FMO DATABASE

FMODB ID: V51R1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-535018.56396
FMO2-HF: Nuclear repulsion	503116.903242
FMO2-HF: Total energy	-31901.660717
FMO2-MP2: Total energy	-31997.108427

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.
-17.396	-12.117	12.18	-6.594	-10.863	0.006

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 : 0.018 / q_NPA : 0.000

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	B	260	HIS	0	0.034	0.035	3.174	-3.725	-1.671	0.012	-0.973	-1.093	0.003
4	B	261	ILE	0	0.010	0.005	2.755	-2.023	-0.142	0.370	-0.849	-1.403	-0.009
5	B	262	ALA	0	-0.006	-0.004	4.890	0.222	0.274	-0.001	-0.005	-0.045	0.000
6	B	263	ILE	0	0.021	0.012	8.040	-0.069	-0.069	0.000	0.000	0.000	0.000
7	B	264	GLY	0	-0.018	0.012	10.753	0.038	0.038	0.000	0.000	0.000	0.000
8	B	265	ILE	0	-0.006	-0.017	14.320	-0.027	-0.027	0.000	0.000	0.000	0.000
9	B	266	TYR	0	0.022	0.020	17.316	0.020	0.020	0.000	0.000	0.000	0.000
10	B	267	PHE	0	0.029	-0.010	20.964	-0.015	-0.015	0.000	0.000	0.000	0.000
11	B	268	ASN	0	0.015	0.002	23.932	0.009	0.009	0.000	0.000	0.000	0.000
12	B	269	PRO	0	0.034	0.034	27.539	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	270	GLU	-1	-0.915	-0.954	29.893	-0.047	-0.047	0.000	0.000	0.000	0.000
14	B	271	ILE	0	-0.100	-0.038	27.203	0.001	0.001	0.000	0.000	0.000	0.000
15	B	272	ALA	0	-0.007	-0.013	25.552	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	273	PRO	0	0.019	0.014	27.165	0.001	0.001	0.000	0.000	0.000	0.000
17	B	274	ALA	0	0.019	0.010	22.023	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	275	PRO	0	0.007	-0.001	19.619	0.006	0.006	0.000	0.000	0.000	0.000
19	B	276	PHE	0	-0.008	0.002	19.289	-0.012	-0.012	0.000	0.000	0.000	0.000
20	B	277	ILE	0	0.011	0.005	12.701	0.005	0.005	0.000	0.000	0.000	0.000
21	B	278	SER	0	0.002	-0.003	16.036	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	279	LEU	0	-0.035	-0.013	11.357	0.023	0.023	0.000	0.000	0.000	0.000
23	B	280	ILE	0	0.036	0.010	7.188	-0.058	-0.058	0.000	0.000	0.000	0.000
24	B	281	GLU	-1	-0.808	-0.885	7.471	0.069	0.069	0.000	0.000	0.000	0.000
25	B	282	THR	0	-0.024	-0.028	2.137	-1.221	-0.073	1.968	-1.054	-2.062	0.003
26	B	283	ASN	0	-0.032	-0.046	2.098	-6.699	-8.581	7.713	-2.620	-3.210	0.021
27	B	284	GLN	0	0.096	0.034	5.091	-0.829	-0.764	-0.001	-0.006	-0.058	0.000
28	B	285	CYS	0	0.024	0.023	8.159	-0.206	-0.206	0.000	0.000	0.000	0.000
29	B	286	ALA	0	-0.001	0.005	6.163	-0.207	-0.207	0.000	0.000	0.000	0.000
30	B	287	LEU	0	-0.027	-0.011	8.024	-0.170	-0.170	0.000	0.000	0.000	0.000
31	B	288	ALA	0	0.014	0.014	10.330	-0.110	-0.110	0.000	0.000	0.000	0.000
32	B	289	VAL	0	0.012	0.004	10.983	-0.064	-0.064	0.000	0.000	0.000	0.000
33	B	290	ARG	1	0.831	0.898	7.530	-0.299	-0.299	0.000	0.000	0.000	0.000
34	B	291	LYS	1	0.847	0.926	13.257	-0.205	-0.205	0.000	0.000	0.000	0.000
35	B	292	TYR	0	0.030	0.011	15.962	-0.028	-0.028	0.000	0.000	0.000	0.000
36	B	293	ALA	0	0.019	0.001	15.846	-0.019	-0.019	0.000	0.000	0.000	0.000
37	B	294	ASN	0	-0.041	-0.016	17.545	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	295	GLU	-1	-0.834	-0.917	19.422	0.133	0.133	0.000	0.000	0.000	0.000
