FMO DATABASE

FMODB ID: QV3YY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1789250.775514
FMO2-HF: Nuclear repulsion	1721023.158764
FMO2-HF: Total energy	-68227.61675
FMO2-MP2: Total energy	-68424.423733

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.
-3.26	0.385	1.521	-2.025	-3.141	0.003

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 : -0.038 / q_NPA : -0.033

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	0.026	0.017	3.542	-1.844	0.196	-0.011	-0.817	-1.212	0.000
4	A	25	ARG	1	0.909	0.952	2.182	-0.148	1.468	1.533	-1.172	-1.977	0.003
5	A	26	LEU	0	0.029	0.018	4.290	-1.344	-1.355	-0.001	-0.036	0.048	0.000
6	A	27	ILE	0	-0.027	-0.016	6.930	0.513	0.513	0.000	0.000	0.000	0.000
7	A	28	VAL	0	-0.010	-0.011	9.589	0.010	0.010	0.000	0.000	0.000	0.000
8	A	29	ASP	-1	-0.798	-0.900	12.874	-0.283	-0.283	0.000	0.000	0.000	0.000
9	A	30	GLU	-1	-0.808	-0.874	15.704	-0.198	-0.198	0.000	0.000	0.000	0.000
10	A	31	ALA	0	-0.030	-0.022	19.172	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	32	ILE	0	0.019	0.007	21.122	0.025	0.025	0.000	0.000	0.000	0.000
12	A	33	ASN	0	-0.051	-0.033	23.381	0.001	0.001	0.000	0.000	0.000	0.000
13	A	34	GLU	-1	-0.845	-0.904	24.230	-0.166	-0.166	0.000	0.000	0.000	0.000
14	A	35	ASP	-1	-0.683	-0.831	24.074	-0.163	-0.163	0.000	0.000	0.000	0.000
15	A	36	ASN	0	-0.046	-0.039	23.516	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	37	SER	0	-0.010	0.001	22.857	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	38	VAL	0	0.001	0.019	20.975	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	39	VAL	0	-0.053	-0.021	15.381	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	40	SER	0	-0.007	-0.011	17.013	0.014	0.014	0.000	0.000	0.000	0.000
20	A	41	LEU	0	0.004	0.007	11.488	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	42	SER	0	0.021	-0.011	13.783	0.066	0.066	0.000	0.000	0.000	0.000
22	A	43	GLN	0	0.046	-0.015	15.056	-0.056	-0.056	0.000	0.000	0.000	0.000
23	A	44	PRO	0	0.043	0.029	13.936	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	45	LYS	1	0.804	0.909	6.592	2.241	2.241	0.000	0.000	0.000	0.000
25	A	46	MET	0	-0.062	-0.028	11.445	-0.069	-0.069	0.000	0.000	0.000	0.000
26	A	47	ASP	-1	-0.828	-0.905	14.033	-0.257	-0.257	0.000	0.000	0.000	0.000
27	A	48	GLU	-1	-0.914	-0.947	7.284	-1.046	-1.046	0.000	0.000	0.000	0.000
28	A	49	LEU	0	-0.100	-0.060	6.807	-0.060	-0.060	0.000	0.000	0.000	0.000
29	A	50	GLN	0	-0.066	-0.025	10.586	0.050	0.050	0.000	0.000	0.000	0.000
30	A	51	LEU	0	-0.043	-0.011	12.214	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	52	PHE	0	0.013	-0.005	15.668	0.020	0.020	0.000	0.000	0.000	0.000
32	A	53	ARG	1	0.964	0.965	19.404	0.188	0.188	0.000	0.000	0.000	0.000
33	A	54	GLY	0	0.006	-0.001	21.540	0.023	0.023	0.000	0.000	0.000	0.000
34	A	55	ASP	-1	-0.809	-0.880	18.284	-0.272	-0.272	0.000	0.000	0.000	0.000
35	A	56	THR	0	-0.042	-0.032	19.346	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	57	VAL	0	-0.030	-0.014	14.075	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	58	LEU	0	-0.041	-0.023	14.073	0.046	0.046	0.000	0.000	0.000	0.000
38	A	59	LEU	0	-0.007	-0.010	11.964	-0.108	-0.108	0.000	0.000	0.000	0.000
39	A	60	LYS	1	0.855	0.925	10.218	0.418	0.418	0.000	0.000	0.000	0.000
40	A	61	GLY	0	0.057	0.024	10.867	-0.059	-0.059	0.000	0.000	0.000	0.000
41	A	62	LYS	1	0.801	0.896	13.062	0.068	0.068	0.000	0.000	0.000	0.000
