FMO DATABASE

FMODB ID: 6YV2Z

Calculation Name: 2RE2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RE2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HJC9

Base Structure: X-ray

Registration Date: 2023-09-23

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-916661.633797
FMO2-HF: Nuclear repulsion	872399.826525
FMO2-HF: Total energy	-44261.807273
FMO2-MP2: Total energy	-44390.518314

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:-3:TYR)

Summations of interaction energy for fragment #1(A:-3:TYR)

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.
-17.862	-13.551	8.043	-5.59	-6.765	-0.042

Interaction energy analysis for fragmet #1(A:-3:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.024

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	-1	GLN	0	-0.040	0.001	1.922	-6.801	-6.210	7.634	-4.090	-4.135	-0.030
4	A	0	GLY	0	-0.012	-0.019	4.938	-0.436	-0.394	-0.001	-0.005	-0.036	0.000
5	A	1	MET	0	-0.037	0.003	3.678	-0.825	0.115	0.156	-0.275	-0.821	0.002
6	A	2	LYS	1	0.969	0.976	7.673	0.922	0.922	0.000	0.000	0.000	0.000
7	A	3	PHE	0	-0.020	-0.008	5.297	-0.263	-0.263	0.000	0.000	0.000	0.000
8	A	4	ALA	0	0.010	0.001	10.273	0.246	0.246	0.000	0.000	0.000	0.000
9	A	5	VAL	0	0.001	-0.010	12.820	-0.114	-0.114	0.000	0.000	0.000	0.000
10	A	6	ALA	0	-0.006	0.012	14.841	0.068	0.068	0.000	0.000	0.000	0.000
11	A	7	VAL	0	-0.023	-0.012	17.954	0.006	0.006	0.000	0.000	0.000	0.000
12	A	8	SER	0	0.097	0.042	20.428	0.006	0.006	0.000	0.000	0.000	0.000
13	A	9	GLY	0	0.016	0.026	23.920	0.005	0.005	0.000	0.000	0.000	0.000
14	A	10	ASP	-1	-0.972	-0.996	21.193	-0.222	-0.222	0.000	0.000	0.000	0.000
15	A	11	ARG	1	0.922	0.962	20.738	0.169	0.169	0.000	0.000	0.000	0.000
16	A	12	VAL	0	0.010	0.006	15.414	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	13	ASN	0	0.011	-0.004	18.436	0.065	0.065	0.000	0.000	0.000	0.000
18	A	14	GLY	0	0.095	0.062	18.536	-0.060	-0.060	0.000	0.000	0.000	0.000
19	A	15	PRO	0	-0.018	-0.014	17.809	0.021	0.021	0.000	0.000	0.000	0.000
20	A	16	GLY	0	-0.029	-0.044	19.679	0.014	0.014	0.000	0.000	0.000	0.000
21	A	17	GLU	-1	-0.805	-0.889	23.191	-0.222	-0.222	0.000	0.000	0.000	0.000
22	A	18	SER	0	-0.053	-0.014	20.982	0.017	0.017	0.000	0.000	0.000	0.000
23	A	19	GLU	-1	-0.853	-0.941	23.244	-0.213	-0.213	0.000	0.000	0.000	0.000
24	A	20	GLU	-1	-0.926	-0.961	22.310	-0.271	-0.271	0.000	0.000	0.000	0.000
25	A	21	VAL	0	-0.031	-0.013	17.302	-0.037	-0.037	0.000	0.000	0.000	0.000
26	A	22	GLN	0	-0.029	-0.015	17.602	0.028	0.028	0.000	0.000	0.000	0.000
27	A	23	ILE	0	0.006	0.000	14.115	-0.098	-0.098	0.000	0.000	0.000	0.000
28	A	24	TYR	0	0.012	-0.010	12.519	0.118	0.118	0.000	0.000	0.000	0.000
29	A	25	GLU	-1	-0.889	-0.948	11.493	-0.713	-0.713	0.000	0.000	0.000	0.000
30	A	26	THR	0	0.000	-0.006	7.140	0.226	0.226	0.000	0.000	0.000	0.000
31	A	27	ASP	-1	-0.842	-0.902	7.890	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	28	GLY	0	-0.020	-0.023	5.966	0.329	0.329	0.000	0.000	0.000	0.000
33	A	29	GLY	0	0.000	0.006	6.694	0.270	0.270	0.000	0.000	0.000	0.000
34	A	30	ASN	0	-0.102	-0.056	10.218	-0.151	-0.151	0.000	0.000	0.000	0.000
