FMO DATABASE

FMODB ID: LZLV9

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	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	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-557731.864116
FMO2-HF: Nuclear repulsion	525232.020649
FMO2-HF: Total energy	-32499.843467
FMO2-MP2: Total energy	-32594.493421

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.
-5.228	0.425	1.259	-2.62	-4.292	-0.012

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 : 0.035 / 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	0.086	0.062	3.873	-1.014	0.908	-0.021	-0.956	-0.944	-0.001
4	C	414	GLN	0	-0.036	-0.035	6.786	0.352	0.352	0.000	0.000	0.000	0.000
5	C	415	LEU	0	0.018	0.002	9.744	-0.063	-0.063	0.000	0.000	0.000	0.000
6	C	416	MET	0	0.002	0.037	12.970	0.076	0.076	0.000	0.000	0.000	0.000
7	C	417	LEU	0	0.040	0.019	16.147	-0.023	-0.023	0.000	0.000	0.000	0.000
8	C	418	ARG	1	0.862	0.902	18.596	0.077	0.077	0.000	0.000	0.000	0.000
9	C	419	TYR	0	0.003	-0.019	20.027	-0.025	-0.025	0.000	0.000	0.000	0.000
10	C	420	PRO	0	0.025	0.018	24.904	0.007	0.007	0.000	0.000	0.000	0.000
11	C	421	ASP	-1	-0.810	-0.895	27.958	-0.025	-0.025	0.000	0.000	0.000	0.000
12	C	422	GLY	0	-0.006	0.002	28.400	0.009	0.009	0.000	0.000	0.000	0.000
13	C	423	LYS	1	0.865	0.935	25.528	0.015	0.015	0.000	0.000	0.000	0.000
14	C	424	ARG	1	0.886	0.897	20.267	-0.021	-0.021	0.000	0.000	0.000	0.000
15	C	425	GLU	-1	-0.746	-0.828	17.771	-0.020	-0.020	0.000	0.000	0.000	0.000
16	C	426	GLN	0	-0.023	-0.007	13.481	-0.031	-0.031	0.000	0.000	0.000	0.000
17	C	427	ILE	0	0.015	0.022	12.556	0.049	0.049	0.000	0.000	0.000	0.000
18	C	428	THR	0	0.002	0.001	7.588	0.081	0.081	0.000	0.000	0.000	0.000
19	C	429	LEU	0	0.000	0.007	8.248	0.123	0.123	0.000	0.000	0.000	0.000
20	C	430	PRO	0	-0.006	-0.014	4.372	-0.476	-0.327	-0.001	-0.059	-0.089	0.000
21	C	431	GLU	-1	-0.833	-0.915	2.523	-4.942	-2.213	1.253	-1.315	-2.668	-0.010
22	C	432	GLN	0	0.064	0.021	3.396	-0.794	-0.028	0.029	-0.285	-0.509	-0.001
23	C	433	ALA	0	-0.046	-0.021	6.190	0.420	0.420	0.000	0.000	0.000	0.000
24	C	434	LYS	1	0.817	0.901	8.782	0.414	0.414	0.000	0.000	0.000	0.000
25	C	435	LEU	0	0.056	0.029	12.112	0.022	0.022	0.000	0.000	0.000	0.000
26	C	436	LEU	0	0.004	-0.012	13.555	0.057	0.057	0.000	0.000	0.000	0.000
27	C	437	ALA	0	-0.054	-0.029	12.297	0.065	0.065	0.000	0.000	0.000	0.000
28	C	438	LEU	0	0.040	0.023	13.290	0.062	0.062	0.000	0.000	0.000	0.000
29	C	439	VAL	0	-0.015	0.001	14.978	0.058	0.058	0.000	0.000	0.000	0.000
30	C	440	LYS	1	0.941	0.969	17.200	0.293	0.293	0.000	0.000	0.000	0.000
31	C	441	HIS	0	-0.026	-0.001	16.205	0.025	0.025	0.000	0.000	0.000	0.000
32	C	442	VAL	0	0.027	0.019	18.249	0.035	0.035	0.000	0.000	0.000	0.000
33	C	443	GLN	0	0.033	0.023	20.522	0.010	0.010	0.000	0.000	0.000	0.000
34	C	444	SER	0	-0.100	-0.068	20.745	0.023	0.023	0.000	0.000	0.000	0.000
35	C	445	LYS	1	0.814	0.894	20.334	0.039	0.039	0.000	0.000	0.000	0.000
36	C	446	GLY	0	0.019	0.019	24.105	0.011	0.011	0.000	0.000	0.000	0.000
37	C	447	TYR	0	-0.053	-0.023	24.230	0.002	0.002	0.000	0.000	0.000	0.000
