FMO DATABASE

FMODB ID: KG693

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1790956.909061
FMO2-HF: Nuclear repulsion	1722728.823402
FMO2-HF: Total energy	-68228.085659
FMO2-MP2: Total energy	-68424.858737

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.
-3.986	0.098	1.949	-2.41	-3.622	0.006

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 : -0.025 / q_NPA : -0.028

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	0.018	0.027	3.616	-1.920	0.066	0.007	-0.833	-1.160	-0.001
4	A	25	ARG	1	0.858	0.914	2.232	-0.466	1.560	1.943	-1.501	-2.467	0.007
5	A	26	LEU	0	0.017	0.021	3.964	-1.421	-1.349	-0.001	-0.076	0.005	0.000
6	A	27	ILE	0	-0.029	-0.020	6.731	0.534	0.534	0.000	0.000	0.000	0.000
7	A	28	VAL	0	-0.026	-0.022	9.616	-0.007	-0.007	0.000	0.000	0.000	0.000
8	A	29	ASP	-1	-0.784	-0.891	12.701	-0.234	-0.234	0.000	0.000	0.000	0.000
9	A	30	GLU	-1	-0.793	-0.877	15.688	-0.204	-0.204	0.000	0.000	0.000	0.000
10	A	31	ALA	0	-0.031	-0.015	19.193	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	32	ILE	0	0.007	-0.002	20.971	0.028	0.028	0.000	0.000	0.000	0.000
12	A	33	ASN	0	-0.034	-0.023	23.165	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	34	GLU	-1	-0.859	-0.906	24.186	-0.178	-0.178	0.000	0.000	0.000	0.000
14	A	35	ASP	-1	-0.689	-0.821	23.887	-0.181	-0.181	0.000	0.000	0.000	0.000
15	A	36	ASN	0	-0.036	-0.035	23.145	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	37	SER	0	-0.018	0.002	22.583	0.000	0.000	0.000	0.000	0.000	0.000
17	A	38	VAL	0	0.004	0.021	20.788	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	39	VAL	0	-0.049	-0.027	15.339	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	40	SER	0	-0.010	-0.010	16.607	0.004	0.004	0.000	0.000	0.000	0.000
20	A	41	LEU	0	0.021	0.012	11.164	-0.079	-0.079	0.000	0.000	0.000	0.000
21	A	42	SER	0	0.017	-0.012	13.752	0.057	0.057	0.000	0.000	0.000	0.000
22	A	43	GLN	0	0.020	-0.018	14.879	-0.065	-0.065	0.000	0.000	0.000	0.000
23	A	44	PRO	0	0.041	0.021	14.001	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	45	LYS	1	0.785	0.885	6.463	2.425	2.425	0.000	0.000	0.000	0.000
25	A	46	MET	0	-0.070	-0.031	11.277	-0.147	-0.147	0.000	0.000	0.000	0.000
26	A	47	ASP	-1	-0.815	-0.898	13.646	-0.369	-0.369	0.000	0.000	0.000	0.000
27	A	48	GLU	-1	-0.902	-0.937	6.893	-1.415	-1.415	0.000	0.000	0.000	0.000
28	A	49	LEU	0	-0.099	-0.056	6.870	-0.217	-0.217	0.000	0.000	0.000	0.000
29	A	50	GLN	0	-0.069	-0.031	10.514	0.076	0.076	0.000	0.000	0.000	0.000
30	A	51	LEU	0	-0.032	-0.002	11.880	0.022	0.022	0.000	0.000	0.000	0.000
31	A	52	PHE	0	0.021	-0.002	15.568	0.032	0.032	0.000	0.000	0.000	0.000
32	A	53	ARG	1	0.930	0.954	19.332	0.227	0.227	0.000	0.000	0.000	0.000
33	A	54	GLY	0	0.025	0.008	20.953	0.034	0.034	0.000	0.000	0.000	0.000
34	A	55	ASP	-1	-0.822	-0.891	18.026	-0.372	-0.372	0.000	0.000	0.000	0.000
35	A	56	THR	0	-0.020	-0.017	19.158	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	57	VAL	0	-0.022	-0.007	13.936	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	58	LEU	0	-0.053	-0.026	13.928	0.067	0.067	0.000	0.000	0.000	0.000
38	A	59	LEU	0	0.008	0.003	11.957	-0.134	-0.134	0.000	0.000	0.000	0.000
39	A	60	LYS	1	0.865	0.919	10.174	0.489	0.489	0.000	0.000	0.000	0.000
40	A	61	GLY	0	0.058	0.018	11.092	-0.049	-0.049	0.000	0.000	0.000	0.000
