FMO DATABASE

FMODB ID: Z6R1N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-875506.28166
FMO2-HF: Nuclear repulsion	827696.750464
FMO2-HF: Total energy	-47809.531196
FMO2-MP2: Total energy	-47949.6215

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.
-3.454	-0.533	0.173	-1.072	-2.023	0.001

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 : 0.041 / 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

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	A	600	GLU	-1	-0.881	-0.943	3.199	-2.533	-0.742	0.008	-0.752	-1.047	0.001
4	A	601	VAL	0	0.019	0.007	3.060	-0.247	0.665	0.166	-0.266	-0.813	0.000
5	A	602	ALA	0	-0.009	-0.006	4.466	0.311	0.529	-0.001	-0.054	-0.163	0.000
6	A	603	GLU	-1	-0.821	-0.900	6.438	0.262	0.262	0.000	0.000	0.000	0.000
7	A	604	LEU	0	0.017	0.012	7.397	0.019	0.019	0.000	0.000	0.000	0.000
8	A	605	LYS	1	0.941	0.977	6.987	-1.005	-1.005	0.000	0.000	0.000	0.000
9	A	606	LYS	1	1.028	1.022	10.391	-0.303	-0.303	0.000	0.000	0.000	0.000
10	A	607	GLN	0	-0.066	-0.038	11.274	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	608	VAL	0	0.018	0.010	13.505	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	609	GLU	-1	-0.913	-0.963	13.064	0.317	0.317	0.000	0.000	0.000	0.000
13	A	610	SER	0	-0.046	-0.028	16.214	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	611	ALA	0	-0.035	-0.009	17.889	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	612	GLU	-1	-0.826	-0.911	19.360	0.063	0.063	0.000	0.000	0.000	0.000
16	A	613	LEU	0	-0.004	0.004	20.547	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	614	LYS	1	0.964	0.971	22.154	-0.087	-0.087	0.000	0.000	0.000	0.000
18	A	615	ASN	0	0.010	0.004	23.675	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	616	GLN	0	-0.031	-0.027	23.741	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	617	ARG	1	0.826	0.879	26.088	-0.075	-0.075	0.000	0.000	0.000	0.000
21	A	618	LEU	0	-0.044	-0.017	26.959	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	619	LYS	1	0.916	0.962	26.924	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	620	GLU	-1	-0.779	-0.844	30.974	0.054	0.054	0.000	0.000	0.000	0.000
24	A	621	VAL	0	0.008	0.004	32.274	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	622	PHE	0	-0.006	-0.008	31.342	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	623	GLN	0	-0.003	0.005	35.765	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	624	THR	0	-0.005	-0.021	37.211	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	625	LYS	1	0.826	0.896	38.484	-0.035	-0.035	0.000	0.000	0.000	0.000
29	A	626	ILE	0	0.011	0.006	38.587	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	627	GLN	0	0.029	0.012	41.825	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	628	GLU	-1	-0.847	-0.889	42.650	0.030	0.030	0.000	0.000	0.000	0.000
32	A	629	PHE	0	0.044	0.018	43.900	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	630	ARG	1	0.866	0.926	45.688	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	631	LYS	1	0.981	0.989	47.778	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	632	ALA	0	-0.002	0.011	48.352	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	633	CYS	0	-0.017	-0.016	48.873	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	634	TYR	0	-0.002	0.019	51.739	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	635	THR	0	-0.060	-0.058	52.647	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	636	LEU	0	-0.041	-0.017	52.026	0.000	0.000	0.000	0.000	0.000	0.000
