FMO DATABASE

FMODB ID: LJY39

Calculation Name: 3JU0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JU0

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D6K1

Base Structure: X-ray

Registration Date: 2023-06-19

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-692456.552312
FMO2-HF: Nuclear repulsion	655242.857795
FMO2-HF: Total energy	-37213.694517
FMO2-MP2: Total energy	-37324.75996

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-17.443	-17.948	13.772	-6.813	-6.451	-0.041

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.001

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	A	4	THR	0	0.083	0.019	3.788	1.099	2.896	0.005	-1.006	-0.795	0.004
4	A	5	ASP	-1	-0.796	-0.922	6.666	0.164	0.164	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.028	0.024	9.957	-0.041	-0.041	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.884	0.937	3.886	-1.536	-1.047	0.000	-0.267	-0.222	0.001
7	A	8	VAL	0	0.000	0.004	8.026	0.008	0.008	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.934	0.979	10.521	-0.105	-0.105	0.000	0.000	0.000	0.000
9	A	10	ASN	0	0.017	-0.009	13.373	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.014	0.019	11.669	0.002	0.002	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.919	0.980	13.805	-0.193	-0.193	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.036	0.031	16.542	0.023	0.023	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.006	-0.020	16.961	0.015	0.015	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.752	-0.860	20.258	0.047	0.047	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.841	0.898	21.224	-0.062	-0.062	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.853	-0.915	17.713	0.050	0.050	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.022	-0.030	12.347	0.021	0.021	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.885	0.933	11.283	-0.091	-0.091	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.014	0.021	7.361	0.134	0.134	0.000	0.000	0.000	0.000
20	A	21	THR	0	0.010	-0.013	4.990	-0.393	-0.393	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.767	-0.847	1.774	-14.955	-19.142	12.452	-4.578	-3.686	-0.050
22	A	23	GLY	0	0.061	0.050	3.343	-1.800	-1.395	0.017	0.012	-0.433	-0.002
23	A	24	PHE	0	0.023	-0.003	5.048	0.178	0.178	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.036	0.027	8.716	0.155	0.155	0.000	0.000	0.000	0.000
25	A	26	MET	0	-0.045	-0.010	5.872	0.228	0.228	0.000	0.000	0.000	0.000
26	A	27	HIS	0	-0.013	-0.017	7.235	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.012	0.018	8.604	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.027	-0.014	10.389	0.085	0.085	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.020	-0.002	12.327	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	31	HIS	0	0.030	-0.005	15.027	0.012	0.012	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.007	0.004	18.762	0.003	0.003	0.000	0.000	0.000	0.000
32	A	33	ASN	0	0.008	0.021	21.870	0.002	0.002	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.043	0.033	20.735	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.052	-0.029	19.378	0.001	0.001	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.837	0.911	14.059	-0.091	-0.091	0.000	0.000	0.000	0.000
36	A	37	TYR	0	0.042	0.025	15.458	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	38	TRP	0	-0.013	-0.012	7.788	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.895	0.940	11.939	0.091	0.091	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.005	0.014	10.969	-0.086	-0.086	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.002	0.014	12.543	0.052	0.052	0.000	0.000	0.000	0.000
41	A	42	TYR	0	-0.067	-0.077	14.124	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.970	0.994	16.901	0.111	0.111	0.000	0.000	0.000	0.000
43	A	44	PHE	0	0.051	0.021	20.201	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.718	-0.829	23.313	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.915	0.962	22.181	0.103	0.103	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.895	0.936	24.722	0.041	0.041	0.000	0.000	0.000	0.000
47	A	48	GLN	0	-0.013	-0.019	16.835	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.775	0.879	19.497	0.074	0.074	0.000	0.000	0.000	0.000
49	A	50	LEU	0	0.002	-0.009	15.147	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.025	0.037	16.225	0.014	0.014	0.000	0.000	0.000	0.000
51	A	52	ALA	0	-0.007	-0.009	16.015	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.001	-0.009	11.699	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.026	-0.001	15.584	0.014	0.014	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.014	-0.006	16.358	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	56	TYR	0	0.006	0.039	12.775	0.008	0.008	0.000	0.000	0.000	0.000
56	A	57	PRO	0	0.026	-0.012	15.424	0.003	0.003	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.004	-0.002	16.872	0.006	0.006	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.033	-0.008	13.194	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	60	SER	0	0.020	-0.020	12.373	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.003	-0.005	4.911	-0.052	-0.052	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.016	0.011	8.322	-0.070	-0.070	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.727	-0.827	9.998	0.018	0.018	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.010	-0.004	9.249	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.815	0.859	2.160	-1.046	-0.055	1.298	-0.974	-1.315	0.006
65	A	66	GLN	0	0.025	0.018	8.758	0.016	0.016	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.836	0.902	12.393	0.019	0.019	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.823	0.871	5.610	0.497	0.497	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.785	-0.859	10.675	-0.187	-0.187	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.815	-0.882	13.062	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.009	-0.009	14.872	0.007	0.007	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.854	0.923	11.777	0.335	0.335	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.877	0.923	15.861	0.045	0.045	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.001	0.007	18.793	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.029	-0.016	16.836	0.003	0.003	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.041	-0.014	19.513	0.004	0.004	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.002	0.009	21.287	0.006	0.006	0.000	0.000	0.000	0.000
77	A	78	GLY	0	0.007	0.013	23.673	0.006	0.006	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.032	-0.023	23.868	0.005	0.005	0.000	0.000	0.000	0.000
79	A	80	ASP	-1	-0.749	-0.824	22.592	-0.083	-0.083	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.013	-0.008	18.356	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.079	-0.072	20.841	0.005	0.005	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.026	0.024	22.399	0.007	0.007	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.817	0.910	20.723	0.036	0.036	0.000	0.000	0.000	0.000
84	A	85	LYS	1	1.001	0.994	22.189	0.011	0.011	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.058	0.014	17.512	0.003	0.003	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.021	-0.004	19.911	0.003	0.003	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.785	-0.880	22.322	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.040	-0.006	17.796	0.012	0.012	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.838	0.896	18.647	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.011	-0.015	16.774	0.008	0.008	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.004	-0.021	13.740	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	GLN	0	0.030	0.014	15.961	0.011	0.011	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.754	-0.848	20.096	0.011	0.011	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.874	0.949	19.637	-0.042	-0.042	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.860	0.943	18.204	-0.100	-0.100	0.000	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)