FMO DATABASE

FMODB ID: VRNK1

Calculation Name: 2AV5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AV5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U151

Base Structure: X-ray

Registration Date: 2023-03-13

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-863945.557174
FMO2-HF: Nuclear repulsion	822239.292479
FMO2-HF: Total energy	-41706.264695
FMO2-MP2: Total energy	-41831.392847

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:15:LYS)

Summations of interaction energy for fragment #1(A:15:LYS)

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.
141.15	144.81	0.833	-1.604	-2.89	-0.002

Interaction energy analysis for fragmet #1(A:15:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.016 / q_NPA : 0.991

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	17	ARG	1	0.940	0.982	3.871	27.990	29.819	-0.021	-0.935	-0.873	0.001
4	A	18	TYR	0	0.010	0.005	7.161	-0.480	-0.480	0.000	0.000	0.000	0.000
5	A	19	ILE	0	0.029	0.011	10.681	0.436	0.436	0.000	0.000	0.000	0.000
6	A	20	ALA	0	-0.011	0.006	14.019	0.209	0.209	0.000	0.000	0.000	0.000
7	A	21	PHE	0	0.024	0.007	17.441	-0.098	-0.098	0.000	0.000	0.000	0.000
8	A	22	LYS	1	0.879	0.938	20.274	10.374	10.374	0.000	0.000	0.000	0.000
9	A	23	VAL	0	0.024	0.027	24.039	-0.211	-0.211	0.000	0.000	0.000	0.000
10	A	24	ILE	0	-0.045	-0.030	26.540	0.198	0.198	0.000	0.000	0.000	0.000
11	A	25	SER	0	-0.005	-0.029	30.007	-0.085	-0.085	0.000	0.000	0.000	0.000
12	A	26	GLU	-1	-0.874	-0.914	32.890	-7.811	-7.811	0.000	0.000	0.000	0.000
13	A	27	ASN	0	-0.040	-0.032	33.323	0.263	0.263	0.000	0.000	0.000	0.000
14	A	28	GLN	0	-0.042	-0.030	31.992	-0.276	-0.276	0.000	0.000	0.000	0.000
15	A	29	PHE	0	0.043	0.038	28.770	0.045	0.045	0.000	0.000	0.000	0.000
16	A	30	ASN	0	0.056	-0.003	28.445	-0.202	-0.202	0.000	0.000	0.000	0.000
17	A	31	LYS	1	0.726	0.820	23.545	11.028	11.028	0.000	0.000	0.000	0.000
18	A	32	ASP	-1	-0.840	-0.907	24.291	-12.318	-12.318	0.000	0.000	0.000	0.000
19	A	33	GLU	-1	-0.709	-0.831	25.547	-10.116	-10.116	0.000	0.000	0.000	0.000
20	A	34	ILE	0	0.004	-0.004	22.296	-0.376	-0.376	0.000	0.000	0.000	0.000
21	A	35	LYS	1	0.795	0.888	20.251	12.343	12.343	0.000	0.000	0.000	0.000
22	A	36	GLU	-1	-0.938	-0.957	21.285	-12.185	-12.185	0.000	0.000	0.000	0.000
23	A	37	ALA	0	0.059	0.038	23.142	-0.363	-0.363	0.000	0.000	0.000	0.000
24	A	38	ILE	0	-0.057	-0.036	17.802	-0.480	-0.480	0.000	0.000	0.000	0.000
25	A	39	TRP	0	0.021	0.007	16.140	-0.656	-0.656	0.000	0.000	0.000	0.000
26	A	40	ASN	0	0.023	0.002	19.904	0.031	0.031	0.000	0.000	0.000	0.000
27	A	41	ALA	0	-0.002	0.011	21.023	0.082	0.082	0.000	0.000	0.000	0.000
28	A	42	CYS	0	-0.073	-0.037	16.880	-0.522	-0.522	0.000	0.000	0.000	0.000
29	A	43	LEU	0	0.001	-0.003	18.824	-0.228	-0.228	0.000	0.000	0.000	0.000