40	A	637	THR	0	-0.049	-0.033	55.385	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	638	GLY	0	0.042	0.032	57.723	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	639	TYR	0	-0.014	-0.028	57.413	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	640	GLN	0	-0.064	-0.031	52.875	0.001	0.001	0.000	0.000	0.000	0.000
44	A	641	ILE	0	0.019	0.008	51.414	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	642	ASP	-1	-0.817	-0.879	50.577	0.018	0.018	0.000	0.000	0.000	0.000
46	A	643	ILE	0	0.005	0.008	46.394	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	644	THR	0	-0.051	-0.032	49.327	0.000	0.000	0.000	0.000	0.000	0.000
48	A	645	THR	0	0.053	0.017	49.004	0.000	0.000	0.000	0.000	0.000	0.000
49	A	646	GLU	-1	-0.887	-0.921	50.890	0.009	0.009	0.000	0.000	0.000	0.000
50	A	647	ASN	0	0.024	0.007	50.378	0.000	0.000	0.000	0.000	0.000	0.000
51	A	648	GLN	0	0.019	0.007	52.034	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	649	TYR	0	0.004	-0.005	49.284	0.001	0.001	0.000	0.000	0.000	0.000
53	A	650	ARG	1	0.919	0.953	53.456	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	651	LEU	0	-0.011	-0.005	55.179	0.001	0.001	0.000	0.000	0.000	0.000
55	A	652	THR	0	0.019	0.003	56.893	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	653	SER	0	0.012	0.013	58.507	0.001	0.001	0.000	0.000	0.000	0.000
57	A	654	LEU	0	-0.020	-0.017	58.768	0.000	0.000	0.000	0.000	0.000	0.000
58	A	655	TYR	0	-0.025	-0.014	61.009	0.000	0.000	0.000	0.000	0.000	0.000
59	A	656	ALA	0	0.005	0.009	63.160	0.000	0.000	0.000	0.000	0.000	0.000
60	A	657	GLU	-1	-0.826	-0.893	65.001	0.010	0.010	0.000	0.000	0.000	0.000
61	A	658	HIS	1	0.811	0.901	66.774	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	659	PRO	0	-0.013	-0.004	63.046	0.000	0.000	0.000	0.000	0.000	0.000
63	A	660	GLY	0	0.022	0.000	62.152	0.000	0.000	0.000	0.000	0.000	0.000
64	A	661	ASP	-1	-0.816	-0.898	62.901	0.011	0.011	0.000	0.000	0.000	0.000
65	A	662	CYS	0	-0.077	-0.036	59.812	0.001	0.001	0.000	0.000	0.000	0.000
66	A	663	LEU	0	0.039	0.043	61.023	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	664	ILE	0	0.015	-0.001	57.267	0.001	0.001	0.000	0.000	0.000	0.000
68	A	665	PHE	0	0.039	0.024	57.517	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	666	LYS	1	0.848	0.905	55.864	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	667	ALA	0	0.036	0.027	53.407	0.000	0.000	0.000	0.000	0.000	0.000
71	A	668	THR	0	-0.012	-0.008	55.332	0.000	0.000	0.000	0.000	0.000	0.000
72	A	669	SER	0	-0.041	-0.033	51.867	0.000	0.000	0.000	0.000	0.000	0.000
73	A	670	PRO	0	0.010	0.011	47.340	0.000	0.000	0.000	0.000	0.000	0.000
74	A	671	SER	0	-0.004	-0.009	47.881	0.001	0.001	0.000	0.000	0.000	0.000
75	A	672	GLY	0	-0.030	-0.011	49.829	0.000	0.000	0.000	0.000	0.000	0.000
76	A	673	SER	0	-0.018	-0.003	52.128	0.000	0.000	0.000	0.000	0.000	0.000
