FMO DATABASE

FMODB ID: 89MNY

Calculation Name: 3JXO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JXO

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0F6

Base Structure: X-ray

Registration Date: 2023-09-23

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	84
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-524434.48727
FMO2-HF: Nuclear repulsion	492943.254786
FMO2-HF: Total energy	-31491.232484
FMO2-MP2: Total energy	-31584.689181

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:-7:ASN)

Summations of interaction energy for fragment #1(A:-7:ASN)

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.
-4.718	-1.704	0.835	-1.329	-2.519	0.011

Interaction energy analysis for fragmet #1(A:-7:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.037

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	-5	TYR	0	-0.006	-0.009	2.514	-4.729	-1.714	0.836	-1.327	-2.524	0.011
4	A	-4	PHE	0	0.022	0.023	5.550	-0.415	-0.416	-0.001	-0.002	0.005	0.000
5	A	-3	GLN	0	0.042	0.010	8.690	0.794	0.794	0.000	0.000	0.000	0.000
6	A	-2	GLY	0	0.010	0.022	10.708	-0.108	-0.108	0.000	0.000	0.000	0.000
7	A	-1	MET	0	0.017	0.031	14.529	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	140	ILE	0	-0.026	-0.006	16.250	0.002	0.002	0.000	0.000	0.000	0.000
9	A	141	PRO	0	0.059	0.027	19.125	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	142	LEU	0	-0.088	-0.035	19.031	0.005	0.005	0.000	0.000	0.000	0.000
11	A	143	GLU	-1	-0.887	-0.949	22.809	0.085	0.085	0.000	0.000	0.000	0.000
12	A	144	GLN	0	-0.058	-0.034	26.658	0.010	0.010	0.000	0.000	0.000	0.000
13	A	145	GLY	0	0.022	0.021	28.820	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	146	ILE	0	-0.028	-0.012	24.095	0.001	0.001	0.000	0.000	0.000	0.000
15	A	147	GLU	-1	-0.839	-0.907	20.700	0.298	0.298	0.000	0.000	0.000	0.000
16	A	148	PHE	0	-0.017	-0.003	13.269	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	149	LEU	0	0.029	0.004	16.263	0.029	0.029	0.000	0.000	0.000	0.000
18	A	150	SER	0	-0.043	-0.027	11.973	0.057	0.057	0.000	0.000	0.000	0.000
19	A	151	VAL	0	0.008	0.007	14.067	0.022	0.022	0.000	0.000	0.000	0.000
20	A	152	ASN	0	-0.050	-0.032	10.577	0.234	0.234	0.000	0.000	0.000	0.000
21	A	153	VAL	0	-0.033	-0.006	13.591	-0.106	-0.106	0.000	0.000	0.000	0.000
22	A	154	GLU	-1	-0.793	-0.898	13.990	0.868	0.868	0.000	0.000	0.000	0.000
23	A	155	GLU	-1	-0.977	-1.017	17.166	0.257	0.257	0.000	0.000	0.000	0.000
24	A	156	ASP	-1	-0.955	-0.965	20.104	0.325	0.325	0.000	0.000	0.000	0.000
25	A	157	SER	0	-0.016	0.002	19.829	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	158	PRO	0	-0.006	-0.008	21.879	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	159	VAL	0	-0.057	-0.033	21.161	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	160	VAL	0	-0.006	0.004	20.042	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	161	GLY	0	-0.020	-0.009	22.452	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	162	LYS	1	0.848	0.930	24.420	-0.181	-0.181	0.000	0.000	0.000	0.000
31	A	163	LYS	1	0.798	0.913	24.059	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	164	LEU	0	0.008	-0.004	20.677	0.003	0.003	0.000	0.000	0.000	0.000
33	A	165	LYS	1	0.800	0.891	24.840	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	166	ASP	-1	-0.865	-0.926	28.051	0.105	0.105	0.000	0.000	0.000	0.000
35	A	167	LEU	0	-0.047	-0.012	23.326	0.004	0.004	0.000	0.000	0.000	0.000
36	A	168	PRO	0	-0.020	-0.001	27.852	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	169	LEU	0	0.043	0.022	24.818	0.016	0.016	0.000	0.000	0.000	0.000
