FMO DATABASE

FMODB ID: 6NR6Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-841908.469269
FMO2-HF: Nuclear repulsion	798051.35096
FMO2-HF: Total energy	-43857.118309
FMO2-MP2: Total energy	-43984.611258

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.
0.611	2.429	-0.016	-0.907	-0.895	0.005

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 : 0.033 / q_NPA : 0.017

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	-0.007	0.008	3.766	0.237	2.055	-0.016	-0.907	-0.895	0.005
4	A	227	ALA	0	-0.003	-0.014	6.128	0.288	0.288	0.000	0.000	0.000	0.000
5	A	228	VAL	0	-0.002	-0.008	9.296	0.008	0.008	0.000	0.000	0.000	0.000
6	A	229	ALA	0	-0.011	-0.001	12.294	0.083	0.083	0.000	0.000	0.000	0.000
7	A	230	GLU	-1	-0.759	-0.844	13.483	-0.359	-0.359	0.000	0.000	0.000	0.000
8	A	231	MET	0	-0.059	-0.020	16.522	0.005	0.005	0.000	0.000	0.000	0.000
9	A	232	ASN	0	0.064	0.023	18.848	0.008	0.008	0.000	0.000	0.000	0.000
10	A	233	PRO	0	-0.045	-0.005	20.397	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	234	ASN	0	-0.017	0.007	22.592	0.005	0.005	0.000	0.000	0.000	0.000
12	A	235	VAL	0	0.023	-0.007	25.382	0.006	0.006	0.000	0.000	0.000	0.000
13	A	236	ASN	0	-0.032	-0.008	27.674	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	237	VAL	0	0.000	-0.021	30.183	0.006	0.006	0.000	0.000	0.000	0.000
15	A	238	PHE	0	-0.019	0.006	30.822	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	239	VAL	0	0.024	0.000	35.269	0.006	0.006	0.000	0.000	0.000	0.000
17	A	240	PRO	0	-0.038	-0.002	38.328	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	241	PRO	0	0.051	0.026	41.276	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	242	ARG	1	0.951	0.961	44.260	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	243	ASP	-1	-0.908	-0.952	47.451	0.008	0.008	0.000	0.000	0.000	0.000
21	A	244	GLY	0	0.009	0.011	43.947	0.001	0.001	0.000	0.000	0.000	0.000
22	A	245	PHE	0	-0.028	-0.006	42.843	0.003	0.003	0.000	0.000	0.000	0.000
23	A	246	SER	0	-0.018	-0.007	43.840	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	247	GLY	0	0.031	0.014	46.004	0.002	0.002	0.000	0.000	0.000	0.000
25	A	248	PRO	0	0.027	-0.004	47.364	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	249	ALA	0	0.004	0.021	48.407	0.001	0.001	0.000	0.000	0.000	0.000
27	A	250	PRO	0	-0.026	-0.022	46.982	0.001	0.001	0.000	0.000	0.000	0.000
28	A	251	ARG	1	0.849	0.898	46.625	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	252	LYS	1	0.952	0.974	41.033	-0.051	-0.051	0.000	0.000	0.000	0.000
30	A	253	SER	0	0.001	-0.011	40.739	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	254	LYS	1	0.956	0.968	34.734	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	255	LEU	0	-0.030	0.015	34.436	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	256	ILE	0	0.006	0.008	30.262	0.006	0.006	0.000	0.000	0.000	0.000
34	A	257	CYS	0	-0.058	-0.009	28.011	0.000	0.000	0.000	0.000	0.000	0.000
35	A	258	GLU	-1	-0.824	-0.898	26.373	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	259	ALA	0	-0.009	-0.001	22.731	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	260	THR	0	0.004	-0.015	22.730	0.000	0.000	0.000	0.000	0.000	0.000
38	A	261	ASN	0	0.011	0.001	21.653	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	262	PHE	0	0.009	0.023	16.626	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	263	THR	0	-0.008	-0.020	14.125	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	264	PRO	0	0.050	0.022	10.528	0.010	0.010	0.000	0.000	0.000	0.000
42	A	265	LYS	1	0.922	0.975	11.579	-0.045	-0.045	0.000	0.000	0.000	0.000
43	A	266	PRO	0	-0.026	-0.011	10.715	0.030	0.030	0.000	0.000	0.000	0.000
44	A	267	ILE	0	-0.005	0.002	13.641	-0.049	-0.049	0.000	0.000	0.000	0.000
45	A	268	THR	0	-0.001	0.005	17.341	0.042	0.042	0.000	0.000	0.000	0.000
46	A	269	VAL	0	0.024	0.013	20.237	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	270	SER	0	-0.025	-0.008	23.715	0.018	0.018	0.000	0.000	0.000	0.000
48	A	271	TRP	0	0.029	0.009	26.821	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	272	LEU	0	-0.017	-0.009	30.471	0.006	0.006	0.000	0.000	0.000	0.000
50	A	273	LYS	1	0.860	0.929	33.397	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	274	ASP	-1	-0.798	-0.902	37.094	0.033	0.033	0.000	0.000	0.000	0.000
52	A	275	GLY	0	-0.042	-0.031	35.738	0.001	0.001	0.000	0.000	0.000	0.000
53	A	276	LYS	1	0.869	0.942	35.321	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	277	LEU	0	0.017	0.007	28.771	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	278	VAL	0	-0.021	-0.014	32.204	0.000	0.000	0.000	0.000	0.000	0.000
56	A	279	GLU	-1	-0.903	-0.949	30.866	0.112	0.112	0.000	0.000	0.000	0.000
