FMO DATABASE

FMODB ID: 536VZ

Calculation Name: 2VQC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VQC

Chain ID: A

ChEMBL ID:

UniProt ID: P20220

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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467274.625625
FMO2-HF: Nuclear repulsion	437805.698027
FMO2-HF: Total energy	-29468.927597
FMO2-MP2: Total energy	-29553.476245

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:4:THR)

Summations of interaction energy for fragment #1(A:4: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.
1.385	4.086	-0.01	-1.277	-1.415	0.006

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.023

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	6	ASN	0	-0.010	-0.011	3.715	-0.176	2.479	-0.009	-1.276	-1.371	0.006
4	A	7	SER	0	0.069	0.012	5.121	0.214	0.260	-0.001	-0.001	-0.044	0.000
5	A	8	TYR	0	0.028	0.017	7.660	0.105	0.105	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.991	0.994	8.227	1.523	1.523	0.000	0.000	0.000	0.000
7	A	10	MET	0	-0.011	0.003	8.353	0.022	0.022	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.032	0.014	10.958	0.129	0.129	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.862	-0.948	13.289	-0.565	-0.565	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.081	-0.032	12.895	0.063	0.063	0.000	0.000	0.000	0.000
11	A	14	MET	0	-0.013	0.002	14.784	0.080	0.080	0.000	0.000	0.000	0.000
12	A	15	TYR	0	0.001	-0.027	17.295	0.055	0.055	0.000	0.000	0.000	0.000
13	A	16	LYS	1	1.006	1.000	18.441	0.576	0.576	0.000	0.000	0.000	0.000
14	A	17	ILE	0	-0.049	-0.024	18.672	0.024	0.024	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.015	-0.010	21.446	0.029	0.029	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.934	-0.948	23.248	-0.235	-0.235	0.000	0.000	0.000	0.000
17	A	20	LYS	1	0.876	0.945	23.934	0.375	0.375	0.000	0.000	0.000	0.000
18	A	21	LYS	1	0.899	0.961	24.035	0.256	0.256	0.000	0.000	0.000	0.000
19	A	22	GLY	0	0.023	0.016	26.848	0.018	0.018	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.954	-0.999	26.428	-0.118	-0.118	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.053	-0.021	19.669	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	25	THR	0	-0.037	-0.029	21.911	0.024	0.024	0.000	0.000	0.000	0.000
23	A	26	LEU	0	0.010	0.001	15.372	-0.030	-0.030	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.775	-0.864	17.715	-0.179	-0.179	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.789	-0.894	19.519	-0.279	-0.279	0.000	0.000	0.000	0.000
26	A	29	ILE	0	-0.039	-0.025	13.578	-0.057	-0.057	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.071	-0.044	14.253	-0.079	-0.079	0.000	0.000	0.000	0.000
28	A	31	ALA	0	0.003	0.013	15.697	-0.040	-0.040	0.000	0.000	0.000	0.000
29	A	32	GLN	0	-0.025	-0.001	15.522	0.030	0.030	0.000	0.000	0.000	0.000
30	A	33	PHE	0	-0.059	-0.060	11.117	-0.087	-0.087	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.906	-0.923	11.975	-0.647	-0.647	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.049	-0.008	8.869	-0.055	-0.055	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.037	0.004	10.067	0.092	0.092	0.000	0.000	0.000	0.000
34	A	37	VAL	0	0.087	0.026	12.061	-0.045	-0.045	0.000	0.000	0.000	0.000
35	A	38	PRO	0	0.001	-0.013	10.601	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.005	-0.002	7.742	0.062	0.062	0.000	0.000	0.000	0.000
37	A	40	ALA	0	0.055	0.033	9.137	-0.119	-0.119	0.000	0.000	0.000	0.000
38	A	41	TYR	0	0.018	0.000	12.205	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.039	-0.015	7.532	0.083	0.083	0.000	0.000	0.000	0.000
40	A	43	ILE	0	0.008	0.013	9.226	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	44	GLN	0	0.040	0.018	11.602	0.005	0.005	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.919	0.961	10.478	-0.199	-0.199	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.007	-0.004	11.204	0.021	0.021	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.003	0.001	13.332	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.925	0.963	16.106	0.067	0.067	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.022	0.020	15.702	0.013	0.013	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.060	-0.032	14.521	0.011	0.011	0.000	0.000	0.000	0.000
48	A	51	CYS	0	-0.072	-0.037	18.367	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.910	-0.952	20.823	-0.046	-0.046	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.881	0.951	15.883	0.201	0.201	0.000	0.000	0.000	0.000
51	A	54	HIS	1	0.873	0.946	21.156	0.208	0.208	0.000	0.000	0.000	0.000
52	A	55	PRO	0	0.057	0.035	25.085	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	56	ASP	-1	-0.894	-0.944	27.482	-0.129	-0.129	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.840	-0.892	25.319	-0.211	-0.211	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.827	-0.914	25.916	-0.077	-0.077	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.036	-0.029	22.392	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	61	GLN	0	-0.017	-0.016	25.145	0.016	0.016	0.000	0.000	0.000	0.000
58	A	62	TYR	0	-0.033	-0.017	23.251	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	63	LYS	1	0.953	0.980	26.604	0.089	0.089	0.000	0.000	0.000	0.000
60	A	64	ASN	0	0.025	-0.007	27.713	0.003	0.003	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.928	0.995	28.661	0.077	0.077	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.878	0.888	24.095	0.107	0.107	0.000	0.000	0.000	0.000
63	A	67	THR	0	0.001	-0.002	21.283	0.006	0.006	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.065	-0.023	23.261	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	69	PHE	0	-0.020	-0.005	18.948	0.012	0.012	0.000	0.000	0.000	0.000
66	A	70	LYS	1	1.008	1.003	24.114	0.102	0.102	0.000	0.000	0.000	0.000
67	A	71	TRP	0	0.040	0.014	24.012	0.000	0.000	0.000	0.000	0.000	0.000
68	A	72	ILE	0	-0.056	-0.035	27.892	0.008	0.008	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.864	0.955	28.343	0.190	0.190	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)