FMO DATABASE

FMODB ID: 2J78R

Calculation Name: 4DZO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DZO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y6D9

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptH
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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-873117.127632
FMO2-HF: Nuclear repulsion	825308.698977
FMO2-HF: Total energy	-47808.428655
FMO2-MP2: Total energy	-47948.584412

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:598:SER)

Summations of interaction energy for fragment #1(A:598: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.
-4.688	-1.039	0.408	-1.523	-2.535	0.003

Interaction energy analysis for fragmet #1(A:598:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.009

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	600	GLU	-1	-0.899	-0.947	2.966	-3.554	-1.181	0.055	-1.065	-1.363	0.003
4	A	601	VAL	0	0.012	0.003	2.661	-0.601	0.412	0.354	-0.378	-0.989	0.000
5	A	602	ALA	0	-0.015	-0.010	4.112	0.237	0.500	-0.001	-0.080	-0.183	0.000
6	A	603	GLU	-1	-0.946	-0.975	6.080	0.471	0.471	0.000	0.000	0.000	0.000
7	A	604	LEU	0	0.049	0.016	7.141	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	605	LYS	1	0.958	0.979	6.527	-0.746	-0.746	0.000	0.000	0.000	0.000
9	A	606	LYS	1	1.002	1.013	10.104	-0.383	-0.383	0.000	0.000	0.000	0.000
10	A	607	GLN	0	-0.066	-0.042	11.835	-0.078	-0.078	0.000	0.000	0.000	0.000
11	A	608	VAL	0	0.004	0.012	13.167	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	609	GLU	-1	-0.924	-0.961	13.974	0.275	0.275	0.000	0.000	0.000	0.000
13	A	610	SER	0	-0.063	-0.030	16.131	-0.026	-0.026	0.000	0.000	0.000	0.000
14	A	611	ALA	0	0.001	-0.006	17.885	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	612	GLU	-1	-0.869	-0.937	19.161	0.067	0.067	0.000	0.000	0.000	0.000
16	A	613	LEU	0	-0.001	0.008	20.516	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	614	LYS	1	0.957	0.963	22.162	-0.117	-0.117	0.000	0.000	0.000	0.000
18	A	615	ASN	0	-0.006	0.001	23.685	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	616	GLN	0	-0.008	-0.009	23.544	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	617	ARG	1	0.840	0.908	26.018	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	618	LEU	0	-0.027	-0.022	27.385	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	619	LYS	1	0.916	0.969	28.734	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	620	GLU	-1	-0.802	-0.878	31.188	0.063	0.063	0.000	0.000	0.000	0.000
24	A	621	VAL	0	0.009	0.003	32.421	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	622	PHE	0	-0.006	-0.012	31.170	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	623	GLN	0	-0.006	0.009	35.781	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	624	THR	0	0.018	-0.003	37.789	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	625	LYS	1	0.898	0.941	38.498	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	626	ILE	0	-0.002	0.003	38.707	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	627	GLN	0	-0.011	-0.008	41.861	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	628	GLU	-1	-0.852	-0.910	42.809	0.039	0.039	0.000	0.000	0.000	0.000
