FMO DATABASE

FMODB ID: JLMV9

Calculation Name: 5X4L-C-Xray372

Preferred Name: Transitional endoplasmic reticulum ATPase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5X4L

Chain ID: C

ChEMBL ID: CHEMBL1075145

UniProt ID: P55072

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-556869.486506
FMO2-HF: Nuclear repulsion	524370.571017
FMO2-HF: Total energy	-32498.915489
FMO2-MP2: Total energy	-32593.626565

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(C:411:PRO)

Summations of interaction energy for fragment #1(C:411:PRO)

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.
-7	-0.528	1.412	-2.979	-4.905	-0.007

Interaction energy analysis for fragmet #1(C:411:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.073 / q_NPA : 0.020

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	C	413	ALA	0	0.095	0.058	3.780	-1.980	0.705	-0.036	-1.304	-1.345	0.000
4	C	414	GLN	0	-0.047	-0.033	6.901	0.510	0.510	0.000	0.000	0.000	0.000
5	C	415	LEU	0	0.020	0.013	9.846	-0.036	-0.036	0.000	0.000	0.000	0.000
6	C	416	MET	0	-0.050	-0.028	13.212	0.099	0.099	0.000	0.000	0.000	0.000
7	C	417	LEU	0	0.034	0.020	16.638	-0.022	-0.022	0.000	0.000	0.000	0.000
8	C	418	ARG	1	0.848	0.927	18.954	0.106	0.106	0.000	0.000	0.000	0.000
9	C	419	TYR	0	0.008	-0.022	19.769	-0.023	-0.023	0.000	0.000	0.000	0.000
10	C	420	PRO	0	0.038	0.017	24.915	0.007	0.007	0.000	0.000	0.000	0.000
11	C	421	ASP	-1	-0.825	-0.904	27.914	-0.041	-0.041	0.000	0.000	0.000	0.000
12	C	422	GLY	0	-0.033	-0.009	27.758	0.009	0.009	0.000	0.000	0.000	0.000
13	C	423	LYS	1	0.920	0.959	25.539	0.011	0.011	0.000	0.000	0.000	0.000
14	C	424	ARG	1	0.904	0.926	21.432	0.011	0.011	0.000	0.000	0.000	0.000
15	C	425	GLU	-1	-0.794	-0.862	17.772	-0.033	-0.033	0.000	0.000	0.000	0.000
16	C	426	GLN	0	-0.020	-0.003	13.206	-0.027	-0.027	0.000	0.000	0.000	0.000
17	C	427	ILE	0	0.014	0.018	12.604	0.058	0.058	0.000	0.000	0.000	0.000
18	C	428	THR	0	-0.002	-0.008	7.719	0.022	0.022	0.000	0.000	0.000	0.000
19	C	429	LEU	0	-0.012	-0.005	8.180	0.122	0.122	0.000	0.000	0.000	0.000
20	C	430	PRO	0	-0.039	-0.023	4.174	-0.546	-0.357	-0.001	-0.069	-0.120	0.000
21	C	431	GLU	-1	-0.829	-0.924	2.587	-4.932	-2.955	0.353	-0.670	-1.660	-0.004
22	C	432	GLN	0	0.030	0.008	2.226	-1.586	0.035	1.096	-0.936	-1.780	-0.003
23	C	433	ALA	0	-0.065	-0.026	6.479	0.517	0.517	0.000	0.000	0.000	0.000
24	C	434	LYS	1	0.946	0.982	9.149	0.402	0.402	0.000	0.000	0.000	0.000
25	C	435	LEU	0	0.068	0.041	12.698	0.022	0.022	0.000	0.000	0.000	0.000
26	C	436	LEU	0	-0.001	-0.012	14.192	0.068	0.068	0.000	0.000	0.000	0.000
27	C	437	ALA	0	-0.061	-0.039	12.450	0.075	0.075	0.000	0.000	0.000	0.000
28	C	438	LEU	0	0.021	0.021	13.804	0.066	0.066	0.000	0.000	0.000	0.000
29	C	439	VAL	0	-0.005	0.000	15.410	0.067	0.067	0.000	0.000	0.000	0.000
30	C	440	LYS	1	0.936	0.965	17.151	0.290	0.290	0.000	0.000	0.000	0.000
31	C	441	HIS	0	-0.021	-0.015	15.743	0.032	0.032	0.000	0.000	0.000	0.000
32	C	442	VAL	0	0.035	0.022	17.852	0.040	0.040	0.000	0.000	0.000	0.000
33	C	443	GLN	0	0.022	0.015	20.588	0.011	0.011	0.000	0.000	0.000	0.000
34	C	444	SER	0	-0.109	-0.059	20.111	0.026	0.026	0.000	0.000	0.000	0.000
35	C	445	LYS	1	0.877	0.948	20.182	0.039	0.039	0.000	0.000	0.000	0.000
