FMO DATABASE

FMODB ID: R8J98

Calculation Name: 5X4L-A-Xray372

Preferred Name: Transitional endoplasmic reticulum ATPase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5X4L

Chain ID: A

ChEMBL ID: CHEMBL1075145

UniProt ID: P55072

Base Structure: X-ray

Registration Date: 2023-09-24

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	170
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1788253.271728
FMO2-HF: Nuclear repulsion	1720026.881795
FMO2-HF: Total energy	-68226.389932
FMO2-MP2: Total energy	-68423.222455

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:22:SER)

Summations of interaction energy for fragment #1(A:22: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.
-1.06	1.414	2.186	-1.82	-2.841	0.001

Interaction energy analysis for fragmet #1(A:22:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.025

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	24	ASN	0	0.024	0.020	3.534	-2.003	-0.058	-0.011	-0.780	-1.155	0.001
4	A	25	ARG	1	0.916	0.949	2.069	1.517	2.083	2.198	-1.020	-1.744	0.000
5	A	26	LEU	0	0.028	0.019	4.211	-1.083	-1.120	-0.001	-0.020	0.058	0.000
6	A	27	ILE	0	-0.022	-0.011	7.426	0.462	0.462	0.000	0.000	0.000	0.000
7	A	28	VAL	0	-0.001	-0.008	9.943	0.069	0.069	0.000	0.000	0.000	0.000
8	A	29	ASP	-1	-0.833	-0.931	13.308	-0.391	-0.391	0.000	0.000	0.000	0.000
9	A	30	GLU	-1	-0.869	-0.927	16.089	-0.267	-0.267	0.000	0.000	0.000	0.000
10	A	31	ALA	0	-0.040	-0.029	19.593	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	32	ILE	0	0.019	0.003	21.588	0.026	0.026	0.000	0.000	0.000	0.000
12	A	33	ASN	0	-0.045	-0.028	23.851	0.003	0.003	0.000	0.000	0.000	0.000
13	A	34	GLU	-1	-0.895	-0.938	24.479	-0.212	-0.212	0.000	0.000	0.000	0.000
14	A	35	ASP	-1	-0.681	-0.842	24.158	-0.191	-0.191	0.000	0.000	0.000	0.000
15	A	36	ASN	0	-0.059	-0.043	23.411	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	37	SER	0	-0.006	0.014	22.706	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	38	VAL	0	0.015	0.025	20.940	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	39	VAL	0	-0.054	-0.025	15.255	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	40	SER	0	-0.012	-0.007	17.164	0.035	0.035	0.000	0.000	0.000	0.000
20	A	41	LEU	0	0.001	-0.008	11.968	-0.104	-0.104	0.000	0.000	0.000	0.000
21	A	42	SER	0	0.053	0.042	13.989	0.079	0.079	0.000	0.000	0.000	0.000
22	A	43	GLN	0	0.061	0.004	15.264	-0.047	-0.047	0.000	0.000	0.000	0.000
23	A	44	PRO	0	0.048	0.027	13.990	0.003	0.003	0.000	0.000	0.000	0.000
24	A	45	LYS	1	0.797	0.897	6.592	2.116	2.116	0.000	0.000	0.000	0.000
25	A	46	MET	0	-0.064	-0.028	11.445	-0.055	-0.055	0.000	0.000	0.000	0.000
26	A	47	ASP	-1	-0.852	-0.923	14.037	-0.207	-0.207	0.000	0.000	0.000	0.000
27	A	48	GLU	-1	-0.913	-0.941	7.450	-0.415	-0.415	0.000	0.000	0.000	0.000
28	A	49	LEU	0	-0.104	-0.064	6.924	-0.021	-0.021	0.000	0.000	0.000	0.000
29	A	50	GLN	0	-0.054	-0.019	10.607	0.027	0.027	0.000	0.000	0.000	0.000
30	A	51	LEU	0	-0.058	-0.022	12.383	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	52	PHE	0	0.021	-0.004	15.676	0.021	0.021	0.000	0.000	0.000	0.000
32	A	53	ARG	1	0.964	0.965	19.413	0.187	0.187	0.000	0.000	0.000	0.000
33	A	54	GLY	0	-0.003	-0.008	21.448	0.024	0.024	0.000	0.000	0.000	0.000
34	A	55	ASP	-1	-0.804	-0.871	18.412	-0.255	-0.255	0.000	0.000	0.000	0.000
