FMO DATABASE

FMODB ID: 4372N

Calculation Name: 4JE3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JE3

Chain ID: B

ChEMBL ID:

UniProt ID: P38265

Base Structure: X-ray

Registration Date: 2023-06-20

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-448076.454709
FMO2-HF: Nuclear repulsion	418152.193947
FMO2-HF: Total energy	-29924.260762
FMO2-MP2: Total energy	-30011.898161

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(B:374:SER)

Summations of interaction energy for fragment #1(B:374: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.
-18.837	-17.356	11.056	-7.094	-5.443	-0.026

Interaction energy analysis for fragmet #1(B:374:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : -0.005

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

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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	B	376	TYR	0	-0.040	-0.043	3.006	-4.966	-0.743	0.163	-2.429	-1.957	0.008
4	B	377	SER	0	-0.009	0.021	1.772	-14.117	-17.111	10.882	-4.505	-3.384	-0.033
5	B	378	SER	0	0.001	-0.025	3.545	0.083	0.335	0.011	-0.160	-0.102	-0.001
6	B	379	LEU	0	-0.036	-0.024	6.998	-0.347	-0.347	0.000	0.000	0.000	0.000
7	B	380	VAL	0	-0.008	-0.011	9.191	0.001	0.001	0.000	0.000	0.000	0.000
8	B	381	PRO	0	-0.012	0.006	7.203	0.113	0.113	0.000	0.000	0.000	0.000
9	B	382	ILE	0	0.001	0.011	9.778	0.029	0.029	0.000	0.000	0.000	0.000
10	B	383	GLU	-1	-0.879	-0.937	12.762	0.245	0.245	0.000	0.000	0.000	0.000
11	B	384	LYS	1	0.899	0.928	14.255	-0.102	-0.102	0.000	0.000	0.000	0.000
12	B	385	VAL	0	0.017	0.025	17.419	-0.025	-0.025	0.000	0.000	0.000	0.000
13	B	386	GLY	0	-0.022	-0.024	19.324	0.022	0.022	0.000	0.000	0.000	0.000
14	B	387	PHE	0	0.049	0.025	19.218	-0.012	-0.012	0.000	0.000	0.000	0.000
15	B	388	THR	0	-0.068	-0.036	24.630	0.008	0.008	0.000	0.000	0.000	0.000
16	B	389	LEU	0	0.025	0.029	27.569	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	390	LYS	1	0.885	0.917	29.278	-0.044	-0.044	0.000	0.000	0.000	0.000
18	B	391	ASN	0	0.043	0.013	31.189	-0.006	-0.006	0.000	0.000	0.000	0.000
19	B	392	GLU	-1	-0.886	-0.927	35.011	0.024	0.024	0.000	0.000	0.000	0.000
20	B	393	ILE	0	-0.015	-0.010	36.209	0.000	0.000	0.000	0.000	0.000	0.000
21	B	394	ASN	0	-0.035	-0.024	40.365	0.000	0.000	0.000	0.000	0.000	0.000
22	B	395	SER	0	0.022	0.003	43.416	0.000	0.000	0.000	0.000	0.000	0.000
23	B	396	ARG	1	0.933	0.978	41.366	-0.039	-0.039	0.000	0.000	0.000	0.000
24	B	397	ILE	0	0.017	0.002	36.948	0.001	0.001	0.000	0.000	0.000	0.000
25	B	398	ILE	0	0.005	0.014	34.735	0.003	0.003	0.000	0.000	0.000	0.000
26	B	399	THR	0	-0.022	-0.017	32.883	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	400	ILE	0	0.002	0.013	28.209	0.003	0.003	0.000	0.000	0.000	0.000
28	B	401	LYS	1	0.936	0.954	27.935	-0.076	-0.076	0.000	0.000	0.000	0.000
29	B	402	LEU	0	0.058	0.041	22.454	0.006	0.006	0.000	0.000	0.000	0.000
30	B	403	LYS	1	0.905	0.942	21.761	-0.130	-0.130	0.000	0.000	0.000	0.000
31	B	404	PHE	0	0.033	0.025	16.549	0.012	0.012	0.000	0.000	0.000	0.000
32	B	405	ASN	0	-0.007	-0.026	16.858	-0.051	-0.051	0.000	0.000	0.000	0.000
33	B	406	GLY	0	0.019	0.015	13.167	0.046	0.046	0.000	0.000	0.000	0.000
34	B	407	ASN	0	0.013	0.010	9.401	0.045	0.045	0.000	0.000	0.000	0.000