77	A	674	LYS	1	0.858	0.917	54.502	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	675	MET	0	-0.003	0.010	53.383	0.000	0.000	0.000	0.000	0.000	0.000
79	A	676	GLN	0	-0.032	-0.022	58.460	0.000	0.000	0.000	0.000	0.000	0.000
80	A	677	LEU	0	0.006	0.006	60.628	0.000	0.000	0.000	0.000	0.000	0.000
81	A	678	LEU	0	-0.047	-0.023	59.229	0.000	0.000	0.000	0.000	0.000	0.000
82	A	679	GLU	-1	-0.866	-0.917	63.214	0.008	0.008	0.000	0.000	0.000	0.000
83	A	680	THR	0	-0.064	-0.052	62.508	0.000	0.000	0.000	0.000	0.000	0.000
84	A	681	GLU	-1	-0.880	-0.941	65.632	0.009	0.009	0.000	0.000	0.000	0.000
85	A	682	PHE	0	0.099	0.047	65.227	0.000	0.000	0.000	0.000	0.000	0.000
86	A	683	SER	0	-0.040	-0.024	66.124	0.000	0.000	0.000	0.000	0.000	0.000
87	A	684	HIS	0	-0.049	-0.038	68.032	0.000	0.000	0.000	0.000	0.000	0.000
88	A	685	THR	0	-0.087	-0.045	70.270	0.000	0.000	0.000	0.000	0.000	0.000
89	A	686	VAL	0	-0.003	-0.005	68.451	0.000	0.000	0.000	0.000	0.000	0.000
90	A	687	GLY	0	0.045	0.021	71.799	0.000	0.000	0.000	0.000	0.000	0.000
91	A	688	GLU	-1	-0.787	-0.894	73.534	0.008	0.008	0.000	0.000	0.000	0.000
92	A	689	LEU	0	0.008	0.006	69.859	0.000	0.000	0.000	0.000	0.000	0.000
93	A	690	ILE	0	0.009	0.010	68.316	0.000	0.000	0.000	0.000	0.000	0.000
94	A	691	GLU	-1	-0.769	-0.860	70.399	0.008	0.008	0.000	0.000	0.000	0.000
95	A	692	VAL	0	-0.036	-0.027	72.897	0.000	0.000	0.000	0.000	0.000	0.000
96	A	693	HIS	0	-0.003	0.009	68.266	0.000	0.000	0.000	0.000	0.000	0.000
97	A	694	LEU	0	-0.031	-0.002	65.288	0.000	0.000	0.000	0.000	0.000	0.000
98	A	695	ARG	1	0.858	0.914	68.710	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	696	ARG	1	0.749	0.853	71.876	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	697	GLN	0	-0.037	-0.012	69.501	0.000	0.000	0.000	0.000	0.000	0.000
101	A	698	ASP	-1	-0.856	-0.896	65.294	0.010	0.010	0.000	0.000	0.000	0.000
102	A	699	SER	0	0.006	0.004	64.484	0.001	0.001	0.000	0.000	0.000	0.000
103	A	700	ILE	0	0.050	0.013	60.371	0.000	0.000	0.000	0.000	0.000	0.000
104	A	701	PRO	0	0.008	0.000	60.024	0.000	0.000	0.000	0.000	0.000	0.000
105	A	702	ALA	0	0.019	0.033	62.287	0.000	0.000	0.000	0.000	0.000	0.000
106	A	703	PHE	0	0.027	0.001	64.430	0.000	0.000	0.000	0.000	0.000	0.000
107	A	704	LEU	0	0.002	0.004	59.737	0.000	0.000	0.000	0.000	0.000	0.000
108	A	705	SER	0	-0.022	-0.013	63.746	0.000	0.000	0.000	0.000	0.000	0.000
109	A	706	SER	0	-0.004	-0.036	65.044	0.000	0.000	0.000	0.000	0.000	0.000
110	A	707	LEU	0	0.004	0.017	64.656	0.000	0.000	0.000	0.000	0.000	0.000
111	A	708	THR	0	-0.006	-0.005	62.673	0.000	0.000	0.000	0.000	0.000	0.000
112	A	709	LEU	0	-0.019	-0.013	65.717	0.000	0.000	0.000	0.000	0.000	0.000
113	A	710	GLU	-1	-0.812	-0.877	68.986	0.009	0.009	0.000	0.000	0.000	0.000
114	A	711	LEU	0	-0.012	0.000	65.612	0.000	0.000	0.000	0.000	0.000	0.000
115	A	712	PHE	0	-0.008	-0.004	67.078	0.000	0.000	0.000	0.000	0.000	0.000
116	A	713	SER	0	-0.056	-0.039	68.943	0.000	0.000	0.000	0.000	0.000	0.000
117	A	714	ARG	1	0.781	0.864	71.464	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	715	GLN	0	-0.058	-0.011	66.367	0.000	0.000	0.000	0.000	0.000	0.000
119	A	716	THR	0	-0.090	-0.041	70.712	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)