42	A	63	LYS	1	0.938	0.953	15.041	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	64	ARG	1	0.955	0.961	15.482	0.027	0.027	0.000	0.000	0.000	0.000
44	A	65	ARG	1	0.794	0.922	16.545	0.115	0.115	0.000	0.000	0.000	0.000
45	A	66	GLU	-1	-0.794	-0.892	14.939	-0.226	-0.226	0.000	0.000	0.000	0.000
46	A	67	ALA	0	0.009	0.003	15.893	0.029	0.029	0.000	0.000	0.000	0.000
47	A	68	VAL	0	0.020	0.028	16.396	-0.044	-0.044	0.000	0.000	0.000	0.000
48	A	69	CYS	0	-0.054	-0.028	17.519	0.020	0.020	0.000	0.000	0.000	0.000
49	A	70	ILE	0	0.054	0.038	18.958	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	71	VAL	0	0.004	0.011	15.290	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	72	LEU	0	-0.045	-0.029	18.375	0.047	0.047	0.000	0.000	0.000	0.000
52	A	73	SER	0	0.079	0.025	18.388	-0.037	-0.037	0.000	0.000	0.000	0.000
53	A	74	ASP	-1	-0.808	-0.922	18.220	-0.282	-0.282	0.000	0.000	0.000	0.000
54	A	75	ASP	-1	-0.947	-0.950	18.518	-0.284	-0.284	0.000	0.000	0.000	0.000
55	A	76	THR	0	-0.055	-0.046	20.286	0.024	0.024	0.000	0.000	0.000	0.000
56	A	77	CYS	0	-0.113	-0.042	13.925	0.004	0.004	0.000	0.000	0.000	0.000
57	A	78	SER	0	-0.007	0.001	13.128	0.013	0.013	0.000	0.000	0.000	0.000
58	A	79	ASP	-1	-0.764	-0.848	10.968	-0.629	-0.629	0.000	0.000	0.000	0.000
59	A	80	GLU	-1	-0.866	-0.919	7.281	-0.980	-0.980	0.000	0.000	0.000	0.000
60	A	81	LYS	1	0.793	0.869	8.337	0.344	0.344	0.000	0.000	0.000	0.000
61	A	82	ILE	0	0.008	0.000	10.949	-0.036	-0.036	0.000	0.000	0.000	0.000
62	A	83	ARG	1	0.790	0.902	12.767	0.423	0.423	0.000	0.000	0.000	0.000
63	A	84	MET	0	0.026	0.010	13.712	0.024	0.024	0.000	0.000	0.000	0.000
64	A	85	ASN	0	0.029	0.016	18.084	0.012	0.012	0.000	0.000	0.000	0.000
65	A	86	ARG	1	0.974	0.971	20.743	0.129	0.129	0.000	0.000	0.000	0.000
66	A	87	VAL	0	0.008	0.021	22.571	0.005	0.005	0.000	0.000	0.000	0.000
67	A	88	VAL	0	0.087	0.042	17.589	0.010	0.010	0.000	0.000	0.000	0.000
68	A	89	ARG	1	0.768	0.846	17.197	0.224	0.224	0.000	0.000	0.000	0.000
69	A	90	ASN	0	0.029	0.011	18.895	0.013	0.013	0.000	0.000	0.000	0.000
70	A	91	ASN	0	-0.019	0.010	20.735	0.034	0.034	0.000	0.000	0.000	0.000
71	A	92	LEU	0	0.028	0.018	14.257	0.015	0.015	0.000	0.000	0.000	0.000
72	A	93	ARG	1	0.778	0.875	16.528	0.116	0.116	0.000	0.000	0.000	0.000
73	A	94	VAL	0	-0.021	-0.001	13.567	0.032	0.032	0.000	0.000	0.000	0.000
74	A	95	ARG	1	0.942	0.954	16.277	0.084	0.084	0.000	0.000	0.000	0.000
75	A	96	LEU	0	0.033	0.014	15.540	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	97	GLY	0	0.003	0.009	13.574	0.048	0.048	0.000	0.000	0.000	0.000
77	A	98	ASP	-1	-0.803	-0.874	12.219	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	99	VAL	0	-0.020	-0.010	5.798	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	100	ILE	0	-0.041	-0.007	8.646	0.218	0.218	0.000	0.000	0.000	0.000
80	A	101	SER	0	-0.036	-0.014	6.020	-0.258	-0.258	0.000	0.000	0.000	0.000
81	A	102	ILE	0	0.033	0.016	7.384	0.320	0.320	0.000	0.000	0.000	0.000
82	A	103	GLN	0	0.014	0.015	8.514	-0.222	-0.222	0.000	0.000	0.000	0.000
83	A	104	PRO	0	0.127	0.059	10.980	0.055	0.055	0.000	0.000	0.000	0.000
84	A	105	CYS	0	-0.092	-0.050	14.254	0.034	0.034	0.000	0.000	0.000	0.000
85	A	106	PRO	0	0.072	0.039	17.233	0.016	0.016	0.000	0.000	0.000	0.000
86	A	107	ASP	-1	-0.824	-0.898	20.259	-0.111	-0.111	0.000	0.000	0.000	0.000