30	A	44	ARG	1	0.905	0.950	20.825	12.155	12.155	0.000	0.000	0.000	0.000
31	A	45	THR	0	-0.047	-0.017	20.253	0.542	0.542	0.000	0.000	0.000	0.000
32	A	46	LEU	0	-0.079	-0.033	14.920	-0.566	-0.566	0.000	0.000	0.000	0.000
33	A	47	GLY	0	0.080	0.052	17.616	-0.583	-0.583	0.000	0.000	0.000	0.000
34	A	48	GLU	-1	-0.888	-0.946	17.678	-15.843	-15.843	0.000	0.000	0.000	0.000
35	A	49	LEU	0	0.009	0.009	13.425	-1.574	-1.574	0.000	0.000	0.000	0.000
36	A	50	GLY	0	0.062	0.020	13.347	-2.044	-2.044	0.000	0.000	0.000	0.000
37	A	51	THR	0	0.018	-0.002	12.902	-2.078	-2.078	0.000	0.000	0.000	0.000
38	A	52	ALA	0	0.022	0.010	12.420	-1.943	-1.943	0.000	0.000	0.000	0.000
39	A	53	LYS	1	0.841	0.925	8.844	24.376	24.376	0.000	0.000	0.000	0.000
40	A	54	ALA	0	0.036	0.002	8.184	-4.728	-4.728	0.000	0.000	0.000	0.000
41	A	55	LYS	1	0.800	0.901	5.875	35.168	35.168	0.000	0.000	0.000	0.000
42	A	56	PRO	0	0.045	0.023	10.133	-0.888	-0.888	0.000	0.000	0.000	0.000
43	A	57	TRP	0	-0.013	-0.012	12.483	0.113	0.113	0.000	0.000	0.000	0.000
44	A	58	LEU	0	0.054	0.042	13.930	-0.467	-0.467	0.000	0.000	0.000	0.000
45	A	59	ILE	0	-0.050	-0.023	12.407	0.015	0.015	0.000	0.000	0.000	0.000
46	A	60	LYS	1	0.927	0.953	15.807	14.015	14.015	0.000	0.000	0.000	0.000
47	A	61	PHE	0	0.044	0.019	19.064	-0.465	-0.465	0.000	0.000	0.000	0.000
48	A	62	ASP	-1	-0.858	-0.919	22.197	-10.302	-10.302	0.000	0.000	0.000	0.000
49	A	63	GLU	-1	-0.718	-0.847	25.246	-10.605	-10.605	0.000	0.000	0.000	0.000
50	A	64	THR	0	0.023	0.028	28.363	0.363	0.363	0.000	0.000	0.000	0.000
51	A	65	THR	0	-0.007	-0.018	26.250	0.113	0.113	0.000	0.000	0.000	0.000
52	A	66	GLN	0	-0.015	0.008	27.238	-0.249	-0.249	0.000	0.000	0.000	0.000
53	A	67	THR	0	-0.022	-0.015	22.270	-0.126	-0.126	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.046	0.012	20.430	0.100	0.100	0.000	0.000	0.000	0.000
55	A	69	ILE	0	-0.102	-0.043	13.889	-0.243	-0.243	0.000	0.000	0.000	0.000
56	A	70	ILE	0	0.073	0.046	13.249	-0.130	-0.130	0.000	0.000	0.000	0.000
57	A	71	ARG	1	0.863	0.934	7.819	26.454	26.454	0.000	0.000	0.000	0.000
58	A	72	SER	0	0.062	0.026	8.186	1.591	1.591	0.000	0.000	0.000	0.000
59	A	73	ASP	-1	-0.840	-0.925	3.950	-71.255	-70.754	0.002	-0.185	-0.318	-0.001
60	A	74	ARG	1	0.850	0.910	2.593	44.447	45.408	0.852	-0.444	-1.370	-0.002
61	A	75	ASN	0	-0.037	-0.028	3.781	8.857	9.226	0.000	-0.040	-0.329	0.000
62	A	76	HIS	0	0.065	0.050	6.904	0.142	0.142	0.000	0.000	0.000	0.000
63	A	77	VAL	0	-0.027	-0.006	8.100	1.665	1.665	0.000	0.000	0.000	0.000
64	A	78	TYR	0	0.040	0.001	10.645	0.944	0.944	0.000	0.000	0.000	0.000
65	A	79	ASP	-1	-0.774	-0.858	12.825	-21.336	-21.336	0.000	0.000	0.000	0.000
66	A	80	VAL	0	0.022	0.021	12.527	0.987	0.987	0.000	0.000	0.000	0.000
67	A	81	ILE	0	-0.033	-0.021	14.462	1.037	1.037	0.000	0.000	0.000	0.000
68	A	82	PHE	0	0.016	0.020	16.918	0.851	0.851	0.000	0.000	0.000	0.000