35	A	56	THR	0	-0.039	-0.029	19.426	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	57	VAL	0	-0.029	-0.014	14.038	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	58	LEU	0	-0.028	-0.018	14.245	0.038	0.038	0.000	0.000	0.000	0.000
38	A	59	LEU	0	-0.017	-0.020	11.683	-0.118	-0.118	0.000	0.000	0.000	0.000
39	A	60	LYS	1	0.885	0.955	10.338	0.526	0.526	0.000	0.000	0.000	0.000
40	A	61	GLY	0	0.056	0.028	10.824	-0.105	-0.105	0.000	0.000	0.000	0.000
41	A	62	LYS	1	0.893	0.959	13.067	0.243	0.243	0.000	0.000	0.000	0.000
42	A	63	LYS	1	0.927	0.949	14.993	0.113	0.113	0.000	0.000	0.000	0.000
43	A	64	ARG	1	0.982	0.972	15.655	0.102	0.102	0.000	0.000	0.000	0.000
44	A	65	ARG	1	0.796	0.931	16.666	0.193	0.193	0.000	0.000	0.000	0.000
45	A	66	GLU	-1	-0.835	-0.927	14.885	-0.295	-0.295	0.000	0.000	0.000	0.000
46	A	67	ALA	0	0.010	0.002	15.929	0.035	0.035	0.000	0.000	0.000	0.000
47	A	68	VAL	0	0.012	0.025	16.419	-0.048	-0.048	0.000	0.000	0.000	0.000
48	A	69	CYS	0	-0.045	-0.015	17.450	0.026	0.026	0.000	0.000	0.000	0.000
49	A	70	ILE	0	0.046	0.037	18.928	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	71	VAL	0	0.008	0.012	15.204	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	72	LEU	0	-0.052	-0.034	18.238	0.055	0.055	0.000	0.000	0.000	0.000
52	A	73	SER	0	0.058	0.013	18.681	-0.045	-0.045	0.000	0.000	0.000	0.000
53	A	74	ASP	-1	-0.789	-0.923	18.478	-0.333	-0.333	0.000	0.000	0.000	0.000
54	A	75	ASP	-1	-0.943	-0.958	18.861	-0.289	-0.289	0.000	0.000	0.000	0.000
55	A	76	THR	0	-0.070	-0.032	20.470	0.018	0.018	0.000	0.000	0.000	0.000
56	A	77	CYS	0	-0.111	-0.049	14.281	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	78	SER	0	0.006	0.001	13.462	0.018	0.018	0.000	0.000	0.000	0.000
58	A	79	ASP	-1	-0.811	-0.900	11.036	-0.642	-0.642	0.000	0.000	0.000	0.000
59	A	80	GLU	-1	-0.937	-0.969	7.352	-1.183	-1.183	0.000	0.000	0.000	0.000
60	A	81	LYS	1	0.891	0.937	8.639	0.352	0.352	0.000	0.000	0.000	0.000
61	A	82	ILE	0	0.020	0.009	11.298	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	83	ARG	1	0.797	0.924	13.254	0.462	0.462	0.000	0.000	0.000	0.000
63	A	84	MET	0	0.022	0.009	13.693	0.029	0.029	0.000	0.000	0.000	0.000
64	A	85	ASN	0	0.049	0.015	18.259	0.000	0.000	0.000	0.000	0.000	0.000
65	A	86	ARG	1	0.966	0.968	20.794	0.179	0.179	0.000	0.000	0.000	0.000
66	A	87	VAL	0	0.001	0.016	22.502	0.000	0.000	0.000	0.000	0.000	0.000
67	A	88	VAL	0	0.095	0.048	17.432	0.006	0.006	0.000	0.000	0.000	0.000
68	A	89	ARG	1	0.831	0.917	17.458	0.306	0.306	0.000	0.000	0.000	0.000
69	A	90	ASN	0	0.039	0.014	18.728	0.002	0.002	0.000	0.000	0.000	0.000
70	A	91	ASN	0	0.007	0.025	20.474	0.034	0.034	0.000	0.000	0.000	0.000
71	A	92	LEU	0	0.028	0.010	14.237	0.014	0.014	0.000	0.000	0.000	0.000
72	A	93	ARG	1	0.763	0.878	16.418	0.180	0.180	0.000	0.000	0.000	0.000
73	A	94	VAL	0	-0.036	-0.010	13.847	0.020	0.020	0.000	0.000	0.000	0.000
74	A	95	ARG	1	0.943	0.950	16.480	0.206	0.206	0.000	0.000	0.000	0.000
75	A	96	LEU	0	0.027	0.005	15.911	-0.041	-0.041	0.000	0.000	0.000	0.000
76	A	97	GLY	0	-0.005	0.007	13.803	0.055	0.055	0.000	0.000	0.000	0.000
77	A	98	ASP	-1	-0.853	-0.911	12.436	-0.286	-0.286	0.000	0.000	0.000	0.000
78	A	99	VAL	0	-0.024	-0.012	6.209	-0.060	-0.060	0.000	0.000	0.000	0.000
79	A	100	ILE	0	-0.053	-0.011	8.690	0.252	0.252	0.000	0.000	0.000	0.000
80	A	101	SER	0	-0.032	-0.017	6.192	-0.369	-0.369	0.000	0.000	0.000	0.000
81	A	102	ILE	0	0.036	0.017	7.339	0.348	0.348	0.000	0.000	0.000	0.000
82	A	103	GLN	0	-0.005	-0.002	8.599	-0.249	-0.249	0.000	0.000	0.000	0.000
