FMO DATABASE

FMODB ID: QYL2Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-704748.605315
FMO2-HF: Nuclear repulsion	666406.040738
FMO2-HF: Total energy	-38342.564576
FMO2-MP2: Total energy	-38454.62204

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.
-10.331	-5.452	0.472	-2.316	-3.034	0.014

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 : -0.006 / q_NPA : -0.023

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	0.095	0.056	2.677	-1.281	1.570	0.334	-1.380	-1.805	0.005
4	A	160	VAL	0	0.024	0.017	5.603	0.355	0.355	0.000	0.000	0.000	0.000
5	A	161	TYR	0	-0.001	-0.034	6.620	0.327	0.327	0.000	0.000	0.000	0.000
6	A	162	ASP	-1	-0.825	-0.874	4.439	-1.907	-1.737	-0.001	-0.018	-0.152	0.000
7	A	163	ALA	0	-0.034	-0.011	7.554	0.266	0.266	0.000	0.000	0.000	0.000
8	A	164	LEU	0	0.021	0.008	10.593	0.098	0.098	0.000	0.000	0.000	0.000
9	A	165	ALA	0	-0.004	0.010	10.315	0.104	0.104	0.000	0.000	0.000	0.000
10	A	166	GLY	0	0.031	0.010	11.768	0.095	0.095	0.000	0.000	0.000	0.000
11	A	167	GLU	-1	-0.961	-0.999	13.650	-0.268	-0.268	0.000	0.000	0.000	0.000
12	A	168	PHE	0	-0.013	-0.012	15.253	0.043	0.043	0.000	0.000	0.000	0.000
13	A	169	ILE	0	-0.013	-0.021	15.582	0.045	0.045	0.000	0.000	0.000	0.000
14	A	170	ARG	1	0.886	0.957	14.814	0.285	0.285	0.000	0.000	0.000	0.000
15	A	171	ALA	0	-0.022	0.019	19.760	0.025	0.025	0.000	0.000	0.000	0.000
16	A	172	SER	0	0.005	-0.005	21.727	0.007	0.007	0.000	0.000	0.000	0.000
17	A	173	GLY	0	0.029	0.013	25.169	0.003	0.003	0.000	0.000	0.000	0.000
18	A	174	VAL	0	0.040	0.002	24.807	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	175	GLU	-1	-0.919	-0.960	24.771	-0.130	-0.130	0.000	0.000	0.000	0.000
20	A	176	ALA	0	0.019	0.014	23.201	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	177	ARG	1	0.801	0.876	20.413	0.175	0.175	0.000	0.000	0.000	0.000
22	A	178	GLN	0	0.036	0.023	19.961	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	179	ALA	0	-0.005	-0.002	21.359	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	180	LEU	0	0.024	0.020	16.565	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	181	LEU	0	0.005	0.000	16.444	-0.057	-0.057	0.000	0.000	0.000	0.000
26	A	182	LYS	1	0.797	0.897	17.237	0.210	0.210	0.000	0.000	0.000	0.000
27	A	183	GLN	0	0.068	0.029	15.863	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	184	GLY	0	0.043	0.005	13.492	-0.055	-0.055	0.000	0.000	0.000	0.000
29	A	185	GLN	0	-0.014	-0.003	13.825	-0.059	-0.059	0.000	0.000	0.000	0.000
30	A	186	ASP	-1	-0.824	-0.900	16.266	-0.272	-0.272	0.000	0.000	0.000	0.000
