FMO DATABASE

FMODB ID: QVG2Y

Calculation Name: 2VIM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VIM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9U1G7

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	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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-820540.006505
FMO2-HF: Nuclear repulsion	779437.117332
FMO2-HF: Total energy	-41102.889173
FMO2-MP2: Total energy	-41222.410274

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:1:MET)

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

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.
-16.457	-7.596	12.864	-6.043	-15.683	-0.019

Interaction energy analysis for fragmet #1(A:1:MET)

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 : -0.019

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	A	3	VAL	0	0.023	0.013	3.803	-0.223	1.317	-0.010	-0.551	-0.979	0.003
4	A	4	LEU	0	-0.029	-0.012	6.038	-0.137	-0.137	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.016	0.026	9.017	0.079	0.079	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.037	-0.004	12.274	-0.016	-0.016	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.030	0.006	13.467	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.068	0.036	15.207	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.872	-0.915	11.267	0.099	0.099	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.004	0.010	10.213	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.926	-0.970	12.073	-0.051	-0.051	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.807	0.894	13.056	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.021	0.012	6.713	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.037	0.015	10.561	-0.050	-0.050	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.006	0.001	13.064	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.894	-0.931	9.212	-0.145	-0.145	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.062	-0.041	8.879	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.937	0.984	12.318	0.105	0.105	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.034	0.015	15.795	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.816	0.914	8.763	0.487	0.487	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.020	-0.002	10.844	0.022	0.022	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.007	0.002	7.856	-0.108	-0.108	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.017	-0.016	5.827	0.066	0.066	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.003	-0.010	6.035	0.180	0.180	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.877	-0.948	4.058	-0.892	-0.668	0.000	-0.052	-0.172	0.000
26	A	26	PHE	0	0.006	-0.002	5.950	0.482	0.482	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.010	-0.030	7.481	-0.082	-0.082	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.130	0.054	9.863	0.022	0.022	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.006	-0.013	10.087	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	30	TRP	0	-0.024	-0.020	13.557	-0.049	-0.049	0.000	0.000	0.000	0.000
31	A	31	CYS	0	0.032	0.048	9.355	-0.146	-0.146	0.000	0.000	0.000	0.000
32	A	32	GLY	0	-0.001	-0.005	13.225	0.015	0.015	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.009	-0.012	13.178	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.911	0.957	8.566	-0.174	-0.174	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.041	-0.024	9.735	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.020	-0.005	6.974	-0.038	-0.038	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.068	0.043	5.152	-0.328	-0.328	0.000	0.000	0.000	0.000
38	A	39	PRO	0	0.014	0.002	4.171	-0.814	-0.669	-0.001	-0.025	-0.119	0.000
39	A	40	LYS	1	0.841	0.904	6.123	0.294	0.294	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.019	0.017	2.384	-0.082	-0.993	3.588	-0.607	-2.070	-0.001
41	A	42	GLU	-1	-0.898	-0.955	2.010	-2.376	-1.047	3.821	-1.283	-3.867	-0.007
42	A	43	ALA	0	-0.078	-0.045	3.233	0.733	0.450	0.041	0.484	-0.243	0.000
43	A	44	LEU	0	0.031	0.002	5.416	0.225	0.225	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.005	0.002	2.638	-0.606	0.258	0.293	-0.283	-0.874	-0.002
45	A	46	LYS	1	0.885	0.944	4.739	1.022	1.155	-0.001	-0.012	-0.120	0.000
46	A	47	GLU	-1	-0.857	-0.881	7.564	-0.485	-0.485	0.000	0.000	0.000	0.000
47	A	48	ILE	0	-0.031	-0.017	8.403	0.192	0.192	0.000	0.000	0.000	0.000
48	A	49	PRO	0	0.054	0.022	7.705	-0.151	-0.151	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.918	-0.930	8.797	-0.403	-0.403	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.032	-0.022	7.621	0.105	0.105	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.875	-0.915	5.057	-1.479	-1.429	-0.001	-0.001	-0.047	0.000
52	A	53	PHE	0	-0.008	0.004	2.530	-1.610	-0.055	0.674	-0.524	-1.706	-0.002
53	A	54	ALA	0	-0.012	-0.015	2.615	-3.906	-1.201	1.412	-2.098	-2.018	-0.020
54	A	55	LYS	1	0.894	0.952	2.148	-6.850	-5.346	3.049	-1.078	-3.475	0.010
55	A	56	VAL	0	0.003	0.006	5.366	-0.502	-0.496	-0.001	-0.013	0.007	0.000
56	A	57	ASP	-1	-0.824	-0.898	9.072	0.468	0.468	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.006	-0.042	11.045	-0.075	-0.075	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.853	-0.902	14.097	0.182	0.182	0.000	0.000	0.000	0.000
59	A	60	GLN	0	-0.086	-0.041	12.365	0.023	0.023	0.000	0.000	0.000	0.000
60	A	61	ASN	0	-0.060	-0.047	11.980	-0.079	-0.079	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.861	-0.931	15.075	0.108	0.108	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.830	-0.911	17.778	0.060	0.060	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.028	0.003	13.775	-0.025	-0.025	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.016	0.007	14.860	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.006	-0.005	15.776	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.825	0.905	18.051	-0.061	-0.061	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.003	0.012	15.243	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.016	-0.001	17.241	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.052	-0.025	13.102	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.014	0.004	16.330	0.013	0.013	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.043	0.001	16.204	0.012	0.012	0.000	0.000	0.000	0.000
72	A	73	MET	0	0.020	0.052	12.730	0.024	0.024	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.040	-0.006	8.785	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.036	-0.030	10.407	-0.066	-0.066	0.000	0.000	0.000	0.000
75	A	76	PHE	0	-0.021	0.002	4.887	0.083	0.083	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.011	0.006	9.318	0.004	0.004	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.032	-0.013	9.444	-0.054	-0.054	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.034	0.010	11.996	0.049	0.049	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.892	0.935	13.328	0.245	0.245	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.859	-0.917	15.892	-0.105	-0.105	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.012	-0.019	16.406	0.020	0.020	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.839	0.929	17.667	0.143	0.143	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.767	-0.850	15.354	-0.131	-0.131	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.054	-0.037	15.417	0.011	0.011	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.788	-0.884	14.382	-0.254	-0.254	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.751	0.827	13.297	0.078	0.078	0.000	0.000	0.000	0.000
87	A	88	PHE	0	-0.058	-0.020	10.248	0.019	0.019	0.000	0.000	0.000	0.000
88	A	89	SER	0	0.005	-0.004	12.527	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.020	0.005	12.730	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.010	0.001	10.682	-0.058	-0.058	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.030	-0.015	11.617	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.744	-0.861	10.572	-0.611	-0.611	0.000	0.000	0.000	0.000
93	A	94	THR	0	0.023	0.002	11.812	-0.065	-0.065	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.994	1.016	13.851	0.214	0.214	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.006	0.005	6.108	0.012	0.012	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.815	0.864	10.555	0.652	0.652	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.918	-0.952	11.988	-0.264	-0.264	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.077	-0.051	12.172	0.056	0.056	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.040	0.018	7.430	0.021	0.021	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.112	-0.065	11.646	0.037	0.037	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.816	0.912	14.813	0.318	0.318	0.000	0.000	0.000	0.000
102	A	103	HIS	0	-0.014	-0.007	14.160	0.034	0.034	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.874	0.950	12.776	0.477	0.477	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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