FMO DATABASE

FMODB ID: 2J52R

Calculation Name: 4JVU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JVU

Chain ID: A

ChEMBL ID:

UniProt ID: P01872

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	113
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-841910.441857
FMO2-HF: Nuclear repulsion	798053.842441
FMO2-HF: Total energy	-43856.599416
FMO2-MP2: Total energy	-43984.090968

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:224:GLY)

Summations of interaction energy for fragment #1(A:224:GLY)

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.
1.237	2.25	-0.013	-0.381	-0.619	0.001

Interaction energy analysis for fragmet #1(A:224:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.010

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	226	PRO	0	-0.005	0.011	3.766	0.758	1.771	-0.013	-0.381	-0.619	0.001
4	A	227	ALA	0	-0.007	-0.018	6.120	0.423	0.423	0.000	0.000	0.000	0.000
5	A	228	VAL	0	0.001	-0.007	9.288	-0.021	-0.021	0.000	0.000	0.000	0.000
6	A	229	ALA	0	-0.008	0.001	12.286	0.072	0.072	0.000	0.000	0.000	0.000
7	A	230	GLU	-1	-0.780	-0.864	13.857	-0.514	-0.514	0.000	0.000	0.000	0.000
8	A	231	MET	0	-0.060	-0.023	16.515	0.022	0.022	0.000	0.000	0.000	0.000
9	A	232	ASN	0	0.059	0.021	18.842	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	233	PRO	0	-0.044	-0.003	20.395	0.005	0.005	0.000	0.000	0.000	0.000
11	A	234	ASN	0	-0.002	0.015	22.586	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	235	VAL	0	0.020	-0.009	25.409	0.007	0.007	0.000	0.000	0.000	0.000
13	A	236	ASN	0	-0.049	-0.014	27.670	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	237	VAL	0	0.010	-0.018	30.179	0.004	0.004	0.000	0.000	0.000	0.000
15	A	238	PHE	0	-0.017	0.006	30.947	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	239	VAL	0	0.023	0.001	35.266	0.003	0.003	0.000	0.000	0.000	0.000
17	A	240	PRO	0	-0.030	-0.005	38.325	0.000	0.000	0.000	0.000	0.000	0.000
18	A	241	PRO	0	0.046	0.027	41.273	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	242	ARG	1	0.964	0.964	44.257	0.005	0.005	0.000	0.000	0.000	0.000
20	A	243	ASP	-1	-0.917	-0.953	47.448	0.004	0.004	0.000	0.000	0.000	0.000
21	A	244	GLY	0	0.006	0.008	43.951	0.002	0.002	0.000	0.000	0.000	0.000
22	A	245	PHE	0	-0.028	-0.016	43.032	0.002	0.002	0.000	0.000	0.000	0.000
23	A	246	SER	0	-0.023	-0.003	43.871	0.000	0.000	0.000	0.000	0.000	0.000
24	A	247	GLY	0	0.030	0.009	46.004	0.001	0.001	0.000	0.000	0.000	0.000
25	A	248	PRO	0	0.028	-0.001	47.364	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	249	ALA	0	0.010	0.022	48.407	0.000	0.000	0.000	0.000	0.000	0.000
27	A	250	PRO	0	-0.027	-0.027	47.133	0.001	0.001	0.000	0.000	0.000	0.000
28	A	251	ARG	1	0.841	0.908	46.615	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	252	LYS	1	0.964	0.977	40.999	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	253	SER	0	0.006	0.007	40.739	0.000	0.000	0.000	0.000	0.000	0.000
31	A	254	LYS	1	0.960	0.965	34.920	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	255	LEU	0	-0.036	0.015	34.382	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	256	ILE	0	0.014	0.013	30.368	0.004	0.004	0.000	0.000	0.000	0.000
34	A	257	CYS	0	-0.066	-0.011	28.020	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	258	GLU	-1	-0.904	-0.954	26.369	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	259	ALA	0	0.003	0.001	22.689	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	260	THR	0	-0.009	-0.021	22.700	0.005	0.005	0.000	0.000	0.000	0.000
38	A	261	ASN	0	0.043	0.022	21.693	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	262	PHE	0	0.009	0.024	16.581	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	263	THR	0	0.016	-0.009	13.890	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	264	PRO	0	0.042	0.025	10.591	0.002	0.002	0.000	0.000	0.000	0.000
42	A	265	LYS	1	0.948	0.987	11.587	-0.099	-0.099	0.000	0.000	0.000	0.000
43	A	266	PRO	0	-0.022	-0.010	10.694	0.036	0.036	0.000	0.000	0.000	0.000
44	A	267	ILE	0	0.014	0.011	13.638	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	268	THR	0	-0.015	-0.001	17.338	0.037	0.037	0.000	0.000	0.000	0.000
46	A	269	VAL	0	0.017	0.009	20.235	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	270	SER	0	-0.013	0.004	23.713	0.014	0.014	0.000	0.000	0.000	0.000
48	A	271	TRP	0	0.026	-0.002	26.819	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	272	LEU	0	-0.020	-0.011	30.470	0.002	0.002	0.000	0.000	0.000	0.000
50	A	273	LYS	1	0.881	0.934	33.395	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	274	ASP	-1	-0.818	-0.916	37.093	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	275	GLY	0	-0.044	-0.029	35.739	0.000	0.000	0.000	0.000	0.000	0.000
53	A	276	LYS	1	0.901	0.957	35.320	0.004	0.004	0.000	0.000	0.000	0.000