39	B	296	VAL	0	-0.059	-0.016	20.406	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	297	GLY	0	0.007	0.012	22.381	-0.010	-0.010	0.000	0.000	0.000	0.000
41	B	298	ILE	0	-0.015	-0.006	18.042	-0.012	-0.012	0.000	0.000	0.000	0.000
42	B	299	PRO	0	0.029	0.001	19.110	0.008	0.008	0.000	0.000	0.000	0.000
43	B	300	THR	0	-0.025	0.003	14.906	-0.013	-0.013	0.000	0.000	0.000	0.000
44	B	301	VAL	0	0.006	0.007	16.097	0.005	0.005	0.000	0.000	0.000	0.000
45	B	302	ARG	1	0.840	0.910	10.456	0.184	0.184	0.000	0.000	0.000	0.000
46	B	303	ASP	-1	-0.691	-0.830	12.923	-0.267	-0.267	0.000	0.000	0.000	0.000
47	B	304	VAL	0	-0.024	-0.023	8.691	-0.052	-0.052	0.000	0.000	0.000	0.000
48	B	305	LYS	1	0.943	0.975	9.057	0.198	0.198	0.000	0.000	0.000	0.000
49	B	306	LEU	0	0.081	0.040	10.448	-0.083	-0.083	0.000	0.000	0.000	0.000
50	B	307	ALA	0	-0.010	-0.002	7.966	-0.037	-0.037	0.000	0.000	0.000	0.000
51	B	308	ARG	1	0.936	0.960	5.108	0.703	0.703	0.000	0.000	0.000	0.000
52	B	309	LYS	1	0.836	0.913	6.963	0.237	0.237	0.000	0.000	0.000	0.000
53	B	310	LEU	0	0.062	0.059	10.342	-0.015	-0.015	0.000	0.000	0.000	0.000
54	B	311	TYR	0	-0.013	-0.009	2.675	-3.357	-1.396	2.119	-1.087	-2.992	-0.012
55	B	312	LYS	1	0.846	0.919	5.465	1.124	1.124	0.000	0.000	0.000	0.000
56	B	313	THR	0	0.011	-0.007	8.480	0.083	0.083	0.000	0.000	0.000	0.000
57	B	314	HIS	0	0.016	0.030	10.868	0.094	0.094	0.000	0.000	0.000	0.000
58	B	315	THR	0	0.011	0.011	10.560	-0.071	-0.071	0.000	0.000	0.000	0.000
59	B	316	LYS	1	0.795	0.890	10.562	0.083	0.083	0.000	0.000	0.000	0.000
60	B	317	TYR	0	-0.018	-0.018	13.370	0.008	0.008	0.000	0.000	0.000	0.000
61	B	318	SER	0	-0.005	0.002	14.995	0.006	0.006	0.000	0.000	0.000	0.000
62	B	319	PHE	0	0.018	-0.003	17.735	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	320	VAL	0	-0.042	-0.023	16.567	-0.018	-0.018	0.000	0.000	0.000	0.000
64	B	321	ASP	-1	-0.776	-0.874	17.162	-0.234	-0.234	0.000	0.000	0.000	0.000
65	B	322	PHE	0	0.030	-0.016	19.760	0.001	0.001	0.000	0.000	0.000	0.000
66	B	323	GLU	-1	-0.967	-0.964	19.097	-0.201	-0.201	0.000	0.000	0.000	0.000
67	B	324	HIS	0	-0.087	-0.080	14.800	-0.047	-0.047	0.000	0.000	0.000	0.000
68	B	325	LEU	0	-0.018	0.006	18.203	0.000	0.000	0.000	0.000	0.000	0.000
69	B	326	ASP	-1	-0.814	-0.924	20.968	-0.118	-0.118	0.000	0.000	0.000	0.000
70	B	327	GLU	-1	-0.874	-0.926	15.366	-0.276	-0.276	0.000	0.000	0.000	0.000
71	B	328	VAL	0	0.016	0.006	15.874	-0.007	-0.007	0.000	0.000	0.000	0.000
72	B	329	LEU	0	0.028	0.016	18.308	0.013	0.013	0.000	0.000	0.000	0.000
73	B	330	ARG	1	0.825	0.894	16.383	0.192	0.192	0.000	0.000	0.000	0.000
74	B	331	LEU	0	-0.060	-0.030	16.264	0.009	0.009	0.000	0.000	0.000	0.000
75	B	332	ILE	0	-0.015	-0.007	20.768	0.012	0.012	0.000	0.000	0.000	0.000
76	B	333	VAL	0	0.042	0.019	22.913	0.009	0.009	0.000	0.000	0.000	0.000
77	B	334	TRP	0	-0.015	-0.002	22.894	0.007	0.007	0.000	0.000	0.000	0.000
78	B	335	LEU	0	-0.047	-0.033	20.529	0.008	0.008	0.000	0.000	0.000	0.000
79	B	336	GLU	-1	-0.991	-0.977	25.081	-0.038	-0.038	0.000	0.000	0.000	0.000
80	B	337	GLN	0	0.000	-0.005	28.421	0.004	0.004	0.000	0.000	0.000	0.000
81	B	338	VAL	0	-0.093	-0.029	27.465	0.007	0.007	0.000	0.000	0.000	0.000

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