FMO DATABASE

FMODB ID: KGL43

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

Total energy (hartree)

FMO2-HF: Electronic energy	-823347.611809
FMO2-HF: Nuclear repulsion	782244.36437
FMO2-HF: Total energy	-41103.247439
FMO2-MP2: Total energy	-41222.757558

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.
-16.822	-8.941	15.509	-7.097	-16.293	-0.025

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 : -0.007 / q_NPA : -0.016

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	0.019	0.016	3.868	0.404	1.855	-0.008	-0.498	-0.945	0.002
4	A	4	LEU	0	-0.054	-0.023	5.897	-0.270	-0.270	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.031	0.034	9.262	0.057	0.057	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.021	-0.004	12.417	-0.031	-0.031	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.010	-0.005	13.348	0.001	0.001	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.078	0.039	14.895	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.846	-0.881	11.180	0.152	0.152	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.017	0.022	10.013	-0.052	-0.052	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.864	-0.936	11.897	-0.038	-0.038	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.814	0.886	12.747	-0.105	-0.105	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.019	0.010	6.729	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.027	0.009	10.515	-0.049	-0.049	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.034	-0.019	13.190	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.865	-0.904	8.496	-0.111	-0.111	0.000	0.000	0.000	0.000
17	A	17	ASN	0	0.016	0.016	8.148	0.016	0.016	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.856	0.927	11.952	0.097	0.097	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.029	0.021	15.087	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.762	0.868	7.836	0.523	0.523	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.031	-0.011	10.917	0.011	0.011	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.009	0.003	7.887	-0.106	-0.106	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.014	-0.001	5.578	0.107	0.107	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.001	-0.010	6.282	0.130	0.130	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.879	-0.948	3.954	-1.020	-0.844	0.000	-0.031	-0.145	0.000
26	A	26	PHE	0	0.010	0.002	5.811	0.481	0.481	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.009	-0.025	6.992	-0.078	-0.078	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.101	0.047	9.530	0.050	0.050	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.021	-0.019	10.571	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	30	TRP	0	-0.020	-0.028	13.467	-0.051	-0.051	0.000	0.000	0.000	0.000
31	A	31	CYS	0	0.022	0.051	9.075	-0.132	-0.132	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.006	-0.002	13.002	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.007	-0.014	13.208	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.887	0.945	8.528	-0.175	-0.175	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.030	-0.013	9.668	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.018	0.004	7.367	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.069	0.039	4.808	-0.252	-0.252	0.000	0.000	0.000	0.000
38	A	39	PRO	0	0.018	0.001	4.235	-0.792	-0.668	-0.001	-0.024	-0.100	0.000
39	A	40	LYS	1	0.831	0.903	6.653	0.414	0.414	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.017	0.014	2.460	-0.360	-0.518	2.192	-0.392	-1.641	-0.001
41	A	42	GLU	-1	-0.867	-0.933	2.073	-2.234	-1.102	4.051	-1.412	-3.771	-0.009
42	A	43	ALA	0	-0.075	-0.040	3.591	0.406	0.507	0.023	0.071	-0.195	0.000
43	A	44	LEU	0	0.026	-0.004	5.587	0.155	0.155	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.009	0.004	2.977	-0.595	0.249	0.197	-0.256	-0.786	-0.001
45	A	46	LYS	1	0.883	0.944	4.938	1.042	1.164	-0.001	-0.005	-0.115	0.000
46	A	47	GLU	-1	-0.864	-0.886	7.623	-0.478	-0.478	0.000	0.000	0.000	0.000
47	A	48	ILE	0	-0.012	-0.009	8.802	0.170	0.170	0.000	0.000	0.000	0.000
48	A	49	PRO	0	0.064	0.030	7.469	-0.126	-0.126	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.865	-0.891	8.524	-0.364	-0.364	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.030	-0.011	8.023	0.099	0.099	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.862	-0.916	4.704	-1.663	-1.593	-0.001	-0.003	-0.066	0.000
52	A	53	PHE	0	0.003	-0.001	2.536	-1.526	0.053	0.466	-0.487	-1.559	-0.001
53	A	54	ALA	0	-0.004	0.000	2.377	-3.892	-1.767	3.389	-2.788	-2.725	-0.026
54	A	55	LYS	1	0.845	0.921	2.652	-7.478	-7.200	5.202	-1.260	-4.220	0.011
55	A	56	VAL	0	-0.009	-0.009	5.184	-0.243	-0.206	0.000	-0.012	-0.025	0.000
56	A	57	ASP	-1	-0.787	-0.871	8.873	0.383	0.383	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.002	-0.034	10.814	-0.066	-0.066	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.828	-0.894	13.716	0.164	0.164	0.000	0.000	0.000	0.000
59	A	60	GLN	0	-0.105	-0.061	12.674	0.033	0.033	0.000	0.000	0.000	0.000
60	A	61	ASN	0	-0.053	-0.040	12.140	-0.084	-0.084	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.859	-0.933	15.075	0.084	0.084	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.799	-0.889	17.656	0.066	0.066	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.015	-0.006	13.574	-0.029	-0.029	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.002	0.000	14.715	-0.030	-0.030	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.009	0.008	15.521	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.787	0.879	17.836	-0.057	-0.057	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.004	0.015	14.912	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.015	-0.011	16.914	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.041	-0.015	12.920	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.007	-0.008	16.161	0.013	0.013	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.006	0.017	16.503	0.013	0.013	0.000	0.000	0.000	0.000
72	A	73	MET	0	-0.001	0.035	12.285	0.017	0.017	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.032	-0.015	8.846	0.011	0.011	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.048	-0.033	10.104	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	76	PHE	0	-0.019	0.012	5.061	0.055	0.055	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.014	0.004	9.233	0.037	0.037	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.003	-0.007	9.277	-0.075	-0.075	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.027	0.007	11.897	0.061	0.061	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.895	0.935	13.113	0.248	0.248	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.861	-0.922	15.539	-0.105	-0.105	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.003	0.004	16.299	0.025	0.025	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.797	0.897	17.706	0.144	0.144	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.775	-0.856	15.162	-0.171	-0.171	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.044	-0.027	15.512	0.014	0.014	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.770	-0.879	14.316	-0.281	-0.281	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.780	0.851	13.317	0.107	0.107	0.000	0.000	0.000	0.000
87	A	88	PHE	0	-0.066	-0.031	10.462	0.020	0.020	0.000	0.000	0.000	0.000
88	A	89	SER	0	0.023	0.006	12.671	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.050	0.026	12.951	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.007	-0.007	11.195	-0.061	-0.061	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.010	-0.005	12.281	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.726	-0.847	11.020	-0.618	-0.618	0.000	0.000	0.000	0.000
93	A	94	THR	0	-0.005	0.005	12.112	-0.050	-0.050	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.914	0.957	14.203	0.264	0.264	0.000	0.000	0.000	0.000
95	A	96	LEU	0	0.004	0.021	6.630	0.003	0.003	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.793	0.846	10.906	0.613	0.613	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.891	-0.938	12.323	-0.280	-0.280	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.057	-0.049	12.248	0.049	0.049	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.034	0.016	7.521	0.020	0.020	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.092	-0.057	11.663	0.049	0.049	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.776	0.880	14.918	0.335	0.335	0.000	0.000	0.000	0.000
102	A	103	HIS	0	0.004	0.011	14.325	0.040	0.040	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.837	0.909	13.021	0.460	0.460	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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