FMO DATABASE

FMODB ID: V51V1

Calculation Name: 3BEY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BEY

Chain ID: A

ChEMBL ID:

UniProt ID: O27018

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-497372.6581
FMO2-HF: Nuclear repulsion	463169.714257
FMO2-HF: Total energy	-34202.943843
FMO2-MP2: Total energy	-34300.976512

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:7:ARG)

Summations of interaction energy for fragment #1(A:7: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.
-98.474	-98.042	10.157	-4.925	-5.664	-0.029

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.967 / q_NPA : 0.967

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	9	LEU	0	0.006	-0.009	3.644	1.712	3.749	0.031	-0.807	-1.261	0.003
4	A	10	GLU	-1	-0.934	-0.973	1.618	-47.685	-49.882	10.086	-4.034	-3.855	-0.030
5	A	11	GLU	-1	-0.932	-0.950	3.291	-29.420	-28.828	0.040	-0.084	-0.548	-0.002
6	A	12	LEU	0	-0.084	-0.040	6.253	3.646	3.646	0.000	0.000	0.000	0.000
7	A	13	PRO	0	0.057	0.016	8.231	0.248	0.248	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.894	-0.945	9.166	-14.855	-14.855	0.000	0.000	0.000	0.000
9	A	15	VAL	0	0.010	0.002	10.050	0.357	0.357	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.014	0.026	7.153	0.301	0.301	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.903	-0.941	9.093	-17.481	-17.481	0.000	0.000	0.000	0.000
12	A	18	SER	0	-0.069	-0.046	11.569	0.835	0.835	0.000	0.000	0.000	0.000
13	A	19	PHE	0	-0.026	-0.025	10.113	0.356	0.356	0.000	0.000	0.000	0.000
14	A	20	LYN	0	0.044	0.032	9.898	-0.136	-0.136	0.000	0.000	0.000	0.000
15	A	21	ASN	0	0.044	0.017	12.629	0.538	0.538	0.000	0.000	0.000	0.000
16	A	22	PHE	0	-0.054	-0.021	15.938	0.697	0.697	0.000	0.000	0.000	0.000
17	A	23	ARG	1	0.901	0.939	9.201	21.657	21.657	0.000	0.000	0.000	0.000
18	A	24	GLU	-1	-0.844	-0.939	16.212	-14.703	-14.703	0.000	0.000	0.000	0.000
19	A	25	ALA	0	-0.035	-0.004	17.921	0.685	0.685	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.047	-0.031	18.867	0.545	0.545	0.000	0.000	0.000	0.000
21	A	27	ARG	1	0.861	0.925	17.063	16.309	16.309	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.033	-0.001	20.755	0.428	0.428	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.868	-0.934	23.273	-9.606	-9.606	0.000	0.000	0.000	0.000
24	A	30	GLY	0	0.011	0.004	25.918	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.861	0.932	29.380	9.346	9.346	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.004	0.013	27.109	0.210	0.210	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.002	-0.003	28.315	-0.305	-0.305	0.000	0.000	0.000	0.000
28	A	34	GLU	-1	-0.854	-0.944	23.218	-12.822	-12.822	0.000	0.000	0.000	0.000
29	A	35	ARG	1	0.905	0.946	25.380	9.502	9.502	0.000	0.000	0.000	0.000
30	A	36	GLU	-1	-0.878	-0.951	27.113	-9.707	-9.707	0.000	0.000	0.000	0.000
31	A	37	LYS	1	0.824	0.897	23.183	11.481	11.481	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.027	0.029	20.573	-0.450	-0.450	0.000	0.000	0.000	0.000
33	A	39	LEU	0	0.014	-0.002	22.624	-0.399	-0.399	0.000	0.000	0.000	0.000
34	A	40	ILE	0	-0.023	-0.006	23.524	-0.060	-0.060	0.000	0.000	0.000	0.000
35	A	41	SER	0	-0.007	-0.004	18.974	-0.320	-0.320	0.000	0.000	0.000	0.000
36	A	42	VAL	0	0.003	0.027	19.975	-0.647	-0.647	0.000	0.000	0.000	0.000
37	A	43	ALA	0	0.036	0.020	21.388	-0.190	-0.190	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.016	-0.018	21.068	0.125	0.125	0.000	0.000	0.000	0.000
39	A	45	SER	0	-0.047	-0.025	17.621	-0.595	-0.595	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.021	0.006	19.047	-0.302	-0.302	0.000	0.000	0.000	0.000