83	A	104	PRO	0	0.117	0.056	11.125	0.041	0.041	0.000	0.000	0.000	0.000
84	A	105	CYS	0	-0.089	-0.049	14.236	0.025	0.025	0.000	0.000	0.000	0.000
85	A	106	PRO	0	0.074	0.041	17.272	0.010	0.010	0.000	0.000	0.000	0.000
86	A	107	ASP	-1	-0.897	-0.939	20.241	-0.127	-0.127	0.000	0.000	0.000	0.000
87	A	108	VAL	0	-0.069	-0.029	21.543	0.016	0.016	0.000	0.000	0.000	0.000
88	A	109	LYS	1	0.926	0.967	23.512	0.118	0.118	0.000	0.000	0.000	0.000
89	A	110	TYR	0	0.087	0.028	27.317	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	111	GLY	0	0.001	-0.001	30.047	0.005	0.005	0.000	0.000	0.000	0.000
91	A	112	LYS	1	0.933	0.974	31.218	0.072	0.072	0.000	0.000	0.000	0.000
92	A	113	ARG	1	0.947	0.971	33.459	0.073	0.073	0.000	0.000	0.000	0.000
93	A	114	ILE	0	-0.034	-0.005	30.242	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	115	HIS	0	0.007	0.006	32.677	0.005	0.005	0.000	0.000	0.000	0.000
95	A	116	VAL	0	-0.033	-0.023	31.529	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	117	LEU	0	0.027	0.003	33.542	0.005	0.005	0.000	0.000	0.000	0.000
97	A	118	PRO	0	0.025	0.023	34.035	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	119	ILE	0	-0.012	-0.020	31.273	0.003	0.003	0.000	0.000	0.000	0.000
99	A	120	ASP	-1	-0.797	-0.926	35.173	-0.073	-0.073	0.000	0.000	0.000	0.000
100	A	121	ASP	-1	-0.940	-0.968	35.568	-0.087	-0.087	0.000	0.000	0.000	0.000
101	A	122	THR	0	-0.050	-0.032	34.210	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	123	VAL	0	-0.043	-0.063	37.658	0.000	0.000	0.000	0.000	0.000	0.000
103	A	124	GLU	-1	-0.912	-0.935	40.675	-0.061	-0.061	0.000	0.000	0.000	0.000
104	A	125	GLY	0	-0.017	-0.011	43.261	0.003	0.003	0.000	0.000	0.000	0.000
105	A	126	ILE	0	-0.109	-0.033	40.950	0.001	0.001	0.000	0.000	0.000	0.000
106	A	127	THR	0	0.031	0.025	44.411	0.003	0.003	0.000	0.000	0.000	0.000
107	A	128	GLY	0	0.003	-0.011	46.087	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	129	ASN	0	0.010	0.017	43.578	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	130	LEU	0	0.099	0.031	39.084	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	131	PHE	0	0.031	0.012	38.513	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	132	GLU	-1	-0.929	-0.973	39.930	-0.073	-0.073	0.000	0.000	0.000	0.000
112	A	133	VAL	0	-0.044	-0.011	40.826	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	134	TYR	0	-0.085	-0.080	36.455	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	135	LEU	0	-0.010	-0.017	34.136	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	136	LYS	1	0.972	0.994	35.604	0.069	0.069	0.000	0.000	0.000	0.000
116	A	137	PRO	0	0.024	0.002	36.990	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	138	TYR	0	-0.031	0.003	27.621	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	139	PHE	0	0.022	-0.022	29.194	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	140	LEU	0	-0.005	0.014	33.005	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	141	GLU	-1	-0.962	-0.975	34.291	-0.099	-0.099	0.000	0.000	0.000	0.000
121	A	142	ALA	0	0.008	0.005	29.737	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	143	TYR	0	-0.050	-0.018	28.255	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	144	ARG	1	0.802	0.874	26.267	0.164	0.164	0.000	0.000	0.000	0.000
124	A	145	PRO	0	-0.011	0.005	22.156	0.015	0.015	0.000	0.000	0.000	0.000
125	A	146	ILE	0	-0.011	0.004	24.278	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	147	ARG	1	0.906	0.941	19.097	0.215	0.215	0.000	0.000	0.000	0.000