41	A	62	LYS	1	0.801	0.900	13.438	0.051	0.051	0.000	0.000	0.000	0.000
42	A	63	LYS	1	0.933	0.953	15.437	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	64	ARG	1	0.954	0.974	15.374	0.022	0.022	0.000	0.000	0.000	0.000
44	A	65	ARG	1	0.773	0.880	16.452	0.134	0.134	0.000	0.000	0.000	0.000
45	A	66	GLU	-1	-0.785	-0.876	14.732	-0.270	-0.270	0.000	0.000	0.000	0.000
46	A	67	ALA	0	0.005	0.004	16.074	0.037	0.037	0.000	0.000	0.000	0.000
47	A	68	VAL	0	0.018	0.016	16.505	-0.046	-0.046	0.000	0.000	0.000	0.000
48	A	69	CYS	0	-0.056	-0.026	17.618	0.028	0.028	0.000	0.000	0.000	0.000
49	A	70	ILE	0	0.035	0.028	18.803	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	71	VAL	0	-0.012	-0.002	14.851	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	72	LEU	0	-0.028	-0.023	18.040	0.050	0.050	0.000	0.000	0.000	0.000
52	A	73	SER	0	0.083	0.031	17.930	-0.044	-0.044	0.000	0.000	0.000	0.000
53	A	74	ASP	-1	-0.825	-0.918	18.256	-0.276	-0.276	0.000	0.000	0.000	0.000
54	A	75	ASP	-1	-0.907	-0.945	18.280	-0.307	-0.307	0.000	0.000	0.000	0.000
55	A	76	THR	0	-0.073	-0.048	20.317	0.026	0.026	0.000	0.000	0.000	0.000
56	A	77	CYS	0	-0.102	-0.030	13.746	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	78	SER	0	0.005	0.006	13.377	0.015	0.015	0.000	0.000	0.000	0.000
58	A	79	ASP	-1	-0.777	-0.851	11.022	-0.595	-0.595	0.000	0.000	0.000	0.000
59	A	80	GLU	-1	-0.829	-0.906	7.617	-0.925	-0.925	0.000	0.000	0.000	0.000
60	A	81	LYS	1	0.782	0.869	8.300	0.266	0.266	0.000	0.000	0.000	0.000
61	A	82	ILE	0	0.013	-0.001	10.695	-0.110	-0.110	0.000	0.000	0.000	0.000
62	A	83	ARG	1	0.761	0.877	12.427	0.432	0.432	0.000	0.000	0.000	0.000
63	A	84	MET	0	0.028	0.012	13.221	0.014	0.014	0.000	0.000	0.000	0.000
64	A	85	ASN	0	0.038	0.017	17.539	0.020	0.020	0.000	0.000	0.000	0.000
65	A	86	ARG	1	0.951	0.963	20.214	0.130	0.130	0.000	0.000	0.000	0.000
66	A	87	VAL	0	0.020	0.033	22.207	0.010	0.010	0.000	0.000	0.000	0.000
67	A	88	VAL	0	0.063	0.028	17.091	0.008	0.008	0.000	0.000	0.000	0.000
68	A	89	ARG	1	0.765	0.845	16.751	0.224	0.224	0.000	0.000	0.000	0.000
69	A	90	ASN	0	0.033	0.016	18.428	0.020	0.020	0.000	0.000	0.000	0.000
70	A	91	ASN	0	-0.034	-0.014	20.655	0.037	0.037	0.000	0.000	0.000	0.000
71	A	92	LEU	0	0.014	0.021	13.974	0.012	0.012	0.000	0.000	0.000	0.000
72	A	93	ARG	1	0.808	0.885	16.329	0.125	0.125	0.000	0.000	0.000	0.000
73	A	94	VAL	0	-0.036	-0.008	13.266	0.039	0.039	0.000	0.000	0.000	0.000
74	A	95	ARG	1	0.930	0.949	16.114	0.064	0.064	0.000	0.000	0.000	0.000
75	A	96	LEU	0	0.023	0.011	15.509	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	97	GLY	0	0.017	0.013	13.716	0.047	0.047	0.000	0.000	0.000	0.000
77	A	98	ASP	-1	-0.794	-0.868	12.328	0.017	0.017	0.000	0.000	0.000	0.000
78	A	99	VAL	0	0.014	0.009	5.659	-0.054	-0.054	0.000	0.000	0.000	0.000
79	A	100	ILE	0	-0.010	0.018	8.439	0.290	0.290	0.000	0.000	0.000	0.000
80	A	101	SER	0	-0.040	-0.030	5.987	-0.077	-0.077	0.000	0.000	0.000	0.000
81	A	102	ILE	0	0.027	0.015	7.319	0.354	0.354	0.000	0.000	0.000	0.000
82	A	103	GLN	0	0.030	0.022	8.157	-0.257	-0.257	0.000	0.000	0.000	0.000
83	A	104	PRO	0	0.118	0.059	10.770	0.090	0.090	0.000	0.000	0.000	0.000
84	A	105	CYS	0	-0.099	-0.044	14.211	0.042	0.042	0.000	0.000	0.000	0.000
85	A	106	PRO	0	0.086	0.042	17.107	0.030	0.030	0.000	0.000	0.000	0.000
86	A	107	ASP	-1	-0.844	-0.909	19.981	-0.161	-0.161	0.000	0.000	0.000	0.000
