FMO DATABASE

FMODB ID: YZKY2

Calculation Name: 2VT1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VT1

Chain ID: B

ChEMBL ID:

UniProt ID: P0A1M8

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-533240.29503
FMO2-HF: Nuclear repulsion	501338.870596
FMO2-HF: Total energy	-31901.424434
FMO2-MP2: Total energy	-31996.830841

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:258:PRO)

Summations of interaction energy for fragment #1(B:258:PRO)

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.
-9.371	-2.494	3.226	-3.099	-7.003	-0.002

Interaction energy analysis for fragmet #1(B:258:PRO)

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 : -0.012

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	B	260	HIS	0	0.018	0.024	3.806	-3.209	-1.199	-0.006	-0.961	-1.043	0.005
4	B	261	ILE	0	0.033	0.026	2.621	0.946	2.057	0.293	-0.293	-1.111	0.000
5	B	262	ALA	0	-0.040	-0.018	5.075	-0.200	-0.156	-0.001	-0.004	-0.038	0.000
6	B	263	ILE	0	0.036	0.012	7.383	-0.040	-0.040	0.000	0.000	0.000	0.000
7	B	264	GLY	0	-0.022	0.008	10.612	0.014	0.014	0.000	0.000	0.000	0.000
8	B	265	ILE	0	0.001	-0.016	14.211	-0.033	-0.033	0.000	0.000	0.000	0.000
9	B	266	TYR	0	0.016	0.011	16.911	0.013	0.013	0.000	0.000	0.000	0.000
10	B	267	PHE	0	0.009	-0.022	20.467	-0.011	-0.011	0.000	0.000	0.000	0.000
11	B	268	ASN	0	0.025	0.012	23.424	0.005	0.005	0.000	0.000	0.000	0.000
12	B	269	PRO	0	0.036	0.024	26.993	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	270	GLU	-1	-0.915	-0.951	29.105	-0.015	-0.015	0.000	0.000	0.000	0.000
14	B	271	ILE	0	-0.101	-0.037	27.184	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	272	ALA	0	0.003	-0.009	25.620	-0.005	-0.005	0.000	0.000	0.000	0.000
16	B	273	PRO	0	0.007	0.010	26.698	0.003	0.003	0.000	0.000	0.000	0.000
17	B	274	ALA	0	0.014	0.010	21.697	-0.001	-0.001	0.000	0.000	0.000	0.000
18	B	275	PRO	0	0.012	0.000	18.855	0.006	0.006	0.000	0.000	0.000	0.000
19	B	276	PHE	0	0.001	0.011	19.099	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	277	ILE	0	0.012	0.006	12.512	0.016	0.016	0.000	0.000	0.000	0.000
21	B	278	SER	0	0.007	0.001	15.734	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	279	LEU	0	-0.032	-0.016	11.249	0.022	0.022	0.000	0.000	0.000	0.000
23	B	280	ILE	0	0.027	0.008	7.294	-0.033	-0.033	0.000	0.000	0.000	0.000
24	B	281	GLU	-1	-0.850	-0.898	8.021	0.335	0.335	0.000	0.000	0.000	0.000
25	B	282	THR	0	-0.009	-0.034	3.009	-1.562	-0.187	0.257	-0.459	-1.173	0.002
26	B	283	ASN	0	-0.038	-0.050	2.682	-1.196	-0.241	0.131	-0.392	-0.695	0.001
27	B	284	GLN	0	0.090	0.031	6.231	-0.479	-0.479	0.000	0.000	0.000	0.000
28	B	285	CYS	0	0.052	0.027	9.026	-0.156	-0.156	0.000	0.000	0.000	0.000
29	B	286	ALA	0	0.010	0.014	6.935	-0.176	-0.176	0.000	0.000	0.000	0.000
30	B	287	LEU	0	-0.035	-0.022	8.987	-0.202	-0.202	0.000	0.000	0.000	0.000
31	B	288	ALA	0	0.001	0.012	11.433	-0.116	-0.116	0.000	0.000	0.000	0.000
32	B	289	VAL	0	0.014	0.003	11.661	-0.072	-0.072	0.000	0.000	0.000	0.000
33	B	290	ARG	1	0.832	0.913	7.911	-0.705	-0.705	0.000	0.000	0.000	0.000
34	B	291	LYS	1	0.917	0.978	14.189	-0.250	-0.250	0.000	0.000	0.000	0.000
35	B	292	TYR	0	0.045	0.026	16.958	-0.032	-0.032	0.000	0.000	0.000	0.000
36	B	293	ALA	0	0.021	0.006	16.619	-0.025	-0.025	0.000	0.000	0.000	0.000
