FMO DATABASE

FMODB ID: K3NY3

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-447956.609523
FMO2-HF: Nuclear repulsion	418032.729942
FMO2-HF: Total energy	-29923.879582
FMO2-MP2: Total energy	-30011.53431

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.
-10.406	-5.496	2.116	-3.253	-3.773	-0.003

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 : -0.005 / q_NPA : -0.018

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	B	376	TYR	0	-0.047	-0.060	3.469	-2.827	0.143	-0.002	-1.487	-1.481	0.002
4	B	377	SER	0	-0.057	0.006	2.264	-8.079	-6.184	2.116	-1.725	-2.286	-0.005
5	B	378	SER	0	0.008	-0.019	3.989	-0.729	-0.684	0.002	-0.041	-0.006	0.000
6	B	379	LEU	0	-0.035	-0.023	7.194	-0.256	-0.256	0.000	0.000	0.000	0.000
7	B	380	VAL	0	-0.012	-0.016	9.144	-0.029	-0.029	0.000	0.000	0.000	0.000
8	B	381	PRO	0	-0.002	0.014	7.862	0.110	0.110	0.000	0.000	0.000	0.000
9	B	382	ILE	0	-0.007	0.012	10.516	-0.050	-0.050	0.000	0.000	0.000	0.000
10	B	383	GLU	-1	-0.883	-0.933	13.216	0.391	0.391	0.000	0.000	0.000	0.000
11	B	384	LYS	1	0.919	0.935	15.111	-0.190	-0.190	0.000	0.000	0.000	0.000
12	B	385	VAL	0	0.012	0.021	17.883	-0.035	-0.035	0.000	0.000	0.000	0.000
13	B	386	GLY	0	-0.034	-0.027	20.008	0.027	0.027	0.000	0.000	0.000	0.000
14	B	387	PHE	0	0.060	0.031	19.928	-0.017	-0.017	0.000	0.000	0.000	0.000
15	B	388	THR	0	-0.064	-0.028	25.199	0.010	0.010	0.000	0.000	0.000	0.000
16	B	389	LEU	0	0.013	0.020	28.384	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	390	LYS	1	0.892	0.921	30.123	-0.088	-0.088	0.000	0.000	0.000	0.000
18	B	391	ASN	0	0.045	0.019	31.911	-0.009	-0.009	0.000	0.000	0.000	0.000
19	B	392	GLU	-1	-0.885	-0.944	35.740	0.056	0.056	0.000	0.000	0.000	0.000
20	B	393	ILE	0	-0.019	-0.019	36.688	0.000	0.000	0.000	0.000	0.000	0.000
21	B	394	ASN	0	-0.024	-0.015	40.929	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	395	SER	0	0.028	0.024	43.947	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	396	ARG	1	0.941	0.981	42.095	-0.078	-0.078	0.000	0.000	0.000	0.000
24	B	397	ILE	0	0.014	0.011	37.948	0.003	0.003	0.000	0.000	0.000	0.000
25	B	398	ILE	0	-0.028	-0.009	35.475	0.003	0.003	0.000	0.000	0.000	0.000
26	B	399	THR	0	-0.008	-0.010	33.227	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	400	ILE	0	0.019	0.024	28.910	0.003	0.003	0.000	0.000	0.000	0.000
28	B	401	LYS	1	0.917	0.949	28.500	-0.138	-0.138	0.000	0.000	0.000	0.000
29	B	402	LEU	0	0.024	0.026	23.355	0.009	0.009	0.000	0.000	0.000	0.000
30	B	403	LYS	1	0.939	0.956	22.732	-0.208	-0.208	0.000	0.000	0.000	0.000
31	B	404	PHE	0	0.024	0.020	17.367	0.017	0.017	0.000	0.000	0.000	0.000
32	B	405	ASN	0	-0.021	-0.031	17.713	-0.069	-0.069	0.000	0.000	0.000	0.000
33	B	406	GLY	0	0.008	0.006	13.764	0.064	0.064	0.000	0.000	0.000	0.000
34	B	407	ASN	0	0.041	0.024	10.029	-0.206	-0.206	0.000	0.000	0.000	0.000
35	B	408	ASP	-1	-0.777	-0.885	7.001	0.806	0.806	0.000	0.000	0.000	0.000
36	B	409	ILE	0	-0.050	-0.008	10.092	0.194	0.194	0.000	0.000	0.000	0.000
37	B	410	PHE	0	0.020	-0.004	11.995	0.043	0.043	0.000	0.000	0.000	0.000