31	A	187	ASN	0	-0.064	-0.045	12.006	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	188	LEU	0	0.038	0.023	11.507	-0.077	-0.077	0.000	0.000	0.000	0.000
33	A	189	SER	0	-0.087	-0.041	13.457	0.009	0.009	0.000	0.000	0.000	0.000
34	A	190	SER	0	-0.001	0.008	12.172	0.064	0.064	0.000	0.000	0.000	0.000
35	A	191	VAL	0	-0.049	-0.006	8.461	-0.141	-0.141	0.000	0.000	0.000	0.000
36	A	192	LYS	1	0.965	0.987	7.172	0.197	0.197	0.000	0.000	0.000	0.000
37	A	193	GLU	-1	-0.833	-0.929	10.676	0.034	0.034	0.000	0.000	0.000	0.000
38	A	194	THR	0	-0.007	-0.009	10.103	0.021	0.021	0.000	0.000	0.000	0.000
39	A	195	GLN	0	-0.083	-0.057	3.425	-2.939	-2.255	0.026	-0.397	-0.312	0.004
40	A	196	LYS	1	0.973	0.988	7.566	0.081	0.081	0.000	0.000	0.000	0.000
41	A	197	LYS	1	1.035	1.024	9.027	-0.492	-0.492	0.000	0.000	0.000	0.000
42	A	198	TRP	0	-0.053	-0.027	4.892	0.205	0.205	0.000	0.000	0.000	0.000
43	A	199	ALA	0	0.059	0.031	6.985	-0.285	-0.285	0.000	0.000	0.000	0.000
44	A	200	GLU	-1	-0.904	-0.961	8.223	-0.176	-0.176	0.000	0.000	0.000	0.000
45	A	201	GLN	0	-0.044	-0.015	8.454	0.058	0.058	0.000	0.000	0.000	0.000
46	A	202	TYR	0	-0.054	-0.080	4.700	-0.432	-0.344	-0.001	-0.006	-0.080	0.000
47	A	203	LEU	0	0.028	0.021	10.080	0.069	0.069	0.000	0.000	0.000	0.000
48	A	204	LYS	1	0.916	0.957	13.153	0.204	0.204	0.000	0.000	0.000	0.000
49	A	205	ILE	0	-0.035	-0.011	10.516	0.044	0.044	0.000	0.000	0.000	0.000
50	A	206	MET	0	-0.004	0.007	12.653	0.037	0.037	0.000	0.000	0.000	0.000
51	A	207	GLY	0	0.033	0.017	16.098	0.033	0.033	0.000	0.000	0.000	0.000
52	A	208	LYS	1	0.941	0.972	17.627	0.167	0.167	0.000	0.000	0.000	0.000
53	A	209	ILE	0	-0.052	-0.009	15.899	0.016	0.016	0.000	0.000	0.000	0.000
54	A	210	LEU	0	-0.053	-0.022	19.767	0.017	0.017	0.000	0.000	0.000	0.000
55	A	211	ASP	-1	-0.934	-0.949	22.112	-0.128	-0.128	0.000	0.000	0.000	0.000
56	A	212	GLN	0	-0.087	-0.065	22.358	0.014	0.014	0.000	0.000	0.000	0.000
57	A	213	GLY	0	0.031	0.026	23.128	0.010	0.010	0.000	0.000	0.000	0.000
58	A	214	GLU	-1	-0.846	-0.916	21.545	-0.178	-0.178	0.000	0.000	0.000	0.000
59	A	215	ASP	-1	-0.888	-0.935	20.977	-0.123	-0.123	0.000	0.000	0.000	0.000
60	A	216	PHE	0	-0.016	-0.006	15.717	0.004	0.004	0.000	0.000	0.000	0.000
61	A	217	PRO	0	0.047	0.014	15.031	0.004	0.004	0.000	0.000	0.000	0.000
62	A	218	ALA	0	0.052	0.029	16.686	0.005	0.005	0.000	0.000	0.000	0.000
63	A	219	SER	0	-0.041	-0.016	18.974	0.016	0.016	0.000	0.000	0.000	0.000
64	A	220	GLU	-1	-0.788	-0.892	15.295	-0.113	-0.113	0.000	0.000	0.000	0.000
