FMO DATABASE

FMODB ID: K9V43

Calculation Name: 5V8Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5V8Z

Chain ID: A

ChEMBL ID:

UniProt ID: E2RA18

Base Structure: X-ray

Registration Date: 2023-06-22

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-704951.835449
FMO2-HF: Nuclear repulsion	666608.351518
FMO2-HF: Total energy	-38343.48393
FMO2-MP2: Total energy	-38455.496339

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:157:SER)

Summations of interaction energy for fragment #1(A:157:SER)

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.
-6.506	-2.324	0.342	-1.855	-2.67	0.007

Interaction energy analysis for fragmet #1(A:157:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.011

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	159	PRO	0	0.100	0.059	2.574	-1.161	1.641	0.307	-1.372	-1.737	0.004
4	A	160	VAL	0	0.012	0.012	5.525	0.452	0.452	0.000	0.000	0.000	0.000
5	A	161	TYR	0	0.002	-0.028	6.665	0.339	0.339	0.000	0.000	0.000	0.000
6	A	162	ASP	-1	-0.817	-0.889	4.185	-1.888	-1.711	-0.001	-0.044	-0.132	0.000
7	A	163	ALA	0	-0.023	-0.005	7.546	0.262	0.262	0.000	0.000	0.000	0.000
8	A	164	LEU	0	0.019	0.006	10.596	0.109	0.109	0.000	0.000	0.000	0.000
9	A	165	ALA	0	-0.001	0.008	10.269	0.104	0.104	0.000	0.000	0.000	0.000
10	A	166	GLY	0	0.034	0.011	11.758	0.092	0.092	0.000	0.000	0.000	0.000
11	A	167	GLU	-1	-0.953	-0.997	13.642	-0.280	-0.280	0.000	0.000	0.000	0.000
12	A	168	PHE	0	-0.005	-0.016	15.238	0.043	0.043	0.000	0.000	0.000	0.000
13	A	169	ILE	0	-0.034	-0.030	15.418	0.043	0.043	0.000	0.000	0.000	0.000
14	A	170	ARG	1	0.896	0.967	14.765	0.268	0.268	0.000	0.000	0.000	0.000
15	A	171	ALA	0	-0.026	0.016	19.747	0.022	0.022	0.000	0.000	0.000	0.000
16	A	172	SER	0	0.005	-0.002	21.715	0.007	0.007	0.000	0.000	0.000	0.000
17	A	173	GLY	0	0.026	0.007	25.154	0.002	0.002	0.000	0.000	0.000	0.000
18	A	174	VAL	0	0.036	0.001	24.816	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	175	GLU	-1	-0.916	-0.956	24.778	-0.127	-0.127	0.000	0.000	0.000	0.000
20	A	176	ALA	0	0.014	0.009	23.273	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	177	ARG	1	0.823	0.896	20.179	0.161	0.161	0.000	0.000	0.000	0.000
22	A	178	GLN	0	0.037	0.027	19.969	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	179	ALA	0	-0.011	-0.006	21.366	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	180	LEU	0	0.022	0.021	16.697	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	181	LEU	0	0.000	-0.002	16.333	-0.056	-0.056	0.000	0.000	0.000	0.000
26	A	182	LYS	1	0.781	0.875	17.241	0.220	0.220	0.000	0.000	0.000	0.000
27	A	183	GLN	0	0.053	0.027	15.990	0.013	0.013	0.000	0.000	0.000	0.000