54	A	277	LEU	0	0.016	0.007	28.785	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	278	VAL	0	-0.024	-0.017	32.190	0.003	0.003	0.000	0.000	0.000	0.000
56	A	279	GLU	-1	-0.907	-0.948	30.866	0.028	0.028	0.000	0.000	0.000	0.000
57	A	280	SER	0	-0.067	-0.035	31.581	0.007	0.007	0.000	0.000	0.000	0.000
58	A	281	GLY	0	0.030	0.008	33.049	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	282	PHE	0	-0.019	-0.011	26.322	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	283	THR	0	0.008	0.014	26.991	0.007	0.007	0.000	0.000	0.000	0.000
61	A	284	THR	0	-0.021	-0.012	22.340	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	285	ASP	-1	-0.874	-0.916	23.337	0.077	0.077	0.000	0.000	0.000	0.000
63	A	286	PRO	0	-0.027	-0.030	18.303	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	287	VAL	0	-0.016	0.001	16.091	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	288	THR	0	-0.062	-0.028	16.989	0.027	0.027	0.000	0.000	0.000	0.000
66	A	289	ILE	0	0.018	-0.003	14.127	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	290	GLU	-1	-0.743	-0.825	17.664	-0.073	-0.073	0.000	0.000	0.000	0.000
68	A	291	ASN	0	-0.083	-0.073	18.901	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	292	LYS	1	0.847	0.915	21.701	0.135	0.135	0.000	0.000	0.000	0.000
70	A	293	GLY	0	0.067	0.017	22.603	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	294	SER	0	0.021	0.018	21.211	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	295	THR	0	-0.045	-0.005	19.400	0.006	0.006	0.000	0.000	0.000	0.000
73	A	296	PRO	0	-0.040	0.001	16.698	-0.021	-0.021	0.000	0.000	0.000	0.000
74	A	297	GLN	0	0.038	0.007	13.769	0.037	0.037	0.000	0.000	0.000	0.000
75	A	298	THR	0	-0.031	-0.042	15.790	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	299	TYR	0	-0.042	-0.035	11.904	0.062	0.062	0.000	0.000	0.000	0.000
77	A	300	LYS	1	0.938	0.976	18.020	0.007	0.007	0.000	0.000	0.000	0.000
78	A	301	VAL	0	-0.033	-0.017	20.064	0.018	0.018	0.000	0.000	0.000	0.000
79	A	302	ILE	0	0.062	0.038	22.016	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	303	SER	0	0.014	0.008	25.051	0.010	0.010	0.000	0.000	0.000	0.000
81	A	304	THR	0	0.028	0.008	27.160	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	305	LEU	0	0.009	0.010	30.745	0.006	0.006	0.000	0.000	0.000	0.000
83	A	306	THR	0	-0.039	-0.021	33.105	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	307	ILE	0	-0.030	-0.009	36.474	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	308	SER	0	0.006	-0.006	39.251	0.002	0.002	0.000	0.000	0.000	0.000
86	A	309	GLU	-1	-0.744	-0.862	42.942	0.007	0.007	0.000	0.000	0.000	0.000
87	A	310	ILE	0	-0.010	-0.008	45.675	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	311	ASP	-1	-0.822	-0.899	42.251	0.008	0.008	0.000	0.000	0.000	0.000
89	A	312	TRP	0	0.011	-0.005	39.618	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	313	LEU	0	-0.006	-0.006	44.140	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	314	ASN	0	-0.040	-0.004	46.970	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	315	LEU	0	-0.047	-0.018	45.500	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	316	ASN	0	-0.024	0.003	41.398	0.000	0.000	0.000	0.000	0.000	0.000
94	A	317	VAL	0	-0.012	-0.013	37.875	0.000	0.000	0.000	0.000	0.000	0.000
95	A	318	TYR	0	-0.006	-0.003	35.608	0.001	0.001	0.000	0.000	0.000	0.000
96	A	319	THR	0	-0.023	-0.035	31.106	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	321	ARG	1	0.865	0.901	24.964	0.038	0.038	0.000	0.000	0.000	0.000
98	A	322	VAL	0	0.026	0.007	22.213	0.008	0.008	0.000	0.000	0.000	0.000
99	A	323	ASP	-1	-0.792	-0.849	21.031	-0.067	-0.067	0.000	0.000	0.000	0.000
100	A	324	HIS	0	-0.024	-0.044	15.481	0.018	0.018	0.000	0.000	0.000	0.000
101	A	325	ARG	1	0.796	0.866	11.170	0.466	0.466	0.000	0.000	0.000	0.000
102	A	326	GLY	0	0.029	0.024	16.769	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	327	LEU	0	-0.024	0.008	19.694	0.012	0.012	0.000	0.000	0.000	0.000
104	A	328	THR	0	-0.010	-0.043	22.170	0.005	0.005	0.000	0.000	0.000	0.000
105	A	329	PHE	0	-0.015	-0.007	22.043	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	330	LEU	0	0.012	0.005	26.728	0.008	0.008	0.000	0.000	0.000	0.000
107	A	331	LYS	1	0.925	0.976	29.796	0.033	0.033	0.000	0.000	0.000	0.000
108	A	332	ASN	0	0.023	0.015	32.078	0.007	0.007	0.000	0.000	0.000	0.000
109	A	333	VAL	0	-0.007	-0.008	35.428	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	334	SER	0	0.018	0.008	38.075	0.002	0.002	0.000	0.000	0.000	0.000
111	A	335	SER	0	0.007	-0.014	41.494	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	336	THR	0	-0.043	-0.006	44.497	0.000	0.000	0.000	0.000	0.000	0.000
113	A	337	CYS	0	0.002	0.004	45.319	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:224:GLY)