36	C	446	GLY	0	0.010	0.010	23.412	0.008	0.008	0.000	0.000	0.000	0.000
37	C	447	TYR	0	-0.035	-0.023	24.477	0.001	0.001	0.000	0.000	0.000	0.000
38	C	448	PRO	0	0.018	0.008	24.652	-0.018	-0.018	0.000	0.000	0.000	0.000
39	C	449	ASN	0	0.141	0.068	23.494	-0.010	-0.010	0.000	0.000	0.000	0.000
40	C	450	GLU	-1	-0.986	-0.984	25.263	-0.108	-0.108	0.000	0.000	0.000	0.000
41	C	451	ARG	1	0.959	0.982	28.428	0.089	0.089	0.000	0.000	0.000	0.000
42	C	452	PHE	0	-0.033	-0.018	25.880	0.007	0.007	0.000	0.000	0.000	0.000
43	C	453	GLU	-1	-0.951	-0.978	24.056	-0.192	-0.192	0.000	0.000	0.000	0.000
44	C	454	LEU	0	-0.017	-0.019	18.080	0.006	0.006	0.000	0.000	0.000	0.000
45	C	455	LEU	0	-0.002	-0.009	21.543	-0.013	-0.013	0.000	0.000	0.000	0.000
46	C	456	THR	0	0.057	0.055	17.092	-0.004	-0.004	0.000	0.000	0.000	0.000
47	C	457	ASN	0	-0.043	-0.034	20.366	0.011	0.011	0.000	0.000	0.000	0.000
48	C	458	PHE	0	-0.055	-0.003	21.064	-0.010	-0.010	0.000	0.000	0.000	0.000
49	C	459	PRO	0	0.109	0.056	20.577	-0.007	-0.007	0.000	0.000	0.000	0.000
50	C	460	ARG	1	0.958	0.953	22.169	0.139	0.139	0.000	0.000	0.000	0.000
51	C	461	ARG	1	0.883	0.952	15.429	0.465	0.465	0.000	0.000	0.000	0.000
52	C	462	LYS	1	0.993	0.988	21.684	0.179	0.179	0.000	0.000	0.000	0.000
53	C	463	LEU	0	0.048	0.023	16.613	-0.008	-0.008	0.000	0.000	0.000	0.000
54	C	464	SER	0	0.007	0.002	19.898	-0.014	-0.014	0.000	0.000	0.000	0.000
55	C	465	HIS	0	-0.037	-0.020	22.249	0.014	0.014	0.000	0.000	0.000	0.000
56	C	466	LEU	0	-0.031	-0.004	17.112	0.002	0.002	0.000	0.000	0.000	0.000
57	C	467	ASP	-1	-0.773	-0.880	19.485	-0.383	-0.383	0.000	0.000	0.000	0.000
58	C	468	TYR	0	-0.071	-0.065	17.765	-0.043	-0.043	0.000	0.000	0.000	0.000
59	C	469	ASP	-1	-0.962	-0.994	16.456	-0.412	-0.412	0.000	0.000	0.000	0.000
60	C	470	ILE	0	0.026	0.023	13.833	-0.055	-0.055	0.000	0.000	0.000	0.000
61	C	471	THR	0	-0.055	-0.038	8.949	-0.101	-0.101	0.000	0.000	0.000	0.000
62	C	472	MET	0	0.009	-0.008	7.978	0.190	0.190	0.000	0.000	0.000	0.000
63	C	473	GLN	0	0.011	-0.003	5.450	0.375	0.375	0.000	0.000	0.000	0.000
64	C	474	GLU	-1	-0.846	-0.893	8.642	-0.688	-0.688	0.000	0.000	0.000	0.000
65	C	475	ALA	0	-0.030	-0.011	12.027	0.121	0.121	0.000	0.000	0.000	0.000
66	C	476	GLY	0	-0.003	-0.009	11.957	0.123	0.123	0.000	0.000	0.000	0.000
67	C	477	LEU	0	-0.057	-0.036	10.906	0.109	0.109	0.000	0.000	0.000	0.000
68	C	478	CYS	0	-0.061	0.021	6.478	-0.139	-0.139	0.000	0.000	0.000	0.000
69	C	479	PRO	0	0.047	0.021	7.167	0.080	0.080	0.000	0.000	0.000	0.000
70	C	480	GLN	0	-0.006	-0.021	8.163	0.101	0.101	0.000	0.000	0.000	0.000
71	C	481	GLU	-1	-0.850	-0.914	11.413	-0.343	-0.343	0.000	0.000	0.000	0.000
72	C	482	THR	0	-0.095	-0.047	14.389	0.049	0.049	0.000	0.000	0.000	0.000
73	C	483	VAL	0	-0.017	-0.010	15.623	-0.020	-0.020	0.000	0.000	0.000	0.000
74	C	484	PHE	0	-0.030	-0.037	18.578	0.035	0.035	0.000	0.000	0.000	0.000
75	C	485	VAL	0	0.002	0.006	21.505	-0.018	-0.018	0.000	0.000	0.000	0.000
76	C	486	GLN	0	0.000	-0.003	23.734	0.019	0.019	0.000	0.000	0.000	0.000
77	C	487	GLU	-1	-0.920	-0.968	27.109	-0.093	-0.093	0.000	0.000	0.000	0.000
78	C	488	ARG	1	0.853	0.941	25.456	0.173	0.173	0.000	0.000	0.000	0.000
79	C	489	ASN	0	0.008	0.008	30.667	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:411:PRO)