.415	-0.023	-0.023	0.000	0.000	0.000	0.000
66	J	91	MET	0	-0.054	-0.005	14.835	-0.023	-0.023	0.000	0.000	0.000	0.000
67	J	92	VAL	0	0.021	-0.011	15.335	0.059	0.059	0.000	0.000	0.000	0.000
68	J	93	GLY	0	0.012	0.006	15.451	-0.039	-0.039	0.000	0.000	0.000	0.000
69	J	94	ILE	0	-0.006	0.005	15.059	-0.017	-0.017	0.000	0.000	0.000	0.000
70	J	95	GLU	-1	-0.848	-0.922	10.861	0.678	0.678	0.000	0.000	0.000	0.000
71	J	96	LEU	0	0.019	0.009	11.952	-0.029	-0.029	0.000	0.000	0.000	0.000
72	J	97	ASP	-1	-0.823	-0.899	11.910	0.029	0.029	0.000	0.000	0.000	0.000
73	J	98	PRO	0	-0.076	-0.020	10.867	-0.033	-0.033	0.000	0.000	0.000	0.000
74	J	99	PRO	0	-0.036	-0.003	13.743	0.024	0.024	0.000	0.000	0.000	0.000
75	J	100	VAL	0	0.049	0.015	14.022	0.032	0.032	0.000	0.000	0.000	0.000
76	J	101	THR	0	-0.034	-0.024	15.996	-0.053	-0.053	0.000	0.000	0.000	0.000
77	J	102	PHE	0	0.015	0.003	13.382	0.026	0.026	0.000	0.000	0.000	0.000
78	J	103	ARG	1	0.799	0.886	18.895	0.081	0.081	0.000	0.000	0.000	0.000
79	J	104	LEU	0	-0.027	-0.014	22.294	0.013	0.013	0.000	0.000	0.000	0.000
80	J	105	LYS	1	0.844	0.912	23.992	0.062	0.062	0.000	0.000	0.000	0.000
81	J	106	ALA	0	-0.005	-0.005	26.785	0.007	0.007	0.000	0.000	0.000	0.000
82	J	107	GLY	0	0.020	0.020	26.520	-0.004	-0.004	0.000	0.000	0.000	0.000
83	J	108	SER	0	-0.063	-0.053	26.838	-0.007	-0.007	0.000	0.000	0.000	0.000
84	J	109	GLY	0	0.017	0.018	22.776	-0.014	-0.014	0.000	0.000	0.000	0.000
85	J	110	PRO	0	-0.020	-0.010	19.587	0.014	0.014	0.000	0.000	0.000	0.000
86	J	111	LEU	0	-0.013	-0.008	18.239	0.019	0.019	0.000	0.000	0.000	0.000
87	J	112	TYR	0	-0.047	-0.046	14.311	-0.019	-0.019	0.000	0.000	0.000	0.000
88	J	113	ILE	0	0.008	0.005	13.300	0.056	0.056	0.000	0.000	0.000	0.000
89	J	114	SER	0	-0.028	-0.015	10.010	-0.083	-0.083	0.000	0.000	0.000	0.000
90	J	115	GLY	0	0.083	0.015	8.722	0.165	0.165	0.000	0.000	0.000	0.000
91	J	116	GLN	0	-0.038	-0.009	4.736	-0.882	-0.625	-0.001	-0.048	-0.208	0.000
92	J	117	HIS	0	0.010	0.015	2.209	-2.277	-0.276	1.126	-1.167	-1.960	0.000
93	J	118	VAL	0	0.001	0.012	4.062	1.848	2.030	0.000	-0.008	-0.173	0.000

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