35	B	408	ASP	-1	-0.759	-0.864	6.571	-0.146	-0.146	0.000	0.000	0.000	0.000
36	B	409	ILE	0	-0.052	0.004	9.361	0.180	0.180	0.000	0.000	0.000	0.000
37	B	410	PHE	0	0.032	0.009	11.233	0.034	0.034	0.000	0.000	0.000	0.000
38	B	411	GLY	0	0.082	0.053	7.315	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	412	GLY	0	-0.020	-0.013	8.186	0.173	0.173	0.000	0.000	0.000	0.000
40	B	413	LEU	0	-0.023	-0.019	10.489	-0.053	-0.053	0.000	0.000	0.000	0.000
41	B	414	HIS	0	-0.011	0.006	9.749	0.051	0.051	0.000	0.000	0.000	0.000
42	B	415	GLU	-1	-0.807	-0.901	8.392	0.973	0.973	0.000	0.000	0.000	0.000
43	B	416	LEU	0	-0.027	-0.024	10.710	-0.139	-0.139	0.000	0.000	0.000	0.000
44	B	417	CYS	0	-0.069	-0.024	14.071	-0.088	-0.088	0.000	0.000	0.000	0.000
45	B	418	ASP	-1	-0.783	-0.868	11.288	0.215	0.215	0.000	0.000	0.000	0.000
46	B	419	LYS	1	0.758	0.866	10.123	-0.749	-0.749	0.000	0.000	0.000	0.000
47	B	420	ASN	0	-0.070	-0.039	15.133	-0.040	-0.040	0.000	0.000	0.000	0.000
48	B	421	LEU	0	-0.025	0.001	16.071	-0.018	-0.018	0.000	0.000	0.000	0.000
49	B	422	ILE	0	-0.025	-0.006	16.757	-0.013	-0.013	0.000	0.000	0.000	0.000
50	B	423	ASN	0	-0.040	-0.047	19.344	-0.009	-0.009	0.000	0.000	0.000	0.000
51	B	424	ILE	0	0.097	0.028	17.734	-0.005	-0.005	0.000	0.000	0.000	0.000
52	B	425	ASP	-1	-0.885	-0.918	20.212	0.044	0.044	0.000	0.000	0.000	0.000
53	B	426	LYS	1	0.856	0.930	23.294	-0.066	-0.066	0.000	0.000	0.000	0.000
54	B	427	VAL	0	-0.014	0.008	18.579	0.006	0.006	0.000	0.000	0.000	0.000
55	B	428	PRO	0	-0.021	0.007	21.933	-0.013	-0.013	0.000	0.000	0.000	0.000
56	B	429	GLY	0	0.102	0.041	21.071	0.012	0.012	0.000	0.000	0.000	0.000
57	B	430	TRP	0	0.043	-0.002	20.070	0.010	0.010	0.000	0.000	0.000	0.000
58	B	431	LEU	0	-0.078	-0.027	18.991	0.005	0.005	0.000	0.000	0.000	0.000
59	B	432	ALA	0	0.009	0.000	16.814	0.029	0.029	0.000	0.000	0.000	0.000
60	B	433	GLY	0	0.034	0.011	15.376	0.017	0.017	0.000	0.000	0.000	0.000
61	B	434	GLU	-1	-0.940	-0.953	16.730	-0.021	-0.021	0.000	0.000	0.000	0.000
62	B	435	ASN	0	-0.025	-0.029	19.791	0.005	0.005	0.000	0.000	0.000	0.000
63	B	436	GLY	0	0.026	0.018	17.111	0.002	0.002	0.000	0.000	0.000	0.000
64	B	437	SER	0	-0.014	-0.022	16.381	-0.027	-0.027	0.000	0.000	0.000	0.000
65	B	438	PHE	0	-0.006	0.005	17.470	0.008	0.008	0.000	0.000	0.000	0.000
66	B	439	SER	0	0.030	0.009	21.145	0.017	0.017	0.000	0.000	0.000	0.000
67	B	440	GLY	0	0.023	0.009	22.905	-0.012	-0.012	0.000	0.000	0.000	0.000
68	B	441	THR	0	-0.068	-0.023	26.114	0.012	0.012	0.000	0.000	0.000	0.000
69	B	442	ILE	0	0.002	0.006	25.105	-0.004	-0.004	0.000	0.000	0.000	0.000
70	B	443	MET	0	-0.016	-0.022	29.336	0.004	0.004	0.000	0.000	0.000	0.000
71	B	444	ASN	0	0.016	0.006	33.007	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	445	GLY	0	0.006	0.009	30.426	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	446	ASP	-1	-0.857	-0.907	29.644	0.011	0.011	0.000	0.000	0.000	0.000
74	B	447	PHE	0	-0.029	-0.017	23.627	0.009	0.009	0.000	0.000	0.000	0.000
75	B	448	GLN	0	-0.023	-0.016	28.283	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	449	ARG	1	0.837	0.919	21.523	0.020	0.020	0.000	0.000	0.000	0.000
77	B	450	GLU	-1	-0.975	-0.981	26.256	0.024	0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:374:SER)