FMO DATABASE

FMODB ID: M3YJZ

Calculation Name: 2R39-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R39

Chain ID: A

ChEMBL ID:

UniProt ID: Q87KC5

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	OptHSide
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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-865245.332928
FMO2-HF: Nuclear repulsion	821680.551308
FMO2-HF: Total energy	-43564.78162
FMO2-MP2: Total energy	-43693.261363

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:377:VAL)

Summations of interaction energy for fragment #1(A:377:VAL)

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.
-4.548	-0.881	0.311	-1.629	-2.349	-0.002

Interaction energy analysis for fragmet #1(A:377:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.010

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	379	PRO	0	0.029	0.025	2.858	-2.675	0.217	0.287	-1.479	-1.701	-0.003
4	A	380	ALA	0	0.043	0.023	5.161	0.747	0.843	-0.001	-0.003	-0.092	0.000
5	A	381	GLY	0	-0.006	-0.028	6.816	-0.200	-0.200	0.000	0.000	0.000	0.000
6	A	382	MET	0	0.018	0.015	8.691	0.079	0.079	0.000	0.000	0.000	0.000
7	A	383	SER	0	-0.058	-0.023	12.329	0.078	0.078	0.000	0.000	0.000	0.000
8	A	384	VAL	0	0.030	0.012	14.642	-0.018	-0.018	0.000	0.000	0.000	0.000
9	A	385	ILE	0	-0.016	0.001	18.411	0.034	0.034	0.000	0.000	0.000	0.000
10	A	386	ARG	1	0.897	0.953	21.316	0.055	0.055	0.000	0.000	0.000	0.000
11	A	387	ASP	-1	-0.858	-0.890	24.692	-0.058	-0.058	0.000	0.000	0.000	0.000
12	A	388	ARG	1	0.962	0.969	27.304	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	389	ASN	0	-0.047	-0.029	29.547	0.001	0.001	0.000	0.000	0.000	0.000
14	A	390	GLN	0	0.001	0.014	28.832	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	391	LEU	0	0.014	-0.003	33.285	0.003	0.003	0.000	0.000	0.000	0.000
16	A	392	PHE	0	-0.046	-0.037	35.044	0.002	0.002	0.000	0.000	0.000	0.000
17	A	393	ARG	1	0.885	0.923	36.001	0.063	0.063	0.000	0.000	0.000	0.000
18	A	394	VAL	0	-0.053	-0.032	38.352	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	395	ASN	0	0.177	0.129	35.595	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	396	SER	0	-0.134	-0.069	36.829	0.002	0.002	0.000	0.000	0.000	0.000
21	A	397	ALA	0	-0.023	-0.017	38.017	0.002	0.002	0.000	0.000	0.000	0.000
22	A	398	GLY	0	0.009	0.046	40.136	0.004	0.004	0.000	0.000	0.000	0.000
23	A	399	GLU	-1	-0.794	-0.842	35.963	-0.101	-0.101	0.000	0.000	0.000	0.000
24	A	400	VAL	0	-0.027	-0.035	35.489	0.005	0.005	0.000	0.000	0.000	0.000
25	A	401	GLU	-1	-0.787	-0.889	32.532	-0.094	-0.094	0.000	0.000	0.000	0.000
26	A	402	ASN	0	-0.083	-0.034	29.293	0.010	0.010	0.000	0.000	0.000	0.000
27	A	403	THR	0	-0.013	-0.043	28.506	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	404	TYR	0	0.005	-0.044	23.195	0.008	0.008	0.000	0.000	0.000	0.000
29	A	405	THR	0	-0.010	0.003	20.311	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	406	LEU	0	0.006	0.004	17.780	0.006	0.006	0.000	0.000	0.000	0.000
31	A	407	LYS	1	0.922	0.967	13.967	0.083	0.083	0.000	0.000	0.000	0.000