38	B	411	GLY	0	0.104	0.072	8.103	-0.061	-0.061	0.000	0.000	0.000	0.000
39	B	412	GLY	0	-0.016	-0.010	8.981	0.151	0.151	0.000	0.000	0.000	0.000
40	B	413	LEU	0	-0.036	-0.033	10.901	-0.070	-0.070	0.000	0.000	0.000	0.000
41	B	414	HIS	0	0.002	0.019	9.933	0.024	0.024	0.000	0.000	0.000	0.000
42	B	415	GLU	-1	-0.807	-0.893	7.808	1.860	1.860	0.000	0.000	0.000	0.000
43	B	416	LEU	0	-0.046	-0.028	10.867	-0.144	-0.144	0.000	0.000	0.000	0.000
44	B	417	CYS	0	-0.066	-0.029	14.399	-0.109	-0.109	0.000	0.000	0.000	0.000
45	B	418	ASP	-1	-0.800	-0.866	11.568	0.485	0.485	0.000	0.000	0.000	0.000
46	B	419	LYS	1	0.779	0.867	11.143	-1.255	-1.255	0.000	0.000	0.000	0.000
47	B	420	ASN	0	-0.056	-0.022	15.447	-0.050	-0.050	0.000	0.000	0.000	0.000
48	B	421	LEU	0	-0.028	0.000	16.032	-0.033	-0.033	0.000	0.000	0.000	0.000
49	B	422	ILE	0	-0.031	-0.015	17.279	-0.036	-0.036	0.000	0.000	0.000	0.000
50	B	423	ASN	0	-0.033	-0.044	19.687	-0.011	-0.011	0.000	0.000	0.000	0.000
51	B	424	ILE	0	0.068	0.021	18.082	-0.013	-0.013	0.000	0.000	0.000	0.000
52	B	425	ASP	-1	-0.842	-0.905	20.807	0.141	0.141	0.000	0.000	0.000	0.000
53	B	426	LYS	1	0.870	0.935	24.140	-0.158	-0.158	0.000	0.000	0.000	0.000
54	B	427	VAL	0	-0.043	-0.007	19.256	0.005	0.005	0.000	0.000	0.000	0.000
55	B	428	PRO	0	-0.028	0.001	22.652	-0.018	-0.018	0.000	0.000	0.000	0.000
56	B	429	GLY	0	0.112	0.044	21.948	0.018	0.018	0.000	0.000	0.000	0.000
57	B	430	TRP	0	0.028	-0.014	20.925	0.016	0.016	0.000	0.000	0.000	0.000
58	B	431	LEU	0	-0.060	-0.018	19.697	0.009	0.009	0.000	0.000	0.000	0.000
59	B	432	ALA	0	0.010	0.004	17.443	0.047	0.047	0.000	0.000	0.000	0.000
60	B	433	GLY	0	0.027	0.009	16.355	0.010	0.010	0.000	0.000	0.000	0.000
61	B	434	GLU	-1	-0.929	-0.950	17.497	0.023	0.023	0.000	0.000	0.000	0.000
62	B	435	ASN	0	-0.011	0.001	19.166	-0.008	-0.008	0.000	0.000	0.000	0.000
63	B	436	GLY	0	0.052	0.009	16.893	0.000	0.000	0.000	0.000	0.000	0.000
64	B	437	SER	0	-0.062	-0.026	16.927	-0.042	-0.042	0.000	0.000	0.000	0.000
65	B	438	PHE	0	-0.009	-0.007	17.972	0.000	0.000	0.000	0.000	0.000	0.000
66	B	439	SER	0	0.024	0.009	21.596	0.026	0.026	0.000	0.000	0.000	0.000
67	B	440	GLY	0	0.033	0.012	23.445	-0.020	-0.020	0.000	0.000	0.000	0.000
68	B	441	THR	0	-0.068	-0.023	26.570	0.020	0.020	0.000	0.000	0.000	0.000
69	B	442	ILE	0	0.010	0.012	25.530	-0.007	-0.007	0.000	0.000	0.000	0.000
70	B	443	MET	0	-0.012	-0.014	29.796	0.007	0.007	0.000	0.000	0.000	0.000
71	B	444	ASN	0	0.032	0.009	33.531	0.000	0.000	0.000	0.000	0.000	0.000
72	B	445	GLY	0	-0.016	-0.013	30.647	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	446	ASP	-1	-0.892	-0.933	30.364	0.040	0.040	0.000	0.000	0.000	0.000
74	B	447	PHE	0	-0.020	-0.019	24.256	0.008	0.008	0.000	0.000	0.000	0.000
75	B	448	GLN	0	-0.014	0.003	28.550	-0.008	-0.008	0.000	0.000	0.000	0.000
76	B	449	ARG	1	0.848	0.915	22.244	-0.013	-0.013	0.000	0.000	0.000	0.000
77	B	450	GLU	-1	-0.976	-0.977	26.828	0.050	0.050	0.000	0.000	0.000	0.000

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