127	A	148	LYS	1	0.977	0.981	23.905	0.102	0.102	0.000	0.000	0.000	0.000
128	A	149	GLY	0	-0.121	-0.071	24.181	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	150	ASP	-1	-0.878	-0.941	22.338	-0.223	-0.223	0.000	0.000	0.000	0.000
130	A	151	ILE	0	-0.049	-0.039	24.880	0.017	0.017	0.000	0.000	0.000	0.000
131	A	152	PHE	0	-0.020	-0.010	25.823	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	153	LEU	0	0.006	0.014	27.876	0.011	0.011	0.000	0.000	0.000	0.000
133	A	154	VAL	0	0.000	0.011	30.182	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	155	ARG	1	0.936	0.953	30.381	0.150	0.150	0.000	0.000	0.000	0.000
135	A	156	GLY	0	0.079	0.036	35.365	0.000	0.000	0.000	0.000	0.000	0.000
136	A	157	GLY	0	0.028	0.010	39.002	0.001	0.001	0.000	0.000	0.000	0.000
137	A	158	MET	0	-0.020	-0.007	42.363	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	159	ARG	1	0.947	0.975	39.438	0.075	0.075	0.000	0.000	0.000	0.000
139	A	160	ALA	0	-0.032	0.027	34.385	0.000	0.000	0.000	0.000	0.000	0.000
140	A	161	VAL	0	0.054	0.040	35.532	0.003	0.003	0.000	0.000	0.000	0.000
141	A	162	GLU	-1	-0.939	-0.972	29.892	-0.139	-0.139	0.000	0.000	0.000	0.000
142	A	163	PHE	0	0.029	0.010	31.351	0.010	0.010	0.000	0.000	0.000	0.000
143	A	164	LYS	1	0.932	0.964	28.411	0.095	0.095	0.000	0.000	0.000	0.000
144	A	165	VAL	0	0.023	0.022	27.513	0.010	0.010	0.000	0.000	0.000	0.000
145	A	166	VAL	0	-0.040	-0.023	28.846	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	167	GLU	-1	-0.981	-0.995	30.434	-0.073	-0.073	0.000	0.000	0.000	0.000
147	A	168	THR	0	-0.039	-0.043	27.438	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	169	ASP	-1	-0.881	-0.920	30.087	-0.076	-0.076	0.000	0.000	0.000	0.000
149	A	170	PRO	0	0.075	0.029	27.756	0.001	0.001	0.000	0.000	0.000	0.000
150	A	171	SER	0	-0.021	0.042	27.408	-0.011	-0.011	0.000	0.000	0.000	0.000
151	A	172	PRO	0	-0.048	-0.031	22.430	0.003	0.003	0.000	0.000	0.000	0.000
152	A	173	TYR	0	0.047	-0.012	19.491	-0.016	-0.016	0.000	0.000	0.000	0.000
153	A	174	CYS	0	-0.036	0.011	24.464	0.011	0.011	0.000	0.000	0.000	0.000
154	A	175	ILE	0	0.022	0.028	24.089	-0.013	-0.013	0.000	0.000	0.000	0.000
155	A	176	VAL	0	-0.045	-0.035	27.340	0.013	0.013	0.000	0.000	0.000	0.000
156	A	177	ALA	0	0.024	0.012	30.476	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	178	PRO	0	0.002	-0.007	32.804	0.003	0.003	0.000	0.000	0.000	0.000
158	A	179	ASP	-1	-0.888	-0.934	36.279	-0.073	-0.073	0.000	0.000	0.000	0.000
159	A	180	THR	0	-0.128	-0.071	32.272	0.000	0.000	0.000	0.000	0.000	0.000
160	A	181	VAL	0	-0.008	-0.008	35.292	0.001	0.001	0.000	0.000	0.000	0.000
161	A	182	ILE	0	0.000	-0.002	34.547	-0.004	-0.004	0.000	0.000	0.000	0.000
162	A	183	HIS	0	-0.030	-0.006	36.497	0.005	0.005	0.000	0.000	0.000	0.000
163	A	184	CYS	0	-0.049	-0.035	36.811	-0.006	-0.006	0.000	0.000	0.000	0.000
164	A	185	GLU	-1	-0.867	-0.943	37.597	-0.068	-0.068	0.000	0.000	0.000	0.000
165	A	186	GLY	0	0.009	0.011	40.642	0.002	0.002	0.000	0.000	0.000	0.000
166	A	187	GLU	-1	-0.971	-0.982	41.694	-0.055	-0.055	0.000	0.000	0.000	0.000
167	A	188	PRO	0	0.017	0.021	38.659	-0.003	-0.003	0.000	0.000	0.000	0.000
168	A	189	ILE	0	-0.031	0.000	32.861	0.003	0.003	0.000	0.000	0.000	0.000
169	A	190	LYS	1	1.014	1.012	35.342	0.054	0.054	0.000	0.000	0.000	0.000
170	A	191	ARG	1	0.899	0.954	27.918	0.083	0.083	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:22:SER)