32	A	408	VAL	0	0.024	0.011	12.421	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	409	ILE	0	-0.050	-0.012	7.968	0.088	0.088	0.000	0.000	0.000	0.000
34	A	410	ASN	0	0.059	0.043	8.809	-0.425	-0.425	0.000	0.000	0.000	0.000
35	A	411	LYS	1	0.764	0.869	3.158	1.019	1.625	0.026	-0.145	-0.486	0.001
36	A	412	THR	0	-0.001	0.006	5.139	-0.236	-0.163	-0.001	-0.002	-0.070	0.000
37	A	413	GLN	0	-0.025	-0.032	7.301	0.208	0.208	0.000	0.000	0.000	0.000
38	A	414	GLN	0	-0.014	-0.009	10.470	0.084	0.084	0.000	0.000	0.000	0.000
39	A	415	VAL	0	0.035	0.027	11.942	-0.086	-0.086	0.000	0.000	0.000	0.000
40	A	416	GLN	0	-0.019	0.000	10.415	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	417	GLU	-1	-0.862	-0.933	13.900	-0.336	-0.336	0.000	0.000	0.000	0.000
42	A	418	TYR	0	-0.016	-0.020	9.857	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	419	ASN	0	0.024	0.018	16.099	0.073	0.073	0.000	0.000	0.000	0.000
44	A	420	LEU	0	-0.059	-0.030	16.449	-0.045	-0.045	0.000	0.000	0.000	0.000
45	A	421	ASP	-1	-0.872	-0.931	19.643	-0.305	-0.305	0.000	0.000	0.000	0.000
46	A	422	VAL	0	0.015	-0.010	21.344	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	423	LYS	1	0.891	0.961	19.688	0.303	0.303	0.000	0.000	0.000	0.000
48	A	424	GLY	0	0.027	-0.010	24.758	0.006	0.006	0.000	0.000	0.000	0.000
49	A	425	LEU	0	-0.032	-0.008	27.309	0.015	0.015	0.000	0.000	0.000	0.000
50	A	426	ASN	0	-0.015	-0.012	30.329	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	427	ASP	-1	-0.875	-0.940	33.328	-0.100	-0.100	0.000	0.000	0.000	0.000
52	A	428	VAL	0	-0.039	-0.039	29.398	0.002	0.002	0.000	0.000	0.000	0.000
53	A	429	SER	0	-0.026	-0.016	32.434	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	430	TRP	0	0.001	-0.022	21.809	0.004	0.004	0.000	0.000	0.000	0.000
55	A	431	TYR	0	-0.055	-0.047	28.596	0.002	0.002	0.000	0.000	0.000	0.000
56	A	432	GLY	0	0.056	0.011	26.143	0.005	0.005	0.000	0.000	0.000	0.000
57	A	433	LYS	1	0.917	0.955	21.810	0.224	0.224	0.000	0.000	0.000	0.000
58	A	434	GLN	0	0.037	0.037	22.718	0.010	0.010	0.000	0.000	0.000	0.000
59	A	435	THR	0	0.041	0.012	20.485	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	436	ILE	0	-0.120	-0.057	16.061	0.045	0.045	0.000	0.000	0.000	0.000
61	A	437	GLN	0	-0.014	-0.004	17.424	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	438	VAL	0	-0.023	-0.009	12.939	0.041	0.041	0.000	0.000	0.000	0.000
63	A	439	GLU	-1	-0.828	-0.932	14.100	-0.430	-0.430	0.000	0.000	0.000	0.000
64	A	440	PRO	0	-0.017	0.002	11.033	-0.052	-0.052	0.000	0.000	0.000	0.000
65	A	441	GLY	0	-0.014	0.000	9.597	0.106	0.106	0.000	0.000	0.000	0.000
66	A	442	GLU	-1	-0.920	-0.951	10.578	-0.226	-0.226	0.000	0.000	0.000	0.000
67	A	443	VAL	0	-0.036	-0.032	11.874	-0.060	-0.060	0.000	0.000	0.000	0.000
68	A	444	LEU	0	0.012	0.015	13.932	0.046	0.046	0.000	0.000	0.000	0.000
69	A	445	ASN	0	-0.044	-0.041	16.525	0.005	0.005	0.000	0.000	0.000	0.000
70	A	446	LEU	0	-0.013	-0.019	17.868	0.010	0.010	0.000	0.000	0.000	0.000