32	A	629	PHE	0	0.001	0.004	44.067	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	630	ARG	1	0.892	0.945	45.857	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	631	LYS	1	0.970	0.985	47.864	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	632	ALA	0	0.004	-0.003	48.590	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	633	CYS	0	-0.009	-0.014	49.124	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	634	TYR	0	-0.012	0.011	52.000	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	635	THR	0	-0.051	-0.034	53.043	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	636	LEU	0	-0.056	-0.021	52.166	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	637	THR	0	-0.048	-0.028	55.109	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	638	GLY	0	0.069	0.047	57.445	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	639	TYR	0	-0.011	-0.027	57.258	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	640	GLN	0	-0.049	-0.019	53.043	0.002	0.002	0.000	0.000	0.000	0.000
44	A	641	ILE	0	0.009	-0.005	51.496	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	642	ASP	-1	-0.858	-0.917	50.600	0.022	0.022	0.000	0.000	0.000	0.000
46	A	643	ILE	0	0.001	-0.011	46.737	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	644	THR	0	-0.058	-0.027	49.021	0.000	0.000	0.000	0.000	0.000	0.000
48	A	645	THR	0	0.057	0.009	48.801	0.000	0.000	0.000	0.000	0.000	0.000
49	A	646	GLU	-1	-0.944	-0.970	50.718	0.012	0.012	0.000	0.000	0.000	0.000
50	A	647	ASN	0	-0.022	-0.012	50.073	0.000	0.000	0.000	0.000	0.000	0.000
51	A	648	GLN	0	0.049	0.026	51.975	0.000	0.000	0.000	0.000	0.000	0.000
52	A	649	TYR	0	0.003	0.008	49.601	0.001	0.001	0.000	0.000	0.000	0.000
53	A	650	ARG	1	0.957	0.991	53.605	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	651	LEU	0	-0.010	-0.008	55.176	0.001	0.001	0.000	0.000	0.000	0.000
55	A	652	THR	0	0.006	-0.001	57.345	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	653	SER	0	0.032	0.030	58.606	0.001	0.001	0.000	0.000	0.000	0.000
57	A	654	LEU	0	0.000	-0.009	58.776	0.000	0.000	0.000	0.000	0.000	0.000
58	A	655	TYR	0	-0.023	-0.020	60.841	0.000	0.000	0.000	0.000	0.000	0.000
59	A	656	ALA	0	-0.006	0.001	63.064	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	657	GLU	-1	-0.851	-0.917	64.865	0.013	0.013	0.000	0.000	0.000	0.000
61	A	658	HIS	1	0.873	0.936	66.778	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	659	PRO	0	0.000	0.007	62.983	0.000	0.000	0.000	0.000	0.000	0.000
63	A	660	GLY	0	0.008	-0.003	61.689	0.000	0.000	0.000	0.000	0.000	0.000
64	A	661	ASP	-1	-0.859	-0.919	62.703	0.013	0.013	0.000	0.000	0.000	0.000
65	A	662	CYS	0	-0.081	-0.044	59.904	0.001	0.001	0.000	0.000	0.000	0.000
66	A	663	LEU	0	0.038	0.031	60.856	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	664	ILE	0	0.035	0.019	57.738	0.001	0.001	0.000	0.000	0.000	0.000
68	A	665	PHE	0	0.026	0.020	57.434	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	666	LYS	1	0.941	0.971	55.728	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	667	ALA	0	0.027	0.006	53.212	0.000	0.000	0.000	0.000	0.000	0.000
71	A	668	THR	0	-0.044	-0.032	55.267	0.000	0.000	0.000	0.000	0.000	0.000
72	A	669	SER	0	0.032	0.019	51.692	0.000	0.000	0.000	0.000	0.000	0.000
73	A	670	PRO	0	-0.045	-0.036	47.541	0.000	0.000	0.000	0.000	0.000	0.000
74	A	671	SER	0	-0.008	-0.008	47.103	0.001	0.001	0.000	0.000	0.000	0.000
75	A	672	GLY	0	-0.029	-0.014	49.211	0.000	0.000	0.000	0.000	0.000	0.000