35	A	31	VAL	0	0.015	0.010	10.887	-0.082	-0.082	0.000	0.000	0.000	0.000
36	A	32	ARG	1	0.879	0.947	12.386	0.358	0.358	0.000	0.000	0.000	0.000
37	A	33	LEU	0	0.015	0.011	15.445	-0.076	-0.076	0.000	0.000	0.000	0.000
38	A	34	ILE	0	-0.041	-0.023	15.563	0.040	0.040	0.000	0.000	0.000	0.000
39	A	35	GLU	-1	-0.848	-0.913	18.624	-0.390	-0.390	0.000	0.000	0.000	0.000
40	A	36	LYS	1	0.946	0.979	19.362	0.213	0.213	0.000	0.000	0.000	0.000
41	A	37	TYR	0	-0.051	-0.024	19.482	0.021	0.021	0.000	0.000	0.000	0.000
42	A	38	SER	0	0.038	0.023	23.250	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	39	ASN	0	0.016	-0.003	22.220	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	40	PRO	0	0.012	-0.004	22.538	0.025	0.025	0.000	0.000	0.000	0.000
45	A	41	ALA	0	-0.043	-0.007	23.235	0.023	0.023	0.000	0.000	0.000	0.000
46	A	42	LEU	0	-0.006	-0.001	25.215	0.021	0.021	0.000	0.000	0.000	0.000
47	A	43	ASN	0	-0.013	-0.008	28.145	0.029	0.029	0.000	0.000	0.000	0.000
48	A	44	ALA	0	-0.062	-0.010	27.425	0.012	0.012	0.000	0.000	0.000	0.000
49	A	45	THR	0	0.008	0.001	29.381	0.007	0.007	0.000	0.000	0.000	0.000
50	A	46	ALA	0	0.027	0.006	29.423	0.005	0.005	0.000	0.000	0.000	0.000
51	A	47	ALA	0	-0.017	-0.013	24.719	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	48	ARG	1	0.871	0.923	24.166	0.206	0.206	0.000	0.000	0.000	0.000
53	A	49	GLY	0	0.054	0.022	21.057	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	50	VAL	0	0.013	0.000	19.650	-0.045	-0.045	0.000	0.000	0.000	0.000
55	A	51	PHE	0	0.004	-0.004	20.166	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	52	MET	0	-0.020	0.034	15.906	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	53	LEU	0	0.012	0.007	14.458	-0.038	-0.038	0.000	0.000	0.000	0.000
58	A	54	LYS	1	0.916	0.952	16.678	0.341	0.341	0.000	0.000	0.000	0.000
59	A	55	SER	0	0.022	0.031	19.111	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	56	ALA	0	0.055	0.010	14.392	0.001	0.001	0.000	0.000	0.000	0.000
61	A	57	LEU	0	-0.032	-0.020	14.035	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	58	ASP	-1	-0.950	-0.965	15.955	-0.387	-0.387	0.000	0.000	0.000	0.000
63	A	59	HIS	1	0.738	0.851	17.626	0.476	0.476	0.000	0.000	0.000	0.000
64	A	60	GLY	0	-0.020	0.002	15.208	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	61	ALA	0	-0.043	-0.006	11.630	-0.066	-0.066	0.000	0.000	0.000	0.000
66	A	62	ASN	0	0.001	-0.019	7.442	0.133	0.133	0.000	0.000	0.000	0.000
67	A	63	ALA	0	0.017	0.015	5.695	-0.574	-0.574	0.000	0.000	0.000	0.000
68	A	64	LEU	0	-0.024	-0.015	7.786	0.509	0.509	0.000	0.000	0.000	0.000
69	A	65	VAL	0	-0.012	-0.001	9.619	-0.232	-0.232	0.000	0.000	0.000	0.000
70	A	66	LEU	0	-0.003	-0.013	11.846	0.131	0.131	0.000	0.000	0.000	0.000
71	A	67	SER	0	0.057	0.034	14.856	-0.033	-0.033	0.000	0.000	0.000	0.000
72	A	68	GLU	-1	-0.950	-0.975	17.338	-0.283	-0.283	0.000	0.000	0.000	0.000
73	A	69	ILE	0	-0.022	-0.021	14.139	-0.053	-0.053	0.000	0.000	0.000	0.000
74	A	70	GLY	0	0.068	0.048	17.492	0.037	0.037	0.000	0.000	0.000	0.000
75	A	71	SER	0	0.034	0.010	18.403	-0.055	-0.055	0.000	0.000	0.000	0.000