41	A	47	ALA	0	-0.048	-0.023	21.344	0.173	0.173	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.074	-0.030	17.924	0.328	0.328	0.000	0.000	0.000	0.000
43	A	49	ARG	1	0.898	0.946	19.250	13.876	13.876	0.000	0.000	0.000	0.000
44	A	50	CYS	0	0.037	0.027	11.619	-1.681	-1.681	0.000	0.000	0.000	0.000
45	A	51	ASP	-1	-0.888	-0.956	14.011	-17.438	-17.438	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.050	-0.035	9.637	-0.170	-0.170	0.000	0.000	0.000	0.000
47	A	54	THR	0	0.030	0.001	13.861	0.779	0.779	0.000	0.000	0.000	0.000
48	A	55	ARG	1	0.941	0.973	11.352	22.380	22.380	0.000	0.000	0.000	0.000
49	A	56	ARG	1	0.966	0.999	10.196	23.733	23.733	0.000	0.000	0.000	0.000
50	A	57	HIS	0	-0.009	-0.016	14.110	0.368	0.368	0.000	0.000	0.000	0.000
51	A	58	ALA	0	-0.001	0.008	17.430	0.823	0.823	0.000	0.000	0.000	0.000
52	A	59	GLU	-1	-0.937	-0.971	13.637	-19.775	-19.775	0.000	0.000	0.000	0.000
53	A	60	GLU	-1	-0.793	-0.885	15.327	-17.504	-17.504	0.000	0.000	0.000	0.000
54	A	61	ALA	0	-0.003	-0.016	19.050	0.695	0.695	0.000	0.000	0.000	0.000
55	A	62	LEU	0	-0.044	-0.020	20.533	0.596	0.596	0.000	0.000	0.000	0.000
56	A	63	GLU	-1	-1.033	-0.994	18.459	-15.699	-15.699	0.000	0.000	0.000	0.000
57	A	64	ALA	0	-0.008	-0.010	22.713	0.200	0.200	0.000	0.000	0.000	0.000
58	A	65	GLY	0	-0.066	-0.031	25.254	0.476	0.476	0.000	0.000	0.000	0.000
59	A	66	ILE	0	-0.058	-0.015	25.280	0.392	0.392	0.000	0.000	0.000	0.000
60	A	67	THR	0	0.035	0.009	26.331	-0.241	-0.241	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.885	-0.958	24.865	-11.688	-11.688	0.000	0.000	0.000	0.000
62	A	69	GLY	0	-0.022	-0.010	26.923	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	70	GLU	-1	-0.835	-0.920	29.037	-9.802	-9.802	0.000	0.000	0.000	0.000
64	A	71	LEU	0	0.011	0.006	22.517	-0.065	-0.065	0.000	0.000	0.000	0.000
65	A	72	ALA	0	-0.024	-0.004	26.254	-0.172	-0.172	0.000	0.000	0.000	0.000
66	A	73	GLU	-1	-0.886	-0.935	27.968	-9.195	-9.195	0.000	0.000	0.000	0.000
67	A	74	ALA	0	-0.007	0.002	26.219	0.099	0.099	0.000	0.000	0.000	0.000
68	A	75	ALA	0	-0.043	-0.034	25.129	-0.086	-0.086	0.000	0.000	0.000	0.000
69	A	76	ALA	0	-0.001	-0.003	26.436	0.023	0.023	0.000	0.000	0.000	0.000
70	A	77	VAL	0	0.031	0.019	29.694	0.163	0.163	0.000	0.000	0.000	0.000
71	A	78	ALA	0	0.013	0.009	25.594	0.129	0.129	0.000	0.000	0.000	0.000
72	A	79	ALA	0	-0.023	-0.017	27.684	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	80	LEU	0	0.012	0.013	29.064	0.218	0.218	0.000	0.000	0.000	0.000
74	A	81	ILE	0	0.012	0.012	29.254	0.257	0.257	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.911	0.970	24.986	11.817	11.817	0.000	0.000	0.000	0.000
76	A	83	ALA	0	0.001	0.007	29.584	0.114	0.114	0.000	0.000	0.000	0.000
77	A	84	GLY	0	0.009	-0.004	32.975	0.252	0.252	0.000	0.000	0.000	0.000
78	A	85	SER	0	-0.040	-0.040	30.829	0.151	0.151	0.000	0.000	0.000	0.000
79	A	86	ALA	0	0.015	0.009	32.613	0.148	0.148	0.000	0.000	0.000	0.000
80	A	87	MET	0	-0.008	-0.015	34.134	0.229	0.229	0.000	0.000	0.000	0.000
81	A	88	ASN	0	-0.020	0.000	35.828	0.396	0.396	0.000	0.000	0.000	0.000
82	A	89	THR	0	-0.019	-0.012	34.554	0.114	0.114	0.000	0.000	0.000	0.000
83	A	90	ALA	0	-0.003	-0.003	37.032	0.154	0.154	0.000	0.000	0.000	0.000
84	A	91	SER	0	-0.024	-0.003	39.556	0.242	0.242	0.000	0.000	0.000	0.000
85	A	92	ALA	0	0.017	-0.001	39.988	0.194	0.194	0.000	0.000	0.000	0.000
86	A	93	ILE	0	-0.061	-0.013	41.577	0.043	0.043	0.000	0.000	0.000	0.000
87	A	94	PHE	0	-0.073	-0.029	43.645	0.195	0.195	0.000	0.000	0.000	0.000
88	A	95	ARG	1	0.976	0.992	46.224	6.087	6.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)