76	A	673	SER	0	-0.043	-0.008	51.680	0.000	0.000	0.000	0.000	0.000	0.000
77	A	674	LYS	1	0.991	1.006	54.045	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	675	MET	0	0.015	0.013	53.315	0.000	0.000	0.000	0.000	0.000	0.000
79	A	676	GLN	0	-0.034	-0.021	58.518	0.000	0.000	0.000	0.000	0.000	0.000
80	A	677	LEU	0	0.006	0.013	60.741	0.000	0.000	0.000	0.000	0.000	0.000
81	A	678	LEU	0	-0.048	-0.036	59.514	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	679	GLU	-1	-0.856	-0.909	63.316	0.010	0.010	0.000	0.000	0.000	0.000
83	A	680	THR	0	-0.074	-0.052	62.467	0.000	0.000	0.000	0.000	0.000	0.000
84	A	681	GLU	-1	-0.881	-0.952	65.609	0.011	0.011	0.000	0.000	0.000	0.000
85	A	682	PHE	0	0.116	0.049	65.340	0.000	0.000	0.000	0.000	0.000	0.000
86	A	683	SER	0	-0.035	-0.007	65.986	0.000	0.000	0.000	0.000	0.000	0.000
87	A	684	HIS	0	-0.079	-0.065	67.913	0.000	0.000	0.000	0.000	0.000	0.000
88	A	685	THR	0	-0.072	-0.025	70.274	0.000	0.000	0.000	0.000	0.000	0.000
89	A	686	VAL	0	-0.036	-0.019	68.495	0.000	0.000	0.000	0.000	0.000	0.000
90	A	687	GLY	0	0.049	0.015	71.681	0.000	0.000	0.000	0.000	0.000	0.000
91	A	688	GLU	-1	-0.894	-0.942	73.779	0.010	0.010	0.000	0.000	0.000	0.000
92	A	689	LEU	0	0.014	-0.001	69.690	0.000	0.000	0.000	0.000	0.000	0.000
93	A	690	ILE	0	-0.001	0.003	68.563	0.000	0.000	0.000	0.000	0.000	0.000
94	A	691	GLU	-1	-0.805	-0.903	70.660	0.010	0.010	0.000	0.000	0.000	0.000
95	A	692	VAL	0	-0.023	-0.026	72.772	0.000	0.000	0.000	0.000	0.000	0.000
96	A	693	HIS	0	-0.046	-0.029	68.275	0.000	0.000	0.000	0.000	0.000	0.000
97	A	694	LEU	0	-0.027	-0.013	65.143	0.000	0.000	0.000	0.000	0.000	0.000
98	A	695	ARG	1	0.864	0.943	68.483	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	696	ARG	1	0.883	0.943	71.415	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	697	GLN	0	-0.018	0.002	69.370	0.000	0.000	0.000	0.000	0.000	0.000
101	A	698	ASP	-1	-0.938	-0.939	65.722	0.013	0.013	0.000	0.000	0.000	0.000
102	A	699	SER	0	0.005	0.003	64.294	0.001	0.001	0.000	0.000	0.000	0.000
103	A	700	ILE	0	0.042	0.009	60.503	0.000	0.000	0.000	0.000	0.000	0.000
104	A	701	PRO	0	-0.005	-0.003	59.775	0.000	0.000	0.000	0.000	0.000	0.000
105	A	702	ALA	0	0.034	0.033	62.189	0.000	0.000	0.000	0.000	0.000	0.000
106	A	703	PHE	0	0.035	0.011	64.265	0.000	0.000	0.000	0.000	0.000	0.000
107	A	704	LEU	0	-0.010	-0.010	59.981	0.000	0.000	0.000	0.000	0.000	0.000
108	A	705	SER	0	-0.038	-0.021	63.523	0.000	0.000	0.000	0.000	0.000	0.000
109	A	706	SER	0	0.007	-0.021	64.915	0.000	0.000	0.000	0.000	0.000	0.000
110	A	707	LEU	0	-0.007	0.014	64.637	0.000	0.000	0.000	0.000	0.000	0.000
111	A	708	THR	0	-0.009	-0.007	62.712	0.000	0.000	0.000	0.000	0.000	0.000
112	A	709	LEU	0	-0.020	-0.014	65.777	0.000	0.000	0.000	0.000	0.000	0.000
113	A	710	GLU	-1	-0.835	-0.892	68.935	0.012	0.012	0.000	0.000	0.000	0.000
114	A	711	LEU	0	-0.002	-0.007	65.725	0.000	0.000	0.000	0.000	0.000	0.000
115	A	712	PHE	0	-0.015	-0.001	66.806	0.000	0.000	0.000	0.000	0.000	0.000
116	A	713	SER	0	-0.054	-0.050	68.886	0.000	0.000	0.000	0.000	0.000	0.000
117	A	714	ARG	1	0.798	0.892	71.439	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	715	GLN	0	-0.044	-0.005	66.266	0.000	0.000	0.000	0.000	0.000	0.000
119	A	716	THR	0	-0.093	-0.031	70.457	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:598:SER)