57	A	280	SER	0	-0.051	-0.028	31.580	0.006	0.006	0.000	0.000	0.000	0.000
58	A	281	GLY	0	0.031	0.012	33.048	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	282	PHE	0	-0.022	-0.013	26.202	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	283	THR	0	0.003	0.009	26.945	0.010	0.010	0.000	0.000	0.000	0.000
61	A	284	THR	0	-0.056	-0.036	22.352	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	285	ASP	-1	-0.875	-0.929	23.336	0.095	0.095	0.000	0.000	0.000	0.000
63	A	286	PRO	0	-0.012	-0.024	18.272	0.006	0.006	0.000	0.000	0.000	0.000
64	A	287	VAL	0	-0.007	0.007	16.061	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	288	THR	0	-0.016	-0.018	16.988	0.023	0.023	0.000	0.000	0.000	0.000
66	A	289	ILE	0	-0.012	-0.009	13.859	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	290	GLU	-1	-0.735	-0.830	17.664	-0.099	-0.099	0.000	0.000	0.000	0.000
68	A	291	ASN	0	-0.096	-0.081	19.096	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	292	LYS	1	0.865	0.921	21.752	0.196	0.196	0.000	0.000	0.000	0.000
70	A	293	GLY	0	0.052	0.032	22.714	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	294	SER	0	0.010	0.029	21.786	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	295	THR	0	-0.010	-0.021	19.191	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	296	PRO	0	-0.049	-0.007	16.700	-0.041	-0.041	0.000	0.000	0.000	0.000
74	A	297	GLN	0	0.048	0.019	14.137	0.061	0.061	0.000	0.000	0.000	0.000
75	A	298	THR	0	-0.011	-0.024	15.793	-0.025	-0.025	0.000	0.000	0.000	0.000
76	A	299	TYR	0	-0.047	-0.034	11.709	0.040	0.040	0.000	0.000	0.000	0.000
77	A	300	LYS	1	0.877	0.925	18.019	0.027	0.027	0.000	0.000	0.000	0.000
78	A	301	VAL	0	-0.039	-0.017	20.063	0.017	0.017	0.000	0.000	0.000	0.000
79	A	302	ILE	0	0.041	0.034	22.016	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	303	SER	0	0.050	0.039	25.051	0.019	0.019	0.000	0.000	0.000	0.000
81	A	304	THR	0	0.030	0.007	27.162	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	305	LEU	0	0.003	0.011	30.744	0.009	0.009	0.000	0.000	0.000	0.000
83	A	306	THR	0	-0.045	-0.029	33.106	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	307	ILE	0	-0.015	0.001	36.474	0.002	0.002	0.000	0.000	0.000	0.000
85	A	308	SER	0	0.025	0.003	39.252	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	309	GLU	-1	-0.742	-0.851	42.943	0.021	0.021	0.000	0.000	0.000	0.000
87	A	310	ILE	0	0.004	-0.002	45.676	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	311	ASP	-1	-0.812	-0.895	42.265	0.039	0.039	0.000	0.000	0.000	0.000
89	A	312	TRP	0	-0.009	-0.010	39.489	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	313	LEU	0	0.009	0.006	44.142	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	314	ASN	0	-0.088	-0.038	47.019	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	315	LEU	0	-0.038	-0.011	45.490	0.000	0.000	0.000	0.000	0.000	0.000
93	A	316	ASN	0	-0.005	0.014	41.403	0.003	0.003	0.000	0.000	0.000	0.000
94	A	317	VAL	0	-0.010	-0.008	37.911	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	318	TYR	0	0.004	-0.001	35.617	0.006	0.006	0.000	0.000	0.000	0.000
96	A	319	THR	0	-0.029	-0.040	31.108	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	321	ARG	1	0.860	0.890	24.832	-0.064	-0.064	0.000	0.000	0.000	0.000
98	A	322	VAL	0	0.026	0.002	22.096	0.012	0.012	0.000	0.000	0.000	0.000
99	A	323	ASP	-1	-0.796	-0.850	20.961	0.044	0.044	0.000	0.000	0.000	0.000
100	A	324	HIS	0	-0.025	-0.039	15.664	0.029	0.029	0.000	0.000	0.000	0.000
101	A	325	ARG	1	0.794	0.855	11.632	0.218	0.218	0.000	0.000	0.000	0.000
102	A	326	GLY	0	0.027	0.021	16.773	-0.015	-0.015	0.000	0.000	0.000	0.000
103	A	327	LEU	0	-0.033	0.007	19.697	0.001	0.001	0.000	0.000	0.000	0.000
104	A	328	THR	0	0.004	-0.030	22.174	0.010	0.010	0.000	0.000	0.000	0.000
105	A	329	PHE	0	-0.018	-0.008	21.836	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	330	LEU	0	0.004	0.006	26.732	0.011	0.011	0.000	0.000	0.000	0.000
107	A	331	LYS	1	0.900	0.960	29.799	0.000	0.000	0.000	0.000	0.000	0.000
108	A	332	ASN	0	0.035	0.025	32.082	0.011	0.011	0.000	0.000	0.000	0.000
109	A	333	VAL	0	-0.011	-0.009	35.432	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	334	SER	0	0.036	0.009	38.078	0.004	0.004	0.000	0.000	0.000	0.000
111	A	335	SER	0	-0.002	-0.019	41.497	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	336	THR	0	-0.029	0.006	44.500	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	337	CYS	0	0.008	0.005	45.322	-0.001	-0.001	0.000	0.000	0.000	0.000

Graph

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Highlights

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