FMO DATABASE

FMODB ID: 9G9K2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-864516.609286
FMO2-HF: Nuclear repulsion	820952.545548
FMO2-HF: Total energy	-43564.063738
FMO2-MP2: Total energy	-43692.597957

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.
-4.938	-2.011	0.274	-1.263	-1.936	-0.007

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 : -0.059 / q_NPA : -0.050

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	0.018	0.012	2.868	-3.443	-0.999	0.259	-1.193	-1.509	-0.007
4	A	380	ALA	0	0.039	0.023	5.316	0.571	0.661	-0.001	-0.003	-0.086	0.000
5	A	381	GLY	0	-0.031	-0.029	6.690	0.043	0.043	0.000	0.000	0.000	0.000
6	A	382	MET	0	0.029	0.025	8.506	-0.033	-0.033	0.000	0.000	0.000	0.000
7	A	383	SER	0	-0.065	-0.025	12.200	0.107	0.107	0.000	0.000	0.000	0.000
8	A	384	VAL	0	0.047	0.019	14.670	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	385	ILE	0	-0.009	0.004	18.439	0.032	0.032	0.000	0.000	0.000	0.000
10	A	386	ARG	1	0.904	0.964	21.324	-0.066	-0.066	0.000	0.000	0.000	0.000
11	A	387	ASP	-1	-0.865	-0.897	24.700	0.027	0.027	0.000	0.000	0.000	0.000
12	A	388	ARG	1	0.963	0.972	27.313	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	389	ASN	0	-0.053	-0.031	29.521	0.000	0.000	0.000	0.000	0.000	0.000
14	A	390	GLN	0	0.010	0.015	28.769	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	391	LEU	0	0.016	-0.004	33.302	0.000	0.000	0.000	0.000	0.000	0.000
16	A	392	PHE	0	-0.058	-0.037	34.501	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	393	ARG	1	0.877	0.906	36.190	0.009	0.009	0.000	0.000	0.000	0.000
18	A	394	VAL	0	-0.065	-0.056	38.162	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	395	ASN	0	0.216	0.114	35.605	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	396	SER	0	-0.114	-0.063	36.859	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	397	ALA	0	-0.064	0.022	38.079	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	398	GLY	0	0.016	0.049	39.993	0.002	0.002	0.000	0.000	0.000	0.000
23	A	399	GLU	-1	-0.765	-0.810	35.864	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	400	VAL	0	-0.029	-0.034	35.615	0.001	0.001	0.000	0.000	0.000	0.000
25	A	401	GLU	-1	-0.790	-0.894	32.328	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	402	ASN	0	-0.083	-0.042	29.151	0.016	0.016	0.000	0.000	0.000	0.000
27	A	403	THR	0	-0.010	-0.042	28.302	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	404	TYR	0	0.003	-0.039	23.033	0.013	0.013	0.000	0.000	0.000	0.000
29	A	405	THR	0	-0.009	0.001	20.300	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	406	LEU	0	-0.001	0.004	17.545	0.022	0.022	0.000	0.000	0.000	0.000
31	A	407	LYS	1	0.933	0.977	13.618	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	408	VAL	0	0.031	0.011	12.275	0.023	0.023	0.000	0.000	0.000	0.000
33	A	409	ILE	0	-0.064	-0.025	7.951	0.050	0.050	0.000	0.000	0.000	0.000
34	A	410	ASN	0	0.059	0.066	8.833	-0.370	-0.370	0.000	0.000	0.000	0.000
35	A	411	LYS	1	0.853	0.923	3.522	0.243	0.636	0.016	-0.067	-0.341	0.000
36	A	412	THR	0	-0.003	-0.012	5.327	-0.312	-0.312	0.000	0.000	0.000	0.000
37	A	413	GLN	0	-0.029	-0.037	7.546	0.179	0.179	0.000	0.000	0.000	0.000
38	A	414	GLN	0	-0.014	-0.009	10.729	0.121	0.121	0.000	0.000	0.000	0.000
39	A	415	VAL	0	0.046	0.032	12.156	-0.075	-0.075	0.000	0.000	0.000	0.000
40	A	416	GLN	0	-0.028	-0.005	10.589	0.034	0.034	0.000	0.000	0.000	0.000
41	A	417	GLU	-1	-0.956	-0.981	14.071	-0.218	-0.218	0.000	0.000	0.000	0.000
42	A	418	TYR	0	-0.038	-0.033	9.908	0.011	0.011	0.000	0.000	0.000	0.000
43	A	419	ASN	0	0.025	0.018	16.153	0.035	0.035	0.000	0.000	0.000	0.000
44	A	420	LEU	0	-0.062	-0.037	16.502	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	421	ASP	-1	-0.888	-0.931	19.588	-0.106	-0.106	0.000	0.000	0.000	0.000
46	A	422	VAL	0	0.007	-0.014	21.230	0.012	0.012	0.000	0.000	0.000	0.000
47	A	423	LYS	1	0.919	0.970	21.449	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	424	GLY	0	0.026	-0.008	24.750	0.013	0.013	0.000	0.000	0.000	0.000
49	A	425	LEU	0	-0.026	-0.002	27.302	0.006	0.006	0.000	0.000	0.000	0.000
50	A	426	ASN	0	-0.020	-0.018	30.321	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	427	ASP	-1	-0.881	-0.941	33.349	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	428	VAL	0	-0.052	-0.042	29.357	0.005	0.005	0.000	0.000	0.000	0.000
53	A	429	SER	0	-0.051	-0.059	32.322	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	430	TRP	0	-0.008	-0.024	21.769	0.012	0.012	0.000	0.000	0.000	0.000
