FMO DATABASE

FMODB ID: 39NML

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	OptHSide
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-557918.34576
FMO2-HF: Nuclear repulsion	525418.706774
FMO2-HF: Total energy	-32499.638986
FMO2-MP2: Total energy	-32594.328272

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.
-8.341	-1.412	0.59	-3.211	-4.308	-0.016

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 : 0.031 / q_NPA : 0.000

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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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	0.081	0.048	3.780	-1.720	0.571	-0.037	-1.078	-1.176	0.000
4	C	414	GLN	0	-0.046	-0.037	6.645	0.604	0.604	0.000	0.000	0.000	0.000
5	C	415	LEU	0	0.036	0.015	9.849	-0.062	-0.062	0.000	0.000	0.000	0.000
6	C	416	MET	0	-0.032	0.007	12.991	0.118	0.118	0.000	0.000	0.000	0.000
7	C	417	LEU	0	0.035	0.018	16.435	-0.028	-0.028	0.000	0.000	0.000	0.000
8	C	418	ARG	1	0.850	0.904	18.808	0.096	0.096	0.000	0.000	0.000	0.000
9	C	419	TYR	0	0.024	-0.014	19.801	-0.028	-0.028	0.000	0.000	0.000	0.000
10	C	420	PRO	0	0.030	0.017	24.809	0.005	0.005	0.000	0.000	0.000	0.000
11	C	421	ASP	-1	-0.830	-0.912	27.860	-0.016	-0.016	0.000	0.000	0.000	0.000
12	C	422	GLY	0	-0.023	-0.004	27.668	0.008	0.008	0.000	0.000	0.000	0.000
13	C	423	LYS	1	0.917	0.967	25.601	-0.007	-0.007	0.000	0.000	0.000	0.000
14	C	424	ARG	1	0.877	0.903	20.800	-0.006	-0.006	0.000	0.000	0.000	0.000
15	C	425	GLU	-1	-0.758	-0.833	17.744	0.042	0.042	0.000	0.000	0.000	0.000
16	C	426	GLN	0	-0.024	-0.003	13.378	-0.051	-0.051	0.000	0.000	0.000	0.000
17	C	427	ILE	0	0.017	0.017	12.717	0.071	0.071	0.000	0.000	0.000	0.000
18	C	428	THR	0	-0.016	-0.008	7.619	0.059	0.059	0.000	0.000	0.000	0.000
19	C	429	LEU	0	-0.001	0.003	8.201	0.168	0.168	0.000	0.000	0.000	0.000
20	C	430	PRO	0	-0.016	-0.014	4.160	-0.520	-0.334	-0.001	-0.065	-0.120	0.000
21	C	431	GLU	-1	-0.834	-0.918	2.601	-7.080	-3.936	0.505	-1.481	-2.168	-0.013
22	C	432	GLN	0	0.048	0.014	2.641	-1.754	-0.446	0.123	-0.587	-0.844	-0.003
23	C	433	ALA	0	-0.055	-0.024	6.325	0.585	0.585	0.000	0.000	0.000	0.000
24	C	434	LYS	1	0.829	0.910	9.099	0.363	0.363	0.000	0.000	0.000	0.000
25	C	435	LEU	0	0.068	0.038	12.670	0.040	0.040	0.000	0.000	0.000	0.000
26	C	436	LEU	0	0.001	-0.007	14.394	0.078	0.078	0.000	0.000	0.000	0.000
27	C	437	ALA	0	-0.062	-0.040	12.366	0.085	0.085	0.000	0.000	0.000	0.000
28	C	438	LEU	0	0.026	0.020	13.842	0.079	0.079	0.000	0.000	0.000	0.000
29	C	439	VAL	0	-0.013	-0.001	15.384	0.069	0.069	0.000	0.000	0.000	0.000
30	C	440	LYS	1	0.941	0.967	17.093	0.229	0.229	0.000	0.000	0.000	0.000
31	C	441	HIS	0	-0.016	-0.006	15.829	0.042	0.042	0.000	0.000	0.000	0.000
32	C	442	VAL	0	0.029	0.015	17.944	0.039	0.039	0.000	0.000	0.000	0.000
33	C	443	GLN	0	0.032	0.028	20.645	0.006	0.006	0.000	0.000	0.000	0.000
34	C	444	SER	0	-0.102	-0.054	20.245	0.026	0.026	0.000	0.000	0.000	0.000
35	C	445	LYS	1	0.813	0.897	20.031	-0.025	-0.025	0.000	0.000	0.000	0.000
36	C	446	GLY	0	0.010	0.011	23.585	0.005	0.005	0.000	0.000	0.000	0.000
37	C	447	TYR	0	-0.035	-0.023	24.528	-0.003	-0.003	0.000	0.000	0.000	0.000