28	A	184	GLY	0	0.045	0.011	13.496	-0.056	-0.056	0.000	0.000	0.000	0.000
29	A	185	GLN	0	-0.019	-0.008	13.829	-0.051	-0.051	0.000	0.000	0.000	0.000
30	A	186	ASP	-1	-0.805	-0.881	16.269	-0.273	-0.273	0.000	0.000	0.000	0.000
31	A	187	ASN	0	-0.064	-0.046	12.373	-0.051	-0.051	0.000	0.000	0.000	0.000
32	A	188	LEU	0	0.030	0.017	11.811	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	189	SER	0	-0.054	-0.021	13.456	0.009	0.009	0.000	0.000	0.000	0.000
34	A	190	SER	0	-0.009	0.002	12.568	0.054	0.054	0.000	0.000	0.000	0.000
35	A	191	VAL	0	-0.058	-0.012	8.295	-0.146	-0.146	0.000	0.000	0.000	0.000
36	A	192	LYS	1	0.955	0.978	6.083	0.178	0.178	0.000	0.000	0.000	0.000
37	A	193	GLU	-1	-0.771	-0.888	10.668	0.004	0.004	0.000	0.000	0.000	0.000
38	A	194	THR	0	-0.020	-0.018	10.102	0.026	0.026	0.000	0.000	0.000	0.000
39	A	195	GLN	0	-0.063	-0.045	3.586	-0.200	0.240	0.021	-0.154	-0.306	0.001
40	A	196	LYS	1	0.920	0.965	7.557	0.018	0.018	0.000	0.000	0.000	0.000
41	A	197	LYS	1	0.949	0.983	8.985	-0.389	-0.389	0.000	0.000	0.000	0.000
42	A	198	TRP	0	-0.038	-0.031	4.880	0.170	0.170	0.000	0.000	0.000	0.000
43	A	199	ALA	0	0.065	0.030	6.975	-0.292	-0.292	0.000	0.000	0.000	0.000
44	A	200	GLU	-1	-0.874	-0.951	8.220	-0.146	-0.146	0.000	0.000	0.000	0.000
45	A	201	GLN	0	-0.054	-0.017	8.436	0.045	0.045	0.000	0.000	0.000	0.000
46	A	202	TYR	0	-0.036	-0.056	4.510	-0.478	-0.384	-0.001	-0.013	-0.081	0.000
47	A	203	LEU	0	0.028	0.020	10.081	0.065	0.065	0.000	0.000	0.000	0.000
48	A	204	LYS	1	0.888	0.938	12.734	0.192	0.192	0.000	0.000	0.000	0.000
49	A	205	ILE	0	-0.039	-0.008	10.498	0.041	0.041	0.000	0.000	0.000	0.000
50	A	206	MET	0	-0.012	0.002	12.412	0.036	0.036	0.000	0.000	0.000	0.000
51	A	207	GLY	0	0.033	0.017	16.101	0.031	0.031	0.000	0.000	0.000	0.000
52	A	208	LYS	1	0.847	0.917	17.554	0.153	0.153	0.000	0.000	0.000	0.000
53	A	209	ILE	0	-0.045	-0.006	15.834	0.017	0.017	0.000	0.000	0.000	0.000
54	A	210	LEU	0	-0.051	-0.021	19.769	0.017	0.017	0.000	0.000	0.000	0.000
55	A	211	ASP	-1	-0.878	-0.909	22.080	-0.115	-0.115	0.000	0.000	0.000	0.000
56	A	212	GLN	0	-0.071	-0.062	22.355	0.010	0.010	0.000	0.000	0.000	0.000
57	A	213	GLY	0	0.034	0.029	23.120	0.010	0.010	0.000	0.000	0.000	0.000
58	A	214	GLU	-1	-0.809	-0.895	21.577	-0.158	-0.158	0.000	0.000	0.000	0.000
59	A	215	ASP	-1	-0.885	-0.939	20.982	-0.098	-0.098	0.000	0.000	0.000	0.000
60	A	216	PHE	0	-0.007	0.011	15.590	0.004	0.004	0.000	0.000	0.000	0.000
61	A	217	PRO	0	0.052	0.019	14.976	0.004	0.004	0.000	0.000	0.000	0.000
62	A	218	ALA	0	0.049	0.029	16.687	0.008	0.008	0.000	0.000	0.000	0.000
