FMO DATABASE

FMODB ID: 49Y1N

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	OptAll
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	-706664.552839
FMO2-HF: Nuclear repulsion	668320.839085
FMO2-HF: Total energy	-38343.713754
FMO2-MP2: Total energy	-38455.637792

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.
-8.144	-3.886	0.085	-1.839	-2.501	-0.002

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 : -0.007

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	0.082	0.043	3.155	-0.413	1.661	0.041	-0.941	-1.174	0.002
4	A	160	VAL	0	0.017	0.020	5.397	0.303	0.395	-0.001	-0.003	-0.088	0.000
5	A	161	TYR	0	0.004	-0.026	6.346	0.304	0.304	0.000	0.000	0.000	0.000
6	A	162	ASP	-1	-0.813	-0.890	3.421	-4.920	-4.010	0.039	-0.510	-0.439	-0.003
7	A	163	ALA	0	-0.004	0.000	6.939	0.332	0.332	0.000	0.000	0.000	0.000
8	A	164	LEU	0	0.029	0.009	10.095	0.113	0.113	0.000	0.000	0.000	0.000
9	A	165	ALA	0	-0.020	-0.006	9.529	0.120	0.120	0.000	0.000	0.000	0.000
10	A	166	GLY	0	0.053	0.025	11.285	0.118	0.118	0.000	0.000	0.000	0.000
11	A	167	GLU	-1	-0.966	-1.006	13.145	-0.336	-0.336	0.000	0.000	0.000	0.000
12	A	168	PHE	0	0.000	-0.008	14.748	0.059	0.059	0.000	0.000	0.000	0.000
13	A	169	ILE	0	-0.032	-0.026	14.878	0.053	0.053	0.000	0.000	0.000	0.000
14	A	170	ARG	1	0.890	0.961	14.147	0.366	0.366	0.000	0.000	0.000	0.000
15	A	171	ALA	0	-0.015	0.014	19.175	0.030	0.030	0.000	0.000	0.000	0.000
16	A	172	SER	0	-0.003	-0.008	21.149	0.004	0.004	0.000	0.000	0.000	0.000
17	A	173	GLY	0	0.025	0.011	24.290	0.005	0.005	0.000	0.000	0.000	0.000
18	A	174	VAL	0	0.032	0.005	23.972	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	175	GLU	-1	-0.913	-0.954	23.725	-0.156	-0.156	0.000	0.000	0.000	0.000
20	A	176	ALA	0	0.024	0.009	22.900	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	177	ARG	1	0.832	0.911	19.352	0.208	0.208	0.000	0.000	0.000	0.000
22	A	178	GLN	0	0.040	0.019	19.170	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	179	ALA	0	-0.020	-0.007	20.668	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	180	LEU	0	0.028	0.018	16.185	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	181	LEU	0	0.006	0.002	15.615	-0.067	-0.067	0.000	0.000	0.000	0.000
26	A	182	LYS	1	0.774	0.872	16.556	0.245	0.245	0.000	0.000	0.000	0.000
27	A	183	GLN	0	0.061	0.032	15.922	0.016	0.016	0.000	0.000	0.000	0.000
28	A	184	GLY	0	0.052	0.023	13.136	-0.062	-0.062	0.000	0.000	0.000	0.000
29	A	185	GLN	0	-0.047	-0.023	13.547	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	186	ASP	-1	-0.805	-0.875	16.042	-0.301	-0.301	0.000	0.000	0.000	0.000
31	A	187	ASN	0	-0.038	-0.027	12.306	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	188	LEU	0	0.013	0.011	12.202	-0.057	-0.057	0.000	0.000	0.000	0.000
33	A	189	SER	0	-0.052	-0.038	13.706	0.024	0.024	0.000	0.000	0.000	0.000
34	A	190	SER	0	-0.012	0.001	12.972	0.064	0.064	0.000	0.000	0.000	0.000
35	A	191	VAL	0	-0.060	-0.010	8.964	-0.143	-0.143	0.000	0.000	0.000	0.000
36	A	192	LYS	1	0.952	0.977	6.228	0.954	0.954	0.000	0.000	0.000	0.000
37	A	193	GLU	-1	-0.747	-0.878	11.027	-0.209	-0.209	0.000	0.000	0.000	0.000
38	A	194	THR	0	-0.032	-0.020	10.020	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	195	GLN	0	-0.060	-0.043	3.460	0.386	0.686	0.003	-0.095	-0.207	0.000
40	A	196	LYS	1	0.896	0.952	8.119	0.172	0.172	0.000	0.000	0.000	0.000
41	A	197	LYS	1	0.947	0.966	9.449	-0.329	-0.329	0.000	0.000	0.000	0.000
42	A	198	TRP	0	-0.042	-0.024	5.022	0.389	0.389	0.000	0.000	0.000	0.000
43	A	199	ALA	0	0.069	0.028	7.130	-0.304	-0.304	0.000	0.000	0.000	0.000
44	A	200	GLU	-1	-0.828	-0.926	8.320	-0.175	-0.175	0.000	0.000	0.000	0.000
45	A	201	GLN	0	-0.045	-0.014	8.035	0.026	0.026	0.000	0.000	0.000	0.000
46	A	202	TYR	0	-0.031	-0.051	3.563	-0.856	-0.449	0.004	-0.184	-0.226	-0.001