87	A	108	VAL	0	-0.065	-0.020	21.672	0.017	0.017	0.000	0.000	0.000	0.000
88	A	109	LYS	1	0.841	0.913	23.334	0.121	0.121	0.000	0.000	0.000	0.000
89	A	110	TYR	0	0.091	0.027	27.138	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	111	GLY	0	-0.014	0.002	29.914	0.005	0.005	0.000	0.000	0.000	0.000
91	A	112	LYS	1	0.848	0.907	31.088	0.066	0.066	0.000	0.000	0.000	0.000
92	A	113	ARG	1	0.954	0.976	33.304	0.060	0.060	0.000	0.000	0.000	0.000
93	A	114	ILE	0	-0.040	-0.009	30.022	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	115	HIS	0	-0.040	-0.034	32.591	0.003	0.003	0.000	0.000	0.000	0.000
95	A	116	VAL	0	-0.037	-0.024	31.426	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	117	LEU	0	0.022	0.012	33.553	0.004	0.004	0.000	0.000	0.000	0.000
97	A	118	PRO	0	0.014	0.022	34.080	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	119	ILE	0	-0.015	-0.020	31.278	0.003	0.003	0.000	0.000	0.000	0.000
99	A	120	ASP	-1	-0.764	-0.907	35.272	-0.042	-0.042	0.000	0.000	0.000	0.000
100	A	121	ASP	-1	-0.921	-0.950	35.718	-0.054	-0.054	0.000	0.000	0.000	0.000
101	A	122	THR	0	-0.040	-0.029	34.377	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	123	VAL	0	-0.030	-0.052	37.828	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	124	GLU	-1	-0.926	-0.939	40.821	-0.038	-0.038	0.000	0.000	0.000	0.000
104	A	125	GLY	0	-0.018	-0.012	43.415	0.002	0.002	0.000	0.000	0.000	0.000
105	A	126	ILE	0	-0.107	-0.038	41.173	0.000	0.000	0.000	0.000	0.000	0.000
106	A	127	THR	0	0.031	0.030	44.564	0.002	0.002	0.000	0.000	0.000	0.000
107	A	128	GLY	0	0.007	-0.010	46.214	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	129	ASN	0	-0.009	0.002	43.636	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	130	LEU	0	0.109	0.037	39.261	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	131	PHE	0	0.041	0.018	38.270	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	132	GLU	-1	-0.816	-0.898	40.005	-0.061	-0.061	0.000	0.000	0.000	0.000
112	A	133	VAL	0	-0.035	-0.005	41.106	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	134	TYR	0	-0.067	-0.051	36.577	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	135	LEU	0	-0.007	-0.015	34.209	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	136	LYS	1	0.828	0.907	35.679	0.055	0.055	0.000	0.000	0.000	0.000
116	A	137	PRO	0	0.025	0.006	37.070	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	138	TYR	0	-0.039	-0.003	27.787	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	139	PHE	0	0.019	-0.024	29.354	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	140	LEU	0	-0.004	0.014	33.072	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	141	GLU	-1	-0.961	-0.976	34.292	-0.088	-0.088	0.000	0.000	0.000	0.000
121	A	142	ALA	0	-0.001	0.002	29.914	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	143	TYR	0	-0.045	-0.017	28.352	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	144	ARG	1	0.821	0.881	26.310	0.137	0.137	0.000	0.000	0.000	0.000
124	A	145	PRO	0	-0.019	0.007	22.035	0.014	0.014	0.000	0.000	0.000	0.000
125	A	146	ILE	0	-0.018	-0.006	24.297	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	147	ARG	1	0.858	0.907	18.467	0.164	0.164	0.000	0.000	0.000	0.000
127	A	148	LYS	1	0.860	0.913	23.839	0.073	0.073	0.000	0.000	0.000	0.000
128	A	149	GLY	0	-0.086	-0.057	24.106	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	150	ASP	-1	-0.880	-0.937	22.345	