FMO DATABASE

FMODB ID: YVG82

Calculation Name: 2VC8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VC8

Chain ID: A

ChEMBL ID:

UniProt ID: Q96F86

Base Structure: X-ray

Registration Date: 2023-09-23

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-400768.010049
FMO2-HF: Nuclear repulsion	373669.60556
FMO2-HF: Total energy	-27098.404488
FMO2-MP2: Total energy	-27177.311676

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:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-4.358	0.46	6.608	-4.4	-7.03	-0.011

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.027

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	TRP	0	0.036	0.017	3.622	0.101	2.096	-0.009	-0.785	-1.202	0.000
4	A	6	LEU	0	-0.003	0.020	3.493	0.851	1.412	0.012	-0.165	-0.409	0.000
5	A	7	GLY	0	0.020	0.019	5.344	0.133	0.140	-0.001	-0.001	-0.005	0.000
6	A	8	SER	0	-0.046	-0.024	8.565	0.426	0.426	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.045	-0.031	10.647	0.100	0.100	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.030	0.021	10.484	0.003	0.003	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.031	-0.046	13.739	0.045	0.045	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.037	0.015	10.965	0.006	0.006	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.033	-0.020	15.183	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	14	CYS	0	0.015	0.000	16.362	0.029	0.029	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.051	0.037	18.831	0.009	0.009	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.895	-0.954	22.269	0.054	0.054	0.000	0.000	0.000	0.000
15	A	17	SER	0	-0.052	-0.023	24.376	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.012	0.000	20.073	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.000	0.011	22.793	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	20	VAL	0	0.009	0.001	19.188	0.011	0.011	0.000	0.000	0.000	0.000
19	A	21	TYR	0	-0.049	-0.025	16.921	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	22	GLN	0	0.036	0.031	16.554	0.001	0.001	0.000	0.000	0.000	0.000
21	A	23	GLY	0	0.014	0.009	15.501	0.029	0.029	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.875	0.943	12.006	0.656	0.656	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.013	0.006	6.749	0.129	0.129	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.072	-0.066	9.079	-0.196	-0.196	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.037	0.013	6.693	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	28	VAL	0	-0.017	-0.017	2.399	-0.865	-0.120	1.414	-0.773	-1.386	0.000
27	A	29	ASP	-1	-0.795	-0.863	3.206	-0.618	0.475	0.075	-0.584	-0.584	-0.005
28	A	30	GLN	0	0.001	-0.008	2.100	-4.062	-3.766	5.118	-2.088	-3.327	-0.006
29	A	31	VAL	0	-0.044	-0.019	5.504	-0.157	-0.157	0.000	0.000	0.000	0.000
30	A	32	SER	0	-0.049	-0.048	8.839	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	33	GLN	0	-0.061	-0.016	7.710	-0.150	-0.150	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.007	-0.002	7.641	-0.135	-0.135	0.000	0.000	0.000	0.000
33	A	35	ILE	0	-0.004	0.004	6.376	0.133	0.133	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.000	-0.010	7.895	0.100	0.100	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.007	0.007	10.067	-0.167	-0.167	0.000	0.000	0.000	0.000
36	A	38	THR	0	0.031	0.017	12.887	0.078	0.078	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.840	0.894	15.376	0.253	0.253	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.052	0.046	16.489	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	41	PHE	0	0.024	0.003	18.438	0.029	0.029	0.000	0.000	0.000	0.000
40	A	42	HIS	1	0.876	0.923	20.483	0.024	0.024	0.000	0.000	0.000	0.000
41	A	43	ASN	0	-0.018	-0.011	22.923	0.000	0.000	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.047	0.034	25.287	0.003	0.003	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.007	-0.005	26.093	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.875	0.941	22.548	0.103	0.103	0.000	0.000	0.000	0.000
45	A	47	CYS	0	-0.013	-0.002	21.054	0.020	0.020	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.008	0.000	23.166	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.011	0.013	19.808	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	50	PRO	0	-0.011	-0.010	19.567	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.801	-0.865	12.415	-0.251	-0.251	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.036	-0.005	15.297	0.034	0.034	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.008	-0.005	10.959	-0.042	-0.042	0.000	0.000	0.000	0.000
52	A	54	PHE	0	-0.004	-0.004	11.723	0.006	0.006	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.866	0.883	10.885	-0.257	-0.257	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.032	0.002	8.814	-0.079	-0.079	0.000	0.000	0.000	0.000
55	A	57	GLY	0	-0.018	-0.010	10.877	-0.065	-0.065	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.802	-0.855	14.234	0.236	0.236	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.045	-0.018	10.871	-0.068	-0.068	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.010	-0.002	15.045	0.025	0.025	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.854	-0.938	16.796	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.002	0.003	9.708	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.836	0.930	14.303	0.048	0.048	0.000	0.000	0.000	0.000
62	A	64	ILE	0	0.037	0.009	11.382	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.092	-0.046	14.372	0.056	0.056	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.893	-0.940	15.098	-0.461	-0.461	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.007	0.005	12.501	-0.100	-0.100	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.002	-0.005	8.189	0.153	0.153	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.016	0.026	10.602	0.140	0.140	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.008	0.005	11.662	-0.141	-0.141	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.005	-0.009	12.413	0.110	0.110	0.000	0.000	0.000	0.000
70	A	72	ASH	0	-0.046	-0.031	10.397	-0.141	-0.141	0.000	0.000	0.000	0.000
71	A	73	ASN	0	-0.001	-0.012	7.348	0.061	0.061	0.000	0.000	0.000	0.000
72	A	74	GLN	0	0.019	0.027	4.345	-0.340	-0.219	-0.001	-0.004	-0.117	0.000

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