38	A	170	PRO	0	0.019	0.022	27.702	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	171	ARG	1	0.821	0.860	29.215	-0.096	-0.096	0.000	0.000	0.000	0.000
40	A	172	ASP	-1	-0.825	-0.856	29.257	0.111	0.111	0.000	0.000	0.000	0.000
41	A	173	SER	0	0.003	-0.018	24.844	0.019	0.019	0.000	0.000	0.000	0.000
42	A	174	ILE	0	0.005	0.005	21.780	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	175	ILE	0	0.036	0.017	18.612	0.027	0.027	0.000	0.000	0.000	0.000
44	A	176	ALA	0	0.000	0.001	17.554	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	177	ALA	0	-0.047	-0.038	13.827	-0.055	-0.055	0.000	0.000	0.000	0.000
46	A	178	ILE	0	0.032	0.026	13.899	0.065	0.065	0.000	0.000	0.000	0.000
47	A	179	VAL	0	-0.042	-0.006	7.271	-0.119	-0.119	0.000	0.000	0.000	0.000
48	A	180	ARG	1	0.811	0.857	10.740	-0.064	-0.064	0.000	0.000	0.000	0.000
49	A	181	GLY	0	0.031	0.013	10.052	-0.152	-0.152	0.000	0.000	0.000	0.000
50	A	182	GLY	0	-0.029	-0.011	6.334	-0.154	-0.154	0.000	0.000	0.000	0.000
51	A	183	VAL	0	-0.021	-0.006	7.078	-0.449	-0.449	0.000	0.000	0.000	0.000
52	A	184	LEU	0	-0.005	0.001	10.067	0.188	0.188	0.000	0.000	0.000	0.000
53	A	185	VAL	0	-0.009	-0.011	11.660	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	186	VAL	0	-0.004	-0.013	15.093	0.038	0.038	0.000	0.000	0.000	0.000
55	A	187	PRO	0	0.034	0.033	17.192	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	188	ARG	1	0.902	0.940	20.069	-0.040	-0.040	0.000	0.000	0.000	0.000
57	A	189	GLY	0	0.054	0.031	23.612	0.015	0.015	0.000	0.000	0.000	0.000
58	A	190	ASP	-1	-0.765	-0.882	26.279	0.070	0.070	0.000	0.000	0.000	0.000
59	A	191	THR	0	-0.006	-0.011	19.245	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	192	GLU	-1	-0.865	-0.936	22.513	0.106	0.106	0.000	0.000	0.000	0.000
61	A	193	ILE	0	0.031	0.027	18.539	0.005	0.005	0.000	0.000	0.000	0.000
62	A	194	LEU	0	-0.042	-0.028	17.562	-0.038	-0.038	0.000	0.000	0.000	0.000
63	A	195	SER	0	0.058	0.037	16.981	0.041	0.041	0.000	0.000	0.000	0.000
64	A	196	GLY	0	-0.013	-0.009	13.307	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	197	ASP	-1	-0.804	-0.862	11.970	0.516	0.516	0.000	0.000	0.000	0.000
66	A	198	LYS	1	0.833	0.917	7.018	-2.541	-2.541	0.000	0.000	0.000	0.000
67	A	199	LEU	0	0.020	0.007	11.721	-0.111	-0.111	0.000	0.000	0.000	0.000
68	A	200	TYR	0	-0.021	-0.021	7.982	0.210	0.210	0.000	0.000	0.000	0.000
69	A	201	VAL	0	-0.027	-0.012	14.906	-0.081	-0.081	0.000	0.000	0.000	0.000
70	A	202	ILE	0	0.005	0.003	18.526	0.015	0.015	0.000	0.000	0.000	0.000
71	A	203	VAL	0	-0.006	-0.007	21.129	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	204	SER	0	0.049	0.029	24.403	0.008	0.008	0.000	0.000	0.000	0.000
73	A	205	ALA	0	-0.006	-0.027	26.902	0.011	0.011	0.000	0.000	0.000	0.000
74	A	206	GLU	-1	-0.972	-0.982	27.892	0.128	0.128	0.000	0.000	0.000	0.000
75	A	207	ALA	0	-0.016	-0.004	28.159	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	208	LYS	1	0.785	0.859	21.822	-0.302	-0.302	0.000	0.000	0.000	0.000
77	A	209	GLU	-1	-0.878	-0.930	24.755	0.224	0.224	0.000	0.000	0.000	0.000
78	A	210	THR	0	0.038	0.017	26.273	0.006	0.006	0.000	0.000	0.000	0.000
79	A	211	VAL	0	-0.047	-0.023	22.243	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	212	GLU	-1	-0.891	-0.967	20.889	0.373	0.373	0.000	0.000	0.000	0.000
81	A	213	GLU	-1	-0.916	-0.959	22.948	0.208	0.208	0.000	0.000	0.000	0.000
82	A	214	THR	0	-0.073	-0.034	25.007	0.002	0.002	0.000	0.000	0.000	0.000
83	A	215	LEU	0	-0.032	-0.022	19.313	0.000	0.000	0.000	0.000	0.000	0.000
84	A	216	LEU	0	-0.056	-0.025	18.462	0.021	0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-7:ASN)