38	C	448	PRO	0	0.029	0.015	24.657	-0.018	-0.018	0.000	0.000	0.000	0.000
39	C	449	ASN	0	0.133	0.060	23.513	-0.017	-0.017	0.000	0.000	0.000	0.000
40	C	450	GLU	-1	-0.976	-0.977	25.350	-0.094	-0.094	0.000	0.000	0.000	0.000
41	C	451	ARG	1	0.888	0.934	28.546	0.069	0.069	0.000	0.000	0.000	0.000
42	C	452	PHE	0	-0.015	-0.013	25.914	0.005	0.005	0.000	0.000	0.000	0.000
43	C	453	GLU	-1	-0.849	-0.913	24.094	-0.188	-0.188	0.000	0.000	0.000	0.000
44	C	454	LEU	0	-0.001	-0.011	18.024	0.009	0.009	0.000	0.000	0.000	0.000
45	C	455	LEU	0	-0.003	-0.006	21.489	-0.016	-0.016	0.000	0.000	0.000	0.000
46	C	456	THR	0	-0.019	0.018	16.792	0.009	0.009	0.000	0.000	0.000	0.000
47	C	457	ASN	0	-0.005	-0.016	20.133	0.020	0.020	0.000	0.000	0.000	0.000
48	C	458	PHE	0	-0.025	0.021	20.733	-0.011	-0.011	0.000	0.000	0.000	0.000
49	C	459	PRO	0	0.102	0.047	20.336	-0.011	-0.011	0.000	0.000	0.000	0.000
50	C	460	ARG	1	0.911	0.930	21.903	0.147	0.147	0.000	0.000	0.000	0.000
51	C	461	ARG	1	0.803	0.903	14.857	0.499	0.499	0.000	0.000	0.000	0.000
52	C	462	LYS	1	0.896	0.923	21.550	0.178	0.178	0.000	0.000	0.000	0.000
53	C	463	LEU	0	0.054	0.025	16.444	-0.006	-0.006	0.000	0.000	0.000	0.000
54	C	464	SER	0	-0.016	-0.014	19.886	-0.012	-0.012	0.000	0.000	0.000	0.000
55	C	465	HIS	0	-0.045	-0.024	22.312	0.014	0.014	0.000	0.000	0.000	0.000
56	C	466	LEU	0	-0.018	0.007	17.167	0.001	0.001	0.000	0.000	0.000	0.000
57	C	467	ASP	-1	-0.793	-0.895	19.614	-0.372	-0.372	0.000	0.000	0.000	0.000
58	C	468	TYR	0	-0.055	-0.058	17.986	-0.045	-0.045	0.000	0.000	0.000	0.000
59	C	469	ASP	-1	-0.817	-0.912	16.503	-0.416	-0.416	0.000	0.000	0.000	0.000
60	C	470	ILE	0	0.003	0.016	14.007	-0.059	-0.059	0.000	0.000	0.000	0.000
61	C	471	THR	0	-0.043	-0.049	8.906	-0.090	-0.090	0.000	0.000	0.000	0.000
62	C	472	MET	0	-0.015	-0.013	8.057	0.203	0.203	0.000	0.000	0.000	0.000
63	C	473	GLN	0	-0.001	-0.024	4.811	0.576	0.576	0.000	0.000	0.000	0.000
64	C	474	GLU	-1	-0.833	-0.875	8.666	-0.739	-0.739	0.000	0.000	0.000	0.000
65	C	475	ALA	0	-0.041	-0.011	12.084	0.128	0.128	0.000	0.000	0.000	0.000
66	C	476	GLY	0	0.014	0.010	11.881	0.131	0.131	0.000	0.000	0.000	0.000
67	C	477	LEU	0	-0.043	-0.034	10.710	0.132	0.132	0.000	0.000	0.000	0.000
68	C	478	CYS	0	-0.057	0.035	5.690	0.081	0.081	0.000	0.000	0.000	0.000
69	C	479	PRO	0	0.055	0.024	6.854	0.108	0.108	0.000	0.000	0.000	0.000
70	C	480	GLN	0	-0.011	-0.028	7.858	0.142	0.142	0.000	0.000	0.000	0.000
71	C	481	GLU	-1	-0.764	-0.867	11.022	-0.381	-0.381	0.000	0.000	0.000	0.000
72	C	482	THR	0	-0.075	-0.031	14.037	0.061	0.061	0.000	0.000	0.000	0.000
73	C	483	VAL	0	-0.019	-0.013	15.412	-0.023	-0.023	0.000	0.000	0.000	0.000
74	C	484	PHE	0	-0.034	-0.038	18.366	0.040	0.040	0.000	0.000	0.000	0.000
75	C	485	VAL	0	0.000	0.004	21.326	-0.019	-0.019	0.000	0.000	0.000	0.000
76	C	486	GLN	0	-0.038	-0.020	23.632	0.022	0.022	0.000	0.000	0.000	0.000
77	C	487	GLU	-1	-0.852	-0.919	27.017	-0.080	-0.080	0.000	0.000	0.000	0.000
78	C	488	ARG	1	0.844	0.929	25.195	0.164	0.164	0.000	0.000	0.000	0.000
79	C	489	ASN	0	0.016	0.013	30.661	0.000	0.000	0.000	0.000	0.000	0.000

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