69	A	83	SER	0	0.028	-0.018	17.559	0.686	0.686	0.000	0.000	0.000	0.000
70	A	84	LEU	0	-0.047	-0.030	17.436	0.584	0.584	0.000	0.000	0.000	0.000
71	A	85	THR	0	-0.028	-0.024	20.848	0.659	0.659	0.000	0.000	0.000	0.000
72	A	86	LEU	0	-0.024	0.008	22.797	0.590	0.590	0.000	0.000	0.000	0.000
73	A	87	VAL	0	-0.047	-0.018	23.771	0.165	0.165	0.000	0.000	0.000	0.000
74	A	88	SER	0	-0.019	-0.033	26.437	0.279	0.279	0.000	0.000	0.000	0.000
75	A	89	ASP	-1	-0.872	-0.912	29.661	-9.268	-9.268	0.000	0.000	0.000	0.000
76	A	90	ILE	0	-0.026	-0.007	26.973	-0.489	-0.489	0.000	0.000	0.000	0.000
77	A	91	ASN	0	-0.011	-0.025	29.705	0.313	0.313	0.000	0.000	0.000	0.000
78	A	92	GLY	0	0.063	0.047	31.945	0.271	0.271	0.000	0.000	0.000	0.000
79	A	93	ASN	0	-0.049	-0.009	33.555	0.445	0.445	0.000	0.000	0.000	0.000
80	A	94	LYS	1	0.904	0.932	32.847	8.738	8.738	0.000	0.000	0.000	0.000
81	A	95	ALA	0	0.018	0.015	29.745	0.098	0.098	0.000	0.000	0.000	0.000
82	A	96	ILE	0	0.018	0.030	27.679	-0.181	-0.181	0.000	0.000	0.000	0.000
83	A	97	ILE	0	0.006	-0.005	21.260	0.019	0.019	0.000	0.000	0.000	0.000
84	A	98	LYS	1	0.948	0.975	22.428	11.489	11.489	0.000	0.000	0.000	0.000
85	A	99	VAL	0	0.031	0.003	16.697	-0.059	-0.059	0.000	0.000	0.000	0.000
86	A	100	LEU	0	-0.051	-0.026	19.551	0.551	0.551	0.000	0.000	0.000	0.000
87	A	101	GLY	0	0.035	0.007	17.559	0.340	0.340	0.000	0.000	0.000	0.000
88	A	102	VAL	0	0.042	0.026	12.103	-0.564	-0.564	0.000	0.000	0.000	0.000
89	A	103	SER	0	-0.042	-0.036	11.337	0.681	0.681	0.000	0.000	0.000	0.000
90	A	104	GLY	0	0.031	0.019	7.339	-1.424	-1.424	0.000	0.000	0.000	0.000
91	A	105	THR	0	0.031	0.006	7.211	-0.707	-0.707	0.000	0.000	0.000	0.000
92	A	106	ILE	0	0.126	0.061	9.800	1.198	1.198	0.000	0.000	0.000	0.000
93	A	107	LYS	1	0.953	0.988	12.642	14.335	14.335	0.000	0.000	0.000	0.000
94	A	108	ARG	1	0.997	0.991	12.953	15.558	15.558	0.000	0.000	0.000	0.000
95	A	109	LEU	0	-0.019	-0.002	12.997	0.593	0.593	0.000	0.000	0.000	0.000
96	A	110	LYS	1	0.959	0.973	14.949	14.987	14.987	0.000	0.000	0.000	0.000
97	A	111	ARG	1	0.904	0.951	17.640	11.846	11.846	0.000	0.000	0.000	0.000
98	A	112	LYS	1	0.877	0.932	17.886	13.522	13.522	0.000	0.000	0.000	0.000
99	A	113	PHE	0	0.027	0.031	16.159	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	114	LEU	0	0.060	0.035	18.984	0.261	0.261	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.091	-0.043	21.687	0.474	0.474	0.000	0.000	0.000	0.000
102	A	116	GLN	0	0.018	0.022	23.608	0.130	0.130	0.000	0.000	0.000	0.000
103	A	117	PHE	0	0.067	0.047	24.429	0.209	0.209	0.000	0.000	0.000	0.000
104	A	118	GLY	0	0.102	0.063	27.008	0.061	0.061	0.000	0.000	0.000	0.000
105	A	119	TRP	0	-0.101	-0.051	18.833	-0.629	-0.629	0.000	0.000	0.000	0.000
106	A	120	ARG	1	0.915	0.940	21.023	10.298	10.298	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:LYS)