38	C	448	PRO	0	0.027	0.010	24.464	-0.017	-0.017	0.000	0.000	0.000	0.000
39	C	449	ASN	0	0.105	0.042	23.054	-0.008	-0.008	0.000	0.000	0.000	0.000
40	C	450	GLU	-1	-0.956	-0.969	24.946	-0.098	-0.098	0.000	0.000	0.000	0.000
41	C	451	ARG	1	0.885	0.937	28.287	0.074	0.074	0.000	0.000	0.000	0.000
42	C	452	PHE	0	-0.012	-0.005	25.499	0.007	0.007	0.000	0.000	0.000	0.000
43	C	453	GLU	-1	-0.820	-0.884	23.619	-0.154	-0.154	0.000	0.000	0.000	0.000
44	C	454	LEU	0	0.002	-0.003	17.466	0.010	0.010	0.000	0.000	0.000	0.000
45	C	455	LEU	0	-0.002	-0.016	20.971	-0.010	-0.010	0.000	0.000	0.000	0.000
46	C	456	THR	0	-0.050	-0.025	16.544	0.003	0.003	0.000	0.000	0.000	0.000
47	C	457	ASN	0	0.000	-0.016	19.989	0.018	0.018	0.000	0.000	0.000	0.000
48	C	458	PHE	0	0.000	0.022	20.821	-0.004	-0.004	0.000	0.000	0.000	0.000
49	C	459	PRO	0	0.094	0.056	20.199	-0.003	-0.003	0.000	0.000	0.000	0.000
50	C	460	ARG	1	0.876	0.916	21.812	0.107	0.107	0.000	0.000	0.000	0.000
51	C	461	ARG	1	0.810	0.885	14.474	0.373	0.373	0.000	0.000	0.000	0.000
52	C	462	LYS	1	0.899	0.924	21.409	0.142	0.142	0.000	0.000	0.000	0.000
53	C	463	LEU	0	0.045	0.022	15.820	-0.006	-0.006	0.000	0.000	0.000	0.000
54	C	464	SER	0	-0.033	-0.020	19.287	-0.011	-0.011	0.000	0.000	0.000	0.000
55	C	465	HIS	0	-0.041	-0.021	21.852	0.016	0.016	0.000	0.000	0.000	0.000
56	C	466	LEU	0	-0.014	0.010	16.340	0.002	0.002	0.000	0.000	0.000	0.000
57	C	467	ASP	-1	-0.809	-0.905	19.106	-0.327	-0.327	0.000	0.000	0.000	0.000
58	C	468	TYR	0	-0.049	-0.055	17.042	-0.033	-0.033	0.000	0.000	0.000	0.000
59	C	469	ASP	-1	-0.799	-0.896	15.924	-0.410	-0.410	0.000	0.000	0.000	0.000
60	C	470	ILE	0	0.014	0.026	13.367	-0.052	-0.052	0.000	0.000	0.000	0.000
61	C	471	THR	0	-0.054	-0.061	8.492	-0.069	-0.069	0.000	0.000	0.000	0.000
62	C	472	MET	0	-0.038	-0.019	7.235	0.177	0.177	0.000	0.000	0.000	0.000
63	C	473	GLN	0	0.016	-0.026	4.626	0.347	0.434	-0.001	-0.005	-0.082	0.000
64	C	474	GLU	-1	-0.850	-0.879	8.040	-0.578	-0.578	0.000	0.000	0.000	0.000
65	C	475	ALA	0	-0.024	-0.004	11.616	0.102	0.102	0.000	0.000	0.000	0.000
66	C	476	GLY	0	0.013	0.017	11.411	0.090	0.090	0.000	0.000	0.000	0.000
67	C	477	LEU	0	-0.063	-0.037	10.192	0.125	0.125	0.000	0.000	0.000	0.000
68	C	478	CYS	0	-0.039	0.033	5.796	-0.021	-0.021	0.000	0.000	0.000	0.000
69	C	479	PRO	0	0.068	0.034	6.558	0.077	0.077	0.000	0.000	0.000	0.000
70	C	480	GLN	0	-0.040	-0.037	7.599	0.155	0.155	0.000	0.000	0.000	0.000
71	C	481	GLU	-1	-0.734	-0.816	11.023	-0.283	-0.283	0.000	0.000	0.000	0.000
72	C	482	THR	0	-0.094	-0.050	13.887	0.050	0.050	0.000	0.000	0.000	0.000
73	C	483	VAL	0	-0.023	-0.013	15.053	-0.015	-0.015	0.000	0.000	0.000	0.000
74	C	484	PHE	0	-0.004	-0.010	18.054	0.030	0.030	0.000	0.000	0.000	0.000
75	C	485	VAL	0	-0.005	0.005	21.013	-0.020	-0.020	0.000	0.000	0.000	0.000
76	C	486	GLN	0	-0.055	-0.035	23.340	0.021	0.021	0.000	0.000	0.000	0.000
77	C	487	GLU	-1	-0.832	-0.915	26.730	-0.078	-0.078	0.000	0.000	0.000	0.000
78	C	488	ARG	1	0.828	0.918	24.523	0.153	0.153	0.000	0.000	0.000	0.000
79	C	489	ASN	0	0.014	0.012	30.204	-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)