37	B	294	ASN	0	-0.057	-0.028	18.369	-0.021	-0.021	0.000	0.000	0.000	0.000
38	B	295	GLU	-1	-0.877	-0.954	20.227	0.163	0.163	0.000	0.000	0.000	0.000
39	B	296	VAL	0	-0.062	-0.023	21.207	-0.013	-0.013	0.000	0.000	0.000	0.000
40	B	297	GLY	0	-0.005	0.008	23.105	-0.011	-0.011	0.000	0.000	0.000	0.000
41	B	298	ILE	0	-0.029	-0.010	18.486	-0.012	-0.012	0.000	0.000	0.000	0.000
42	B	299	PRO	0	0.023	0.007	19.576	0.016	0.016	0.000	0.000	0.000	0.000
43	B	300	THR	0	-0.043	-0.015	15.100	0.012	0.012	0.000	0.000	0.000	0.000
44	B	301	VAL	0	0.049	0.022	15.488	0.000	0.000	0.000	0.000	0.000	0.000
45	B	302	ARG	1	0.870	0.941	9.930	-0.073	-0.073	0.000	0.000	0.000	0.000
46	B	303	ASP	-1	-0.701	-0.857	12.346	-0.127	-0.127	0.000	0.000	0.000	0.000
47	B	304	VAL	0	-0.043	-0.033	8.380	-0.031	-0.031	0.000	0.000	0.000	0.000
48	B	305	LYS	1	0.963	0.981	8.867	0.122	0.122	0.000	0.000	0.000	0.000
49	B	306	LEU	0	0.089	0.054	10.596	-0.066	-0.066	0.000	0.000	0.000	0.000
50	B	307	ALA	0	-0.017	-0.012	7.452	-0.033	-0.033	0.000	0.000	0.000	0.000
51	B	308	ARG	1	0.941	0.957	4.919	0.404	0.404	0.000	0.000	0.000	0.000
52	B	309	LYS	1	0.905	0.950	6.971	0.081	0.081	0.000	0.000	0.000	0.000
53	B	310	LEU	0	0.050	0.055	9.973	-0.033	-0.033	0.000	0.000	0.000	0.000
54	B	311	TYR	0	-0.029	-0.017	2.427	-3.191	-1.809	2.552	-0.990	-2.943	-0.010
55	B	312	LYS	1	0.856	0.921	5.144	1.027	1.027	0.000	0.000	0.000	0.000
56	B	313	THR	0	0.006	-0.010	7.872	0.075	0.075	0.000	0.000	0.000	0.000
57	B	314	HIS	0	0.012	0.035	10.352	0.093	0.093	0.000	0.000	0.000	0.000
58	B	315	THR	0	0.026	0.020	10.276	-0.064	-0.064	0.000	0.000	0.000	0.000
59	B	316	LYS	1	0.817	0.900	11.708	-0.069	-0.069	0.000	0.000	0.000	0.000
60	B	317	TYR	0	-0.025	-0.023	13.633	0.000	0.000	0.000	0.000	0.000	0.000
61	B	318	SER	0	-0.007	0.001	15.197	-0.006	-0.006	0.000	0.000	0.000	0.000
62	B	319	PHE	0	0.013	-0.003	17.549	0.004	0.004	0.000	0.000	0.000	0.000
63	B	320	VAL	0	-0.031	-0.013	15.965	-0.016	-0.016	0.000	0.000	0.000	0.000
64	B	321	ASP	-1	-0.786	-0.881	16.764	-0.179	-0.179	0.000	0.000	0.000	0.000
65	B	322	PHE	0	0.021	-0.020	19.477	0.002	0.002	0.000	0.000	0.000	0.000
66	B	323	GLU	-1	-0.959	-0.957	19.066	-0.154	-0.154	0.000	0.000	0.000	0.000
67	B	324	HIS	0	-0.094	-0.082	15.271	-0.025	-0.025	0.000	0.000	0.000	0.000
68	B	325	LEU	0	-0.019	0.000	18.229	0.006	0.006	0.000	0.000	0.000	0.000
69	B	326	ASP	-1	-0.807	-0.920	20.612	-0.058	-0.058	0.000	0.000	0.000	0.000
70	B	327	GLU	-1	-0.911	-0.944	15.576	-0.164	-0.164	0.000	0.000	0.000	0.000
71	B	328	VAL	0	-0.005	-0.005	15.561	0.006	0.006	0.000	0.000	0.000	0.000
72	B	329	LEU	0	0.035	0.020	18.165	0.015	0.015	0.000	0.000	0.000	0.000
73	B	330	ARG	1	0.834	0.898	16.650	0.084	0.084	0.000	0.000	0.000	0.000
74	B	331	LEU	0	-0.074	-0.036	16.040	0.009	0.009	0.000	0.000	0.000	0.000
75	B	332	ILE	0	-0.001	-0.004	20.509	0.010	0.010	0.000	0.000	0.000	0.000
76	B	333	VAL	0	0.040	0.021	22.649	0.005	0.005	0.000	0.000	0.000	0.000
77	B	334	TRP	0	-0.023	-0.001	22.570	0.003	0.003	0.000	0.000	0.000	0.000
78	B	335	LEU	0	-0.047	-0.041	20.326	0.006	0.006	0.000	0.000	0.000	0.000
79	B	336	GLU	-1	-0.989	-0.979	24.841	0.003	0.003	0.000	0.000	0.000	0.000
80	B	337	GLN	0	-0.019	-0.009	28.022	0.001	0.001	0.000	0.000	0.000	0.000
81	B	338	VAL	0	-0.073	-0.014	27.619	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:258:PRO)