55	A	431	TYR	0	-0.044	-0.027	28.493	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	432	GLY	0	0.053	0.009	26.036	0.005	0.005	0.000	0.000	0.000	0.000
57	A	433	LYS	1	0.915	0.954	21.722	0.146	0.146	0.000	0.000	0.000	0.000
58	A	434	GLN	0	0.037	0.038	22.748	0.003	0.003	0.000	0.000	0.000	0.000
59	A	435	THR	0	0.066	0.026	20.530	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	436	ILE	0	-0.123	-0.062	16.004	0.025	0.025	0.000	0.000	0.000	0.000
61	A	437	GLN	0	0.046	0.020	17.587	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	438	VAL	0	-0.048	-0.020	12.865	0.034	0.034	0.000	0.000	0.000	0.000
63	A	439	GLU	-1	-0.838	-0.944	14.221	-0.455	-0.455	0.000	0.000	0.000	0.000
64	A	440	PRO	0	-0.010	-0.001	11.181	-0.049	-0.049	0.000	0.000	0.000	0.000
65	A	441	GLY	0	-0.009	0.004	9.611	0.091	0.091	0.000	0.000	0.000	0.000
66	A	442	GLU	-1	-0.909	-0.933	10.610	-0.211	-0.211	0.000	0.000	0.000	0.000
67	A	443	VAL	0	-0.048	-0.037	11.754	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	444	LEU	0	0.009	0.011	13.825	0.041	0.041	0.000	0.000	0.000	0.000
69	A	445	ASN	0	-0.027	-0.030	16.377	0.027	0.027	0.000	0.000	0.000	0.000
70	A	446	LEU	0	-0.020	-0.026	17.897	0.000	0.000	0.000	0.000	0.000	0.000
71	A	447	PRO	0	-0.013	0.017	21.037	0.012	0.012	0.000	0.000	0.000	0.000
72	A	448	MET	0	-0.046	-0.014	23.286	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	449	SER	0	-0.053	-0.043	25.905	0.011	0.011	0.000	0.000	0.000	0.000
74	A	450	LEU	0	-0.012	0.010	25.858	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	451	GLY	0	0.043	0.017	29.607	0.006	0.006	0.000	0.000	0.000	0.000
76	A	452	ALA	0	0.041	0.031	33.182	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	453	ASP	-1	-0.779	-0.893	35.041	0.004	0.004	0.000	0.000	0.000	0.000
78	A	454	PRO	0	-0.053	-0.050	38.182	0.004	0.004	0.000	0.000	0.000	0.000
79	A	455	ASP	-1	-0.898	-0.943	39.381	0.013	0.013	0.000	0.000	0.000	0.000
80	A	456	LYS	1	0.864	0.937	38.069	0.001	0.001	0.000	0.000	0.000	0.000
81	A	457	LEU	0	-0.079	-0.016	33.869	0.003	0.003	0.000	0.000	0.000	0.000
82	A	458	ASN	0	0.020	0.008	33.916	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	459	SER	0	-0.005	-0.010	34.592	0.001	0.001	0.000	0.000	0.000	0.000
84	A	460	ALA	0	-0.036	-0.020	35.594	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	461	ILE	0	0.003	0.007	30.188	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	462	THR	0	0.012	0.017	29.039	0.001	0.001	0.000	0.000	0.000	0.000
87	A	463	THR	0	-0.018	-0.012	24.379	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	464	ILE	0	-0.005	0.012	23.826	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	465	GLN	0	0.016	-0.001	18.614	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	466	PHE	0	0.012	0.002	18.894	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	467	ILE	0	-0.009	-0.015	16.758	0.029	0.029	0.000	0.000	0.000	0.000
92	A	468	LEU	0	-0.012	0.003	11.905	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	469	THR	0	0.027	0.002	14.436	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	470	ASP	-1	-0.794	-0.881	10.813	-0.956	-0.956	0.000	0.000	0.000	0.000
95	A	471	LYS	1	1.023	0.983	13.682	0.252	0.252	0.000	0.000	0.000	0.000
96	A	472	SER	0	-0.069	-0.018	13.672	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	473	ASN	0	-0.062	-0.044	9.572	-0.156	-0.156	0.000	0.000	0.000	0.000
98	A	474	GLU	-1	-1.014	-0.996	10.633	-0.380	-0.380	0.000	0.000	0.000	0.000
99	A	475	PHE	0	-0.004	-0.009	7.480	-0.152	-0.152	0.000	0.000	0.000	0.000
100	A	476	THR	0	-0.045	-0.061	11.306	0.014	0.014	0.000	0.000	0.000	0.000
101	A	477	ILE	0	0.000	0.017	9.513	0.057	0.057	0.000	0.000	0.000	0.000
102	A	478	GLU	-1	-0.861	-0.901	12.245	0.050	0.050	0.000	0.000	0.000	0.000
103	A	479	VAL	0	-0.045	-0.021	14.024	0.071	0.071	0.000	0.000	0.000	0.000
104	A	480	GLU	-1	-0.882	-0.921	16.403	0.137	0.137	0.000	0.000	0.000	0.000
105	A	481	SER	0	0.007	-0.001	19.689	0.003	0.003	0.000	0.000	0.000	0.000
106	A	482	ARG	1	0.818	0.876	22.556	-0.123	-0.123	0.000	0.000	0.000	0.000
107	A	483	PHE	0	0.032	0.042	26.366	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	484	ILE	0	-0.044	-0.036	29.349	0.005	0.005	0.000	0.000	0.000	0.000
109	A	485	LYS	1	0.935	0.981	32.397	-0.032	-0.032	0.000	0.000	0.000	0.000
110	A	486	LYS	1	0.978	0.987	36.049	-0.017	-0.017	0.000	0.000	0.000	0.000
111	A	487	LEU	0	0.008	0.008	38.708	0.003	0.003	0.000	0.000	0.000	0.000

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