63	A	219	SER	0	-0.022	-0.016	18.977	0.014	0.014	0.000	0.000	0.000	0.000
64	A	220	GLU	-1	-0.777	-0.858	15.216	-0.087	-0.087	0.000	0.000	0.000	0.000
65	A	221	MET	0	-0.017	-0.022	13.776	0.006	0.006	0.000	0.000	0.000	0.000
66	A	222	THR	0	-0.020	-0.006	16.247	0.027	0.027	0.000	0.000	0.000	0.000
67	A	223	ARG	1	0.761	0.845	17.304	0.082	0.082	0.000	0.000	0.000	0.000
68	A	224	ILE	0	-0.019	-0.019	13.593	0.021	0.021	0.000	0.000	0.000	0.000
69	A	225	ALA	0	0.049	0.030	16.581	0.021	0.021	0.000	0.000	0.000	0.000
70	A	226	ARG	1	0.986	0.994	17.409	0.027	0.027	0.000	0.000	0.000	0.000
71	A	227	LEU	0	-0.070	-0.033	18.655	0.011	0.011	0.000	0.000	0.000	0.000
72	A	228	ILE	0	0.003	-0.007	13.582	0.012	0.012	0.000	0.000	0.000	0.000
73	A	229	GLU	-1	-0.846	-0.900	17.901	0.051	0.051	0.000	0.000	0.000	0.000
74	A	230	LYS	1	0.847	0.894	20.610	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	231	ASN	0	-0.013	0.006	20.548	0.011	0.011	0.000	0.000	0.000	0.000
76	A	232	LYS	1	0.885	0.952	21.616	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	233	MET	0	-0.037	-0.005	17.883	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	234	SER	0	0.050	0.027	19.259	0.007	0.007	0.000	0.000	0.000	0.000
79	A	235	ASP	-1	-0.757	-0.881	17.324	0.155	0.155	0.000	0.000	0.000	0.000
80	A	236	GLY	0	0.037	0.022	14.969	0.021	0.021	0.000	0.000	0.000	0.000
81	A	237	LYS	1	0.866	0.908	14.019	-0.088	-0.088	0.000	0.000	0.000	0.000
82	A	238	LYS	1	0.915	0.940	14.413	-0.146	-0.146	0.000	0.000	0.000	0.000
83	A	239	GLU	-1	-0.919	-0.944	10.545	0.440	0.440	0.000	0.000	0.000	0.000
84	A	240	GLU	-1	-0.865	-0.916	9.773	0.263	0.263	0.000	0.000	0.000	0.000
85	A	241	LEU	0	-0.011	-0.010	10.150	-0.066	-0.066	0.000	0.000	0.000	0.000
86	A	242	GLN	0	0.035	0.016	9.287	-0.046	-0.046	0.000	0.000	0.000	0.000
87	A	243	LYS	1	0.913	0.954	3.472	-4.327	-3.762	0.017	-0.261	-0.321	0.002
88	A	244	SER	0	-0.012	-0.013	6.684	-0.283	-0.283	0.000	0.000	0.000	0.000
89	A	245	LEU	0	-0.023	0.005	9.061	-0.095	-0.095	0.000	0.000	0.000	0.000
90	A	246	ASN	0	0.008	-0.001	4.502	0.051	0.155	-0.001	-0.011	-0.093	0.000
91	A	247	ILE	0	-0.032	-0.007	4.897	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	248	LEU	0	0.018	0.007	7.006	0.045	0.045	0.000	0.000	0.000	0.000
93	A	249	THR	0	-0.056	-0.026	8.808	0.067	0.067	0.000	0.000	0.000	0.000
94	A	250	ALA	0	0.004	0.013	7.800	0.079	0.079	0.000	0.000	0.000	0.000
95	A	251	PHE	0	-0.050	-0.029	9.777	0.016	0.016	0.000	0.000	0.000	0.000
96	A	252	GLN	0	-0.023	-0.012	12.993	0.071	0.071	0.000	0.000	0.000	0.000
97	A	253	LYS	1	0.915	0.958	15.472	0.126	0.126	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:157:SER)