71	A	447	PRO	0	-0.017	0.012	21.180	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	448	MET	0	-0.046	-0.011	23.501	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	449	SER	0	-0.048	-0.052	26.105	0.011	0.011	0.000	0.000	0.000	0.000
74	A	450	LEU	0	-0.014	0.009	25.871	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	451	GLY	0	0.044	0.018	29.770	0.012	0.012	0.000	0.000	0.000	0.000
76	A	452	ALA	0	0.026	0.023	33.204	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	453	ASP	-1	-0.741	-0.854	35.079	-0.066	-0.066	0.000	0.000	0.000	0.000
78	A	454	PRO	0	-0.044	-0.041	38.191	0.000	0.000	0.000	0.000	0.000	0.000
79	A	455	ASP	-1	-0.872	-0.939	39.390	-0.054	-0.054	0.000	0.000	0.000	0.000
80	A	456	LYS	1	0.818	0.905	37.955	0.080	0.080	0.000	0.000	0.000	0.000
81	A	457	LEU	0	-0.083	-0.023	33.828	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	458	ASN	0	0.010	0.000	33.378	0.006	0.006	0.000	0.000	0.000	0.000
83	A	459	SER	0	-0.002	-0.012	34.667	0.006	0.006	0.000	0.000	0.000	0.000
84	A	460	ALA	0	-0.018	-0.007	35.601	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	461	ILE	0	0.000	0.005	30.338	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	462	THR	0	0.016	0.018	29.020	0.001	0.001	0.000	0.000	0.000	0.000
87	A	463	THR	0	-0.021	-0.013	24.341	0.002	0.002	0.000	0.000	0.000	0.000
88	A	464	ILE	0	-0.002	0.016	23.866	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	465	GLN	0	0.021	0.000	18.726	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	466	PHE	0	0.034	0.014	18.895	0.005	0.005	0.000	0.000	0.000	0.000
91	A	467	ILE	0	-0.018	-0.020	16.786	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	468	LEU	0	-0.011	0.001	11.795	0.046	0.046	0.000	0.000	0.000	0.000
93	A	469	THR	0	0.031	0.006	14.473	-0.084	-0.084	0.000	0.000	0.000	0.000
94	A	470	ASP	-1	-0.808	-0.891	10.624	-1.211	-1.211	0.000	0.000	0.000	0.000
95	A	471	LYS	1	0.947	0.942	13.547	0.386	0.386	0.000	0.000	0.000	0.000
96	A	472	SER	0	-0.021	0.005	13.774	0.047	0.047	0.000	0.000	0.000	0.000
97	A	473	ASN	0	-0.123	-0.077	9.762	-0.081	-0.081	0.000	0.000	0.000	0.000
98	A	474	GLU	-1	-0.999	-0.985	10.894	-0.884	-0.884	0.000	0.000	0.000	0.000
99	A	475	PHE	0	0.000	-0.013	7.274	-0.294	-0.294	0.000	0.000	0.000	0.000
100	A	476	THR	0	-0.026	-0.036	11.293	0.134	0.134	0.000	0.000	0.000	0.000
101	A	477	ILE	0	-0.028	0.015	9.425	-0.090	-0.090	0.000	0.000	0.000	0.000
102	A	478	GLU	-1	-0.858	-0.913	12.254	-0.493	-0.493	0.000	0.000	0.000	0.000
103	A	479	VAL	0	-0.041	-0.021	14.077	0.033	0.033	0.000	0.000	0.000	0.000
104	A	480	GLU	-1	-0.871	-0.905	16.411	-0.084	-0.084	0.000	0.000	0.000	0.000
105	A	481	SER	0	0.018	-0.001	19.696	0.021	0.021	0.000	0.000	0.000	0.000
106	A	482	ARG	1	0.792	0.859	22.563	0.077	0.077	0.000	0.000	0.000	0.000
107	A	483	PHE	0	0.031	0.043	26.374	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	484	ILE	0	-0.018	-0.024	29.357	0.007	0.007	0.000	0.000	0.000	0.000
109	A	485	LYS	1	0.899	0.970	32.405	0.057	0.057	0.000	0.000	0.000	0.000
110	A	486	LYS	1	0.968	0.981	36.058	0.039	0.039	0.000	0.000	0.000	0.000
111	A	487	LEU	0	0.013	0.013	38.716	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:377:VAL)