65	A	221	MET	0	-0.016	-0.023	13.796	0.006	0.006	0.000	0.000	0.000	0.000
66	A	222	THR	0	-0.009	0.008	16.248	0.027	0.027	0.000	0.000	0.000	0.000
67	A	223	ARG	1	0.781	0.880	16.995	0.108	0.108	0.000	0.000	0.000	0.000
68	A	224	ILE	0	-0.022	-0.022	13.623	0.022	0.022	0.000	0.000	0.000	0.000
69	A	225	ALA	0	0.059	0.034	16.594	0.021	0.021	0.000	0.000	0.000	0.000
70	A	226	ARG	1	0.995	0.998	17.418	0.051	0.051	0.000	0.000	0.000	0.000
71	A	227	LEU	0	-0.084	-0.044	18.664	0.013	0.013	0.000	0.000	0.000	0.000
72	A	228	ILE	0	0.008	-0.003	13.718	0.015	0.015	0.000	0.000	0.000	0.000
73	A	229	GLU	-1	-0.935	-0.956	17.911	0.028	0.028	0.000	0.000	0.000	0.000
74	A	230	LYS	1	0.905	0.934	20.619	0.001	0.001	0.000	0.000	0.000	0.000
75	A	231	ASN	0	0.009	0.015	20.558	0.010	0.010	0.000	0.000	0.000	0.000
76	A	232	LYS	1	0.906	0.962	21.627	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	233	MET	0	-0.046	-0.014	18.146	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	234	SER	0	0.048	0.028	19.192	0.006	0.006	0.000	0.000	0.000	0.000
79	A	235	ASP	-1	-0.803	-0.909	17.370	0.135	0.135	0.000	0.000	0.000	0.000
80	A	236	GLY	0	0.022	0.011	14.979	0.020	0.020	0.000	0.000	0.000	0.000
81	A	237	LYS	1	0.871	0.917	14.031	-0.073	-0.073	0.000	0.000	0.000	0.000
82	A	238	LYS	1	0.950	0.974	14.425	-0.103	-0.103	0.000	0.000	0.000	0.000
83	A	239	GLU	-1	-0.923	-0.947	10.569	0.416	0.416	0.000	0.000	0.000	0.000
84	A	240	GLU	-1	-0.904	-0.946	9.785	0.235	0.235	0.000	0.000	0.000	0.000
85	A	241	LEU	0	-0.028	-0.022	10.163	-0.066	-0.066	0.000	0.000	0.000	0.000
86	A	242	GLN	0	0.045	0.021	9.234	-0.048	-0.048	0.000	0.000	0.000	0.000
87	A	243	LYS	1	0.906	0.948	2.981	-5.423	-4.456	0.114	-0.485	-0.597	0.005
88	A	244	SER	0	-0.005	-0.011	6.691	-0.294	-0.294	0.000	0.000	0.000	0.000
89	A	245	LEU	0	-0.026	0.005	9.070	-0.102	-0.102	0.000	0.000	0.000	0.000
90	A	246	ASN	0	0.004	-0.004	4.009	0.174	0.293	0.000	-0.030	-0.088	0.000
91	A	247	ILE	0	-0.022	0.006	4.937	-0.051	-0.051	0.000	0.000	0.000	0.000
92	A	248	LEU	0	0.006	-0.001	7.004	0.040	0.040	0.000	0.000	0.000	0.000
93	A	249	THR	0	-0.056	-0.026	8.866	0.060	0.060	0.000	0.000	0.000	0.000
94	A	250	ALA	0	0.006	0.017	7.832	0.087	0.087	0.000	0.000	0.000	0.000
95	A	251	PHE	0	-0.053	-0.031	9.938	0.034	0.034	0.000	0.000	0.000	0.000
96	A	252	GLN	0	-0.028	-0.015	13.109	0.088	0.088	0.000	0.000	0.000	0.000
97	A	253	LYS	1	0.978	0.996	15.492	0.133	0.133	0.000	0.000	0.000	0.000

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