FMO DATABASE

FMODB ID: VRL91

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

Total energy (hartree)

FMO2-HF: Electronic energy	-468319.916616
FMO2-HF: Nuclear repulsion	438850.480314
FMO2-HF: Total energy	-29469.436302
FMO2-MP2: Total energy	-29554.01634

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.
0.614	2.183	-0.009	-0.592	-0.967	0.002

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 : 0.012 / q_NPA : -0.005

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	-0.005	3.858	-0.273	1.227	-0.008	-0.591	-0.901	0.002
4	A	7	SER	0	0.051	0.007	5.173	0.303	0.372	-0.001	-0.001	-0.066	0.000
5	A	8	TYR	0	-0.015	-0.019	7.686	0.125	0.125	0.000	0.000	0.000	0.000
6	A	9	LYS	1	1.014	0.999	8.983	0.995	0.995	0.000	0.000	0.000	0.000
7	A	10	MET	0	-0.030	-0.002	8.374	0.113	0.113	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.041	0.019	11.162	0.068	0.068	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.822	-0.908	13.391	-0.281	-0.281	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.098	-0.047	12.870	0.003	0.003	0.000	0.000	0.000	0.000
11	A	14	MET	0	0.002	0.015	14.812	0.035	0.035	0.000	0.000	0.000	0.000
12	A	15	TYR	0	-0.002	-0.040	17.500	0.009	0.009	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.951	0.979	17.554	0.149	0.149	0.000	0.000	0.000	0.000
14	A	17	ILE	0	-0.031	-0.020	18.531	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.016	-0.008	21.695	0.009	0.009	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.796	-0.876	23.490	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	20	LYS	1	0.883	0.950	23.814	0.013	0.013	0.000	0.000	0.000	0.000
18	A	21	LYS	1	0.820	0.893	23.812	-0.124	-0.124	0.000	0.000	0.000	0.000
19	A	22	GLY	0	0.035	0.033	26.900	0.005	0.005	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.865	-0.940	26.256	0.083	0.083	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.023	0.003	19.865	0.008	0.008	0.000	0.000	0.000	0.000
22	A	25	THR	0	-0.029	-0.046	21.412	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	26	LEU	0	0.013	0.006	15.357	0.005	0.005	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.738	-0.851	17.304	0.275	0.275	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.762	-0.857	19.345	0.169	0.169	0.000	0.000	0.000	0.000
26	A	29	ILE	0	-0.021	-0.021	13.174	0.005	0.005	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.063	-0.037	13.970	0.052	0.052	0.000	0.000	0.000	0.000
28	A	31	ALA	0	0.013	0.009	15.715	0.032	0.032	0.000	0.000	0.000	0.000
29	A	32	GLN	0	-0.054	-0.020	15.985	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	33	PHE	0	-0.045	-0.043	11.296	-0.047	-0.047	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.895	-0.926	12.396	0.493	0.493	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.054	-0.007	8.823	0.159	0.159	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.043	0.015	9.641	-0.137	-0.137	0.000	0.000	0.000	0.000
34	A	37	VAL	0	0.075	0.021	11.464	0.025	0.025	0.000	0.000	0.000	0.000
35	A	38	PRO	0	0.031	0.000	10.356	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.016	-0.008	7.645	0.151	0.151	0.000	0.000	0.000	0.000
37	A	40	ALA	0	0.052	0.028	8.943	-0.153	-0.153	0.000	0.000	0.000	0.000
38	A	41	TYR	0	0.039	0.006	12.090	-0.133	-0.133	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.014	0.004	8.110	-0.249	-0.249	0.000	0.000	0.000	0.000
40	A	43	ILE	0	-0.006	0.008	8.881	-0.136	-0.136	0.000	0.000	0.000	0.000
41	A	44	GLN	0	0.014	0.012	11.707	-0.097	-0.097	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.886	0.935	9.883	-0.453	-0.453	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.018	-0.008	11.264	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.032	0.017	13.421	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.798	0.888	16.401	-0.116	-0.116	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.008	0.002	15.265	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.044	-0.011	14.597	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	51	CYS	0	-0.038	-0.036	18.353	0.007	0.007	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.808	-0.878	21.093	0.066	0.066	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.850	0.930	15.162	0.109	0.109	0.000	0.000	0.000	0.000
51	A	54	HIS	1	0.823	0.903	22.325	0.037	0.037	0.000	0.000	0.000	0.000
52	A	55	PRO	0	0.041	0.029	25.100	0.007	0.007	0.000	0.000	0.000	0.000
53	A	56	ASP	-1	-0.819	-0.891	27.811	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.808	-0.878	24.989	-0.040	-0.040	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.809	-0.887	26.074	0.054	0.054	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.009	-0.019	22.325	0.011	0.011	0.000	0.000	0.000	0.000
57	A	61	GLN	0	0.027	0.015	24.997	0.010	0.010	0.000	0.000	0.000	0.000
58	A	62	TYR	0	-0.012	-0.013	23.439	0.011	0.011	0.000	0.000	0.000	0.000
59	A	63	LYS	1	0.887	0.933	26.392	-0.119	-0.119	0.000	0.000	0.000	0.000
60	A	64	ASN	0	0.037	0.010	27.749	0.014	0.014	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.952	0.982	28.655	-0.121	-0.121	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.780	0.885	23.466	-0.190	-0.190	0.000	0.000	0.000	0.000
63	A	67	THR	0	0.001	0.004	21.560	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.086	-0.052	23.617	0.010	0.010	0.000	0.000	0.000	0.000
65	A	69	PHE	0	-0.018	-0.003	19.341	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.881	0.935	23.996	-0.064	-0.064	0.000	0.000	0.000	0.000
67	A	71	TRP	0	0.001	-0.011	23.709	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	72	ILE	0	-0.046	-0.027	28.255	0.004	0.004	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.761	0.897	27.163	0.027	0.027	0.000	0.000	0.000	0.000

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