87	A	108	VAL	0	-0.047	-0.011	21.253	0.023	0.023	0.000	0.000	0.000	0.000
88	A	109	LYS	1	0.833	0.896	22.882	0.175	0.175	0.000	0.000	0.000	0.000
89	A	110	TYR	0	0.074	0.027	26.737	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	111	GLY	0	-0.008	0.006	29.572	0.005	0.005	0.000	0.000	0.000	0.000
91	A	112	LYS	1	0.851	0.910	30.938	0.086	0.086	0.000	0.000	0.000	0.000
92	A	113	ARG	1	0.909	0.960	33.295	0.077	0.077	0.000	0.000	0.000	0.000
93	A	114	ILE	0	-0.016	0.002	29.972	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	115	HIS	0	-0.039	-0.028	32.471	0.004	0.004	0.000	0.000	0.000	0.000
95	A	116	VAL	0	-0.019	-0.017	31.566	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	117	LEU	0	0.009	0.015	33.823	0.005	0.005	0.000	0.000	0.000	0.000
97	A	118	PRO	0	0.022	0.017	34.261	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	119	ILE	0	-0.015	-0.015	31.224	0.004	0.004	0.000	0.000	0.000	0.000
99	A	120	ASP	-1	-0.771	-0.881	35.097	-0.044	-0.044	0.000	0.000	0.000	0.000
100	A	121	ASP	-1	-0.912	-0.948	35.452	-0.055	-0.055	0.000	0.000	0.000	0.000
101	A	122	THR	0	-0.034	-0.027	34.141	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	123	VAL	0	-0.025	-0.045	37.565	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	124	GLU	-1	-0.959	-0.966	40.623	-0.040	-0.040	0.000	0.000	0.000	0.000
104	A	125	GLY	0	0.021	0.014	43.417	0.003	0.003	0.000	0.000	0.000	0.000
105	A	126	ILE	0	-0.099	-0.038	40.840	0.000	0.000	0.000	0.000	0.000	0.000
106	A	127	THR	0	0.000	0.009	44.282	0.002	0.002	0.000	0.000	0.000	0.000
107	A	128	GLY	0	0.014	-0.008	45.891	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	129	ASN	0	0.006	0.007	43.698	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	130	LEU	0	0.087	0.030	39.467	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	131	PHE	0	0.041	0.020	37.921	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	132	GLU	-1	-0.818	-0.907	39.827	-0.070	-0.070	0.000	0.000	0.000	0.000
112	A	133	VAL	0	-0.028	-0.008	41.194	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	134	TYR	0	-0.054	-0.039	36.481	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	135	LEU	0	-0.004	-0.008	34.006	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	136	LYS	1	0.835	0.910	35.356	0.064	0.064	0.000	0.000	0.000	0.000
116	A	137	PRO	0	0.001	-0.002	36.878	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	138	TYR	0	-0.023	0.004	27.716	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	139	PHE	0	0.025	-0.011	29.083	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	140	LEU	0	-0.006	0.009	33.058	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	141	GLU	-1	-0.946	-0.974	34.137	-0.103	-0.103	0.000	0.000	0.000	0.000
121	A	142	ALA	0	-0.021	-0.005	30.010	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	143	TYR	0	-0.036	-0.017	28.174	-0.011	-0.011	0.000	0.000	0.000	0.000
123	A	144	ARG	1	0.821	0.879	26.175	0.154	0.154	0.000	0.000	0.000	0.000
124	A	145	PRO	0	-0.010	0.010	21.759	0.012	0.012	0.000	0.000	0.000	0.000
125	A	146	ILE	0	-0.035	-0.011	23.905	0.001	0.001	0.000	0.000	0.000	0.000
126	A	147	ARG	1	0.842	0.894	17.879	0.195	0.195	0.000	0.000	0.000	0.000
127	A	148	LYS	1	0.839	0.913	23.913	0.090	0.090	0.000	0.000	0.000	0.000