47	A	203	LEU	0	0.036	0.018	9.700	0.077	0.077	0.000	0.000	0.000	0.000
48	A	204	LYS	1	0.818	0.908	12.394	0.224	0.224	0.000	0.000	0.000	0.000
49	A	205	ILE	0	-0.027	-0.004	9.858	0.049	0.049	0.000	0.000	0.000	0.000
50	A	206	MET	0	-0.025	-0.005	11.651	0.039	0.039	0.000	0.000	0.000	0.000
51	A	207	GLY	0	0.030	0.014	15.351	0.036	0.036	0.000	0.000	0.000	0.000
52	A	208	LYS	1	0.857	0.919	16.772	0.186	0.186	0.000	0.000	0.000	0.000
53	A	209	ILE	0	-0.037	-0.009	14.885	0.019	0.019	0.000	0.000	0.000	0.000
54	A	210	LEU	0	-0.061	-0.025	18.923	0.020	0.020	0.000	0.000	0.000	0.000
55	A	211	ASP	-1	-0.867	-0.914	21.339	-0.147	-0.147	0.000	0.000	0.000	0.000
56	A	212	GLN	0	-0.079	-0.054	21.423	0.014	0.014	0.000	0.000	0.000	0.000
57	A	213	GLY	0	0.034	0.033	22.208	0.011	0.011	0.000	0.000	0.000	0.000
58	A	214	GLU	-1	-0.809	-0.897	20.358	-0.217	-0.217	0.000	0.000	0.000	0.000
59	A	215	ASP	-1	-0.871	-0.931	19.530	-0.140	-0.140	0.000	0.000	0.000	0.000
60	A	216	PHE	0	-0.004	0.021	14.829	0.005	0.005	0.000	0.000	0.000	0.000
61	A	217	PRO	0	0.037	0.007	13.928	0.007	0.007	0.000	0.000	0.000	0.000
62	A	218	ALA	0	0.041	0.026	15.485	0.008	0.008	0.000	0.000	0.000	0.000
63	A	219	SER	0	-0.020	-0.016	17.874	0.022	0.022	0.000	0.000	0.000	0.000
64	A	220	GLU	-1	-0.764	-0.840	14.712	-0.088	-0.088	0.000	0.000	0.000	0.000
65	A	221	MET	0	-0.008	-0.013	12.805	0.015	0.015	0.000	0.000	0.000	0.000
66	A	222	THR	0	-0.034	-0.021	15.363	0.038	0.038	0.000	0.000	0.000	0.000
67	A	223	ARG	1	0.747	0.833	17.356	0.091	0.091	0.000	0.000	0.000	0.000
68	A	224	ILE	0	-0.010	-0.011	13.136	0.027	0.027	0.000	0.000	0.000	0.000
69	A	225	ALA	0	0.048	0.021	15.957	0.030	0.030	0.000	0.000	0.000	0.000
70	A	226	ARG	1	0.978	0.993	16.826	0.035	0.035	0.000	0.000	0.000	0.000
71	A	227	LEU	0	-0.049	-0.031	18.409	0.011	0.011	0.000	0.000	0.000	0.000
72	A	228	ILE	0	0.016	0.000	13.415	0.013	0.013	0.000	0.000	0.000	0.000
73	A	229	GLU	-1	-0.838	-0.884	17.763	0.054	0.054	0.000	0.000	0.000	0.000
74	A	230	LYS	1	0.838	0.895	20.168	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	231	ASN	0	0.018	0.013	20.802	0.010	0.010	0.000	0.000	0.000	0.000
76	A	232	LYS	1	0.837	0.922	21.548	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	233	MET	0	-0.027	0.008	17.590	0.001	0.001	0.000	0.000	0.000	0.000
78	A	234	SER	0	0.060	0.034	20.052	0.007	0.007	0.000	0.000	0.000	0.000
79	A	235	ASP	-1	-0.787	-0.896	17.160	0.200	0.200	0.000	0.000	0.000	0.000
80	A	236	GLY	0	0.071	0.043	15.009	0.033	0.033	0.000	0.000	0.000	0.000
81	A	237	LYS	1	0.854	0.901	14.084	-0.111	-0.111	0.000	0.000	0.000	0.000
82	A	238	LYS	1	0.888	0.928	14.525	-0.183	-0.183	0.000	0.000	0.000	0.000
83	A	239	GLU	-1	-0.914	-0.947	10.664	0.579	0.579	0.000	0.000	0.000	0.000
84	A	240	GLU	-1	-0.855	-0.909	9.738	0.361	0.361	0.000	0.000	0.000	0.000
85	A	241	LEU	0	-0.001	0.002	10.253	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	242	GLN	0	0.029	0.013	9.092	-0.070	-0.070	0.000	0.000	0.000	0.000
87	A	243	LYS	1	0.923	0.963	4.243	-4.750	-4.557	0.000	-0.054	-0.139	0.000
88	A	244	SER	0	0.004	-0.011	6.345	-0.320	-0.320	0.000	0.000	0.000	0.000
89	A	245	LEU	0	-0.033	-0.001	8.844	-0.157	-0.157	0.000	0.000	0.000	0.000
90	A	246	ASN	0	0.012	-0.001	4.089	-0.097	0.099	0.000	-0.041	-0.154	0.000
91	A	247	ILE	0	-0.050	-0.009	4.198	-0.245	-0.159	-0.001	-0.011	-0.074	0.000
92	A	248	LEU	0	0.006	0.001	6.140	0.004	0.004	0.000	0.000	0.000	0.000
93	A	249	THR	0	-0.051	-0.038	7.713	0.064	0.064	0.000	0.000	0.000	0.000
94	A	250	ALA	0	-0.011	0.009	7.148	0.107	0.107	0.000	0.000	0.000	0.000
95	A	251	PHE	0	-0.020	-0.010	9.179	0.046	0.046	0.000	0.000	0.000	0.000
96	A	252	GLN	0	-0.025	-0.012	12.263	0.125	0.125	0.000	0.000	0.000	0.000
97	A	253	LYS	1	0.900	0.949	14.709	0.177	0.177	0.000	0.000	0.000	0.000

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