FMO DATABASE

FMODB ID: R8G78

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	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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-818070.144396
FMO2-HF: Nuclear repulsion	776968.041622
FMO2-HF: Total energy	-41102.102774
FMO2-MP2: Total energy	-41221.62614

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.
-11.711	-5.362	14.7	-6.643	-14.402	-0.04

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 : -0.021 / q_NPA : -0.011

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	3	VAL	0	0.018	0.007	3.803	-0.691	0.876	-0.011	-0.571	-0.985	0.003
4	A	4	LEU	0	-0.028	-0.012	5.923	-0.023	-0.023	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.013	0.029	8.993	0.047	0.047	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.059	0.021	12.151	-0.019	-0.019	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.050	0.021	13.443	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.027	0.012	15.185	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.901	-0.958	11.010	0.162	0.162	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.014	-0.001	10.132	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.928	-0.973	12.053	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.888	0.946	13.329	-0.113	-0.113	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.044	0.029	6.812	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.019	0.019	10.574	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.019	-0.009	13.060	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.973	-0.991	9.247	0.066	0.066	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.116	-0.069	8.735	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.934	0.979	12.311	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.070	0.037	15.780	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.847	0.945	9.332	0.230	0.230	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.025	-0.009	10.219	0.020	0.020	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.016	0.013	7.981	-0.079	-0.079	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.029	-0.026	5.339	0.030	0.030	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.011	-0.016	5.519	0.153	0.153	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.891	-0.944	4.581	-0.166	-0.052	-0.001	-0.011	-0.102	0.000
26	A	26	PHE	0	-0.022	-0.023	6.503	0.370	0.370	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.074	0.008	7.525	-0.029	-0.029	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.115	0.048	10.816	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.013	-0.009	10.462	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	30	TRP	0	-0.098	-0.059	13.779	-0.042	-0.042	0.000	0.000	0.000	0.000
31	A	31	CYS	-1	-0.887	-0.858	13.682	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	32	GLY	0	-0.026	-0.028	13.825	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.039	-0.051	13.666	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	34	CYS	-1	-0.767	-0.874	10.135	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.811	0.912	8.999	-0.073	-0.073	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.054	-0.030	10.130	-0.066	-0.066	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.043	-0.019	7.541	-0.076	-0.076	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.074	0.047	5.477	-0.330	-0.330	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.020	0.009	4.486	-0.882	-0.770	-0.001	-0.007	-0.103	0.000
40	A	40	LYS	1	0.885	0.946	6.252	0.346	0.346	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.026	0.017	2.049	1.144	-1.864	6.170	-0.982	-2.180	-0.006
42	A	42	GLU	-1	-0.952	-0.979	2.365	-4.824	-2.564	2.000	-1.330	-2.930	-0.010
43	A	43	ALA	0	-0.072	-0.041	3.263	0.942	0.598	0.022	0.535	-0.212	0.000
44	A	44	LEU	0	0.010	-0.007	5.389	0.309	0.309	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.004	0.007	2.031	-0.109	-0.062	2.114	-0.774	-1.388	-0.006
46	A	46	LYS	1	0.895	0.945	4.126	1.061	1.293	0.001	-0.071	-0.162	0.000
47	A	47	GLU	-1	-0.881	-0.921	7.347	-0.426	-0.426	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.053	-0.029	7.869	0.217	0.217	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.051	0.019	7.737	-0.121	-0.121	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-1.020	-1.000	8.828	-0.227	-0.227	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.043	-0.024	7.248	0.099	0.099	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.918	-0.949	5.400	-0.830	-0.830	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.007	0.011	2.218	-1.372	-0.521	2.617	-0.929	-2.538	-0.003
54	A	54	ALA	0	-0.014	-0.018	2.610	-3.580	-0.691	1.482	-2.155	-2.215	-0.021
55	A	55	LYS	1	0.950	0.985	3.031	-3.146	-1.513	0.308	-0.340	-1.600	0.003
56	A	56	VAL	0	-0.008	-0.006	5.518	-0.464	-0.468	-0.001	-0.008	0.013	0.000
57	A	57	ASP	-1	-0.836	-0.910	9.252	0.297	0.297	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.016	-0.046	11.139	-0.049	-0.049	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.828	-0.889	14.323	0.105	0.105	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.103	-0.051	12.248	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.078	-0.051	12.003	-0.054	-0.054	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.852	-0.932	14.928	0.078	0.078	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.868	-0.929	17.894	0.064	0.064	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.012	-0.005	13.754	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.044	0.022	15.241	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.017	-0.006	16.128	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.804	0.892	17.973	-0.066	-0.066	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.000	0.013	15.536	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.033	-0.011	17.484	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.044	-0.015	13.783	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.008	-0.013	16.903	0.009	0.009	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.044	-0.001	16.768	0.007	0.007	0.000	0.000	0.000	0.000
73	A	73	MET	0	0.094	0.051	13.666	0.019	0.019	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.145	0.049	9.686	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.071	-0.068	11.144	-0.066	-0.066	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.007	0.006	5.347	0.058	0.058	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.007	0.003	9.498	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	78	PHE	0	-0.044	-0.020	9.067	-0.046	-0.046	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.030	0.005	11.546	0.042	0.042	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.915	0.949	12.993	0.197	0.197	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.890	-0.957	15.660	-0.073	-0.073	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.034	-0.026	16.384	0.015	0.015	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.904	0.971	17.657	0.101	0.101	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.754	-0.844	15.333	-0.110	-0.110	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.078	-0.053	14.826	0.009	0.009	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.800	-0.900	14.095	-0.230	-0.230	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.761	0.843	13.265	0.070	0.070	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.072	-0.021	10.312	0.013	0.013	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.010	0.011	12.883	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.021	0.006	13.431	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.033	0.019	11.437	-0.051	-0.051	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.052	-0.033	12.181	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.836	-0.936	10.249	-0.627	-0.627	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.021	0.005	11.946	-0.064	-0.064	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.988	1.012	13.839	0.208	0.208	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.007	0.014	6.157	0.016	0.016	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.861	0.923	10.441	0.658	0.658	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.939	-0.967	11.687	-0.252	-0.252	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.084	-0.050	11.826	0.056	0.056	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.043	0.017	6.993	0.031	0.031	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.118	-0.069	11.218	0.044	0.044	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.860	0.946	14.529	0.288	0.288	0.000	0.000	0.000	0.000
103	A	103	HIS	0	-0.021	-0.014	13.588	0.039	0.039	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.963	1.004	12.531	0.425	0.425	0.000	0.000	0.000	0.000

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