76	A	72	PRO	0	0.003	-0.002	19.095	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	73	GLY	0	0.027	-0.002	18.146	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	74	PHE	0	0.047	0.014	11.330	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	75	ASN	0	-0.009	-0.026	14.536	-0.061	-0.061	0.000	0.000	0.000	0.000
80	A	76	PHE	0	-0.053	-0.009	16.424	0.012	0.012	0.000	0.000	0.000	0.000
81	A	77	ILE	0	0.010	-0.011	11.337	0.035	0.035	0.000	0.000	0.000	0.000
82	A	78	LYS	1	0.943	0.993	10.826	0.278	0.278	0.000	0.000	0.000	0.000
83	A	79	ASN	0	-0.039	-0.014	9.627	-0.092	-0.092	0.000	0.000	0.000	0.000
84	A	80	LYS	1	0.857	0.930	10.941	0.633	0.633	0.000	0.000	0.000	0.000
85	A	81	MET	0	-0.006	0.004	7.451	0.017	0.017	0.000	0.000	0.000	0.000
86	A	82	ASP	-1	-0.875	-0.912	2.708	-11.692	-9.907	0.150	-0.962	-0.975	-0.012
87	A	83	VAL	0	-0.015	-0.022	6.198	0.424	0.424	0.000	0.000	0.000	0.000
88	A	84	TYR	0	0.023	0.016	2.747	0.002	0.787	0.105	-0.247	-0.642	-0.002
89	A	85	ILE	0	-0.034	-0.020	9.440	0.138	0.138	0.000	0.000	0.000	0.000
90	A	86	VAL	0	-0.018	-0.017	12.120	0.050	0.050	0.000	0.000	0.000	0.000
91	A	87	PRO	0	0.036	0.000	14.764	0.011	0.011	0.000	0.000	0.000	0.000
92	A	88	GLU	-1	-0.894	-0.930	17.888	-0.269	-0.269	0.000	0.000	0.000	0.000
93	A	89	MET	0	-0.106	-0.039	16.876	0.036	0.036	0.000	0.000	0.000	0.000
94	A	90	PRO	0	0.034	0.001	19.184	-0.043	-0.043	0.000	0.000	0.000	0.000
95	A	91	VAL	0	0.073	0.045	15.421	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	92	ALA	0	0.004	0.000	14.965	-0.049	-0.049	0.000	0.000	0.000	0.000
97	A	93	ASP	-1	-0.882	-0.948	14.643	-0.069	-0.069	0.000	0.000	0.000	0.000
98	A	94	ALA	0	-0.006	-0.010	13.508	0.027	0.027	0.000	0.000	0.000	0.000
99	A	95	LEU	0	-0.014	-0.008	10.084	-0.071	-0.071	0.000	0.000	0.000	0.000
100	A	96	LYS	1	0.871	0.935	9.701	-0.275	-0.275	0.000	0.000	0.000	0.000
101	A	97	LEU	0	-0.015	-0.014	10.480	0.153	0.153	0.000	0.000	0.000	0.000
102	A	98	ILE	0	-0.020	-0.011	6.150	0.135	0.135	0.000	0.000	0.000	0.000
103	A	99	LEU	0	-0.006	0.002	5.326	-0.023	-0.023	0.000	0.000	0.000	0.000
104	A	100	GLU	-1	-0.895	-0.930	5.807	1.337	1.337	0.000	0.000	0.000	0.000
105	A	101	GLY	0	-0.032	-0.021	6.724	0.236	0.236	0.000	0.000	0.000	0.000
106	A	102	LYS	1	0.843	0.923	7.359	-0.690	-0.690	0.000	0.000	0.000	0.000
107	A	103	VAL	0	0.026	0.017	9.037	-0.064	-0.064	0.000	0.000	0.000	0.000
108	A	104	SER	0	-0.007	0.005	7.576	-0.188	-0.188	0.000	0.000	0.000	0.000
109	A	105	PRO	0	0.002	-0.001	4.214	-0.053	0.115	-0.001	-0.011	-0.156	0.000
110	A	106	ALA	0	-0.009	0.000	7.030	0.457	0.457	0.000	0.000	0.000	0.000
111	A	107	THR	0	-0.015	-0.026	9.644	-0.121	-0.121	0.000	0.000	0.000	0.000
112	A	108	ALA	0	-0.019	-0.016	11.731	0.079	0.079	0.000	0.000	0.000	0.000
113	A	109	PRO	0	-0.052	-0.005	14.662	-0.065	-0.065	0.000	0.000	0.000	0.000
114	A	110	THR	0	0.042	0.013	16.258	0.024	0.024	0.000	0.000	0.000	0.000
115	A	111	HIS	0	-0.030	-0.006	18.618	0.056	0.056	0.000	0.000	0.000	0.000
116	A	112	ASP	-1	-0.885	-0.966	21.163	-0.248	-0.248	0.000	0.000	0.000	0.000
117	A	113	HIS	0	0.004	0.015	23.263	0.026	0.026	0.000	0.000	0.000	0.000
118	A	114	GLY	0	-0.042	-0.017	25.355	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-3:TYR)