128	A	149	GLY	0	-0.053	-0.034	24.518	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	150	ASP	-1	-0.864	-0.915	22.422	-0.179	-0.179	0.000	0.000	0.000	0.000
130	A	151	ILE	0	-0.044	-0.033	24.946	0.013	0.013	0.000	0.000	0.000	0.000
131	A	152	PHE	0	0.008	0.001	25.785	-0.015	-0.015	0.000	0.000	0.000	0.000
132	A	153	LEU	0	0.022	0.031	27.888	0.009	0.009	0.000	0.000	0.000	0.000
133	A	154	VAL	0	-0.011	0.002	30.035	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	155	ARG	1	0.888	0.916	29.091	0.129	0.129	0.000	0.000	0.000	0.000
135	A	156	GLY	0	0.066	0.027	34.904	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	157	GLY	0	0.022	0.007	38.614	0.002	0.002	0.000	0.000	0.000	0.000
137	A	158	MET	0	-0.017	0.001	42.075	0.000	0.000	0.000	0.000	0.000	0.000
138	A	159	ARG	1	0.940	0.973	39.153	0.055	0.055	0.000	0.000	0.000	0.000
139	A	160	ALA	0	0.002	0.018	34.206	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	161	VAL	0	0.022	0.023	35.190	0.005	0.005	0.000	0.000	0.000	0.000
141	A	162	GLU	-1	-0.921	-0.960	29.534	-0.107	-0.107	0.000	0.000	0.000	0.000
142	A	163	PHE	0	0.031	0.013	31.455	0.008	0.008	0.000	0.000	0.000	0.000
143	A	164	LYS	1	0.939	0.973	28.280	0.066	0.066	0.000	0.000	0.000	0.000
144	A	165	VAL	0	0.006	0.016	27.487	0.007	0.007	0.000	0.000	0.000	0.000
145	A	166	VAL	0	-0.054	-0.037	29.119	0.000	0.000	0.000	0.000	0.000	0.000
146	A	167	GLU	-1	-0.780	-0.878	30.375	-0.080	-0.080	0.000	0.000	0.000	0.000
147	A	168	THR	0	-0.041	-0.050	27.343	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	169	ASP	-1	-0.825	-0.872	29.980	-0.081	-0.081	0.000	0.000	0.000	0.000
149	A	170	PRO	0	0.081	0.020	27.491	0.001	0.001	0.000	0.000	0.000	0.000
150	A	171	SER	0	0.012	0.045	27.269	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	172	PRO	0	-0.052	-0.023	22.264	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	173	TYR	0	0.026	-0.031	18.710	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	174	CYS	0	-0.064	-0.001	24.148	0.005	0.005	0.000	0.000	0.000	0.000
154	A	175	ILE	0	0.035	0.015	23.564	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	176	VAL	0	-0.018	-0.015	26.848	0.014	0.014	0.000	0.000	0.000	0.000
156	A	177	ALA	0	0.028	0.007	30.057	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	178	PRO	0	0.020	-0.001	32.470	0.005	0.005	0.000	0.000	0.000	0.000
158	A	179	ASP	-1	-0.923	-0.951	36.172	-0.087	-0.087	0.000	0.000	0.000	0.000
159	A	180	THR	0	-0.097	-0.046	32.184	0.000	0.000	0.000	0.000	0.000	0.000
160	A	181	VAL	0	-0.013	-0.018	35.159	0.002	0.002	0.000	0.000	0.000	0.000
161	A	182	ILE	0	0.019	0.006	34.055	-0.002	-0.002	0.000	0.000	0.000	0.000
162	A	183	HIS	0	-0.055	-0.017	36.211	0.006	0.006	0.000	0.000	0.000	0.000
163	A	184	CYS	0	0.002	-0.028	36.475	-0.005	-0.005	0.000	0.000	0.000	0.000
164	A	185	GLU	-1	-0.874	-0.918	37.738	-0.058	-0.058	0.000	0.000	0.000	0.000
165	A	186	GLY	0	0.035	0.003	40.457	0.003	0.003	0.000	0.000	0.000	0.000
166	A	187	GLU	-1	-0.944	-0.960	41.477	-0.042	-0.042	0.000	0.000	0.000	0.000
167	A	188	PRO	0	0.007	0.007	38.857	-0.003	-0.003	0.000	0.000	0.000	0.000
168	A	189	ILE	0	-0.034	-0.004	33.418	0.004	0.004	0.000	0.000	0.000	0.000
169	A	190	LYS	1	0.902	0.934	35.544	0.035	0.035	0.000	0.000	0.000	0.000
170	A	191	ARG	1	0.910	0.956	29.057	0.043	0.043	0.000	0.000	0.000	0.000

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