FMO DATABASE

FMODB ID: YY8Q2

Calculation Name: 1WV8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WV8

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJJ5

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-382223.055156
FMO2-HF: Nuclear repulsion	355630.648056
FMO2-HF: Total energy	-26592.4071
FMO2-MP2: Total energy	-26671.13876

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:2:ARG)

Summations of interaction energy for fragment #1(A:2:ARG)

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.
-293.494	-285.156	24.655	-15.151	-17.84	-0.125

Interaction energy analysis for fragmet #1(A:2:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.898 / q_NPA : 0.936

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	4	LEU	0	0.020	0.026	2.925	-7.998	-5.298	0.401	-1.111	-1.989	-0.005
4	A	5	LYS	1	0.828	0.883	4.484	38.874	39.040	-0.001	-0.010	-0.155	0.000
5	A	6	VAL	0	0.026	0.028	6.936	1.819	1.819	0.000	0.000	0.000	0.000
6	A	7	GLN	0	-0.046	-0.025	9.413	1.614	1.614	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.005	-0.003	13.285	0.710	0.710	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.024	-0.027	16.733	0.470	0.470	0.000	0.000	0.000	0.000
9	A	10	TRP	0	-0.060	-0.020	19.734	0.384	0.384	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.814	-0.894	23.193	-10.870	-10.870	0.000	0.000	0.000	0.000
11	A	12	GLY	0	-0.039	-0.034	25.912	0.182	0.182	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-1.008	-1.002	28.988	-9.090	-9.090	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.042	-0.027	28.078	0.283	0.283	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.055	-0.011	29.359	0.070	0.070	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.028	-0.024	24.931	-0.049	-0.049	0.000	0.000	0.000	0.000
16	A	17	TRP	0	-0.038	-0.019	20.080	-0.293	-0.293	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.034	0.007	20.035	-0.023	-0.023	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.033	-0.019	15.621	-0.456	-0.456	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.878	-0.938	14.463	-17.620	-17.620	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.061	-0.067	9.424	-1.949	-1.949	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.898	-0.941	9.379	-23.940	-23.940	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.886	-0.928	5.112	-48.779	-48.705	-0.001	-0.003	-0.069	0.000
23	A	24	VAL	0	-0.063	-0.038	7.721	-0.592	-0.592	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.018	0.004	10.528	1.856	1.856	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.004	-0.001	13.517	0.332	0.332	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.014	-0.004	12.507	0.846	0.846	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.014	0.015	15.648	0.202	0.202	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.020	-0.029	17.284	0.645	0.645	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.861	-0.935	20.022	-13.289	-13.289	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.001	0.004	21.940	0.153	0.153	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.047	0.033	23.606	-0.066	-0.066	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.099	-0.076	24.116	-0.061	-0.061	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.023	0.006	18.279	-0.457	-0.457	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.879	-0.952	19.119	-14.746	-14.746	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.834	-0.900	19.896	-12.330	-12.330	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.011	0.015	17.535	-0.314	-0.314	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.013	-0.007	14.135	-0.869	-0.869	0.000	0.000	0.000	0.000
38	A	39	ALA	0	-0.037	-0.014	15.375	-0.599	-0.599	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.843	0.925	17.219	13.202	13.202	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.007	-0.001	12.574	-0.250	-0.250	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.038	-0.021	12.116	-1.132	-1.132	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.069	-0.017	12.952	-0.113	-0.113	0.000	0.000	0.000	0.000
43	A	44	MET	0	0.055	0.023	13.858	-0.240	-0.240	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.014	0.004	8.233	-0.324	-0.324	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.029	-0.022	9.483	-0.832	-0.832	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.863	-0.932	10.460	-15.285	-15.285	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.019	0.017	12.646	0.232	0.232	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.050	-0.023	6.496	-0.524	-0.524	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.994	-1.000	10.452	-18.400	-18.400	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-1.010	-0.992	12.623	-14.142	-14.142	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.087	-0.049	12.694	0.944	0.944	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.020	-0.006	13.017	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.034	-0.024	7.297	-1.498	-1.498	0.000	0.000	0.000	0.000
54	A	55	ALA	0	-0.034	-0.019	7.807	-1.999	-1.999	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.031	0.031	3.013	-4.068	-3.196	0.155	-0.313	-0.713	0.000
56	A	57	GLU	-1	-0.917	-0.953	1.895	-93.807	-90.206	9.831	-6.338	-7.095	-0.068
57	A	58	LEU	0	0.017	0.011	1.883	-7.294	-10.267	10.043	-3.982	-3.087	-0.039
58	A	59	PRO	0	-0.057	-0.038	4.267	1.445	1.699	-0.001	-0.078	-0.176	0.000
59	A	60	VAL	0	0.020	0.004	2.077	-8.628	-6.315	4.201	-2.900	-3.614	-0.012
60	A	61	GLU	-1	-0.850	-0.883	3.505	-45.990	-44.659	0.027	-0.416	-0.942	-0.001
61	A	62	LEU	0	0.035	0.023	5.523	-4.232	-4.232	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.815	0.885	5.590	42.395	42.395	0.000	0.000	0.000	0.000
63	A	64	LEU	0	0.037	0.028	8.741	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.867	-0.914	8.474	-30.279	-30.279	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.050	0.041	12.804	0.758	0.758	0.000	0.000	0.000	0.000
66	A	67	THR	0	-0.020	-0.018	15.914	-0.317	-0.317	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.937	0.966	18.153	12.525	12.525	0.000	0.000	0.000	0.000
68	A	69	PRO	0	0.013	0.018	21.759	-0.213	-0.213	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.013	-0.015	22.789	0.232	0.232	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.002	-0.004	26.125	0.123	0.123	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.006	0.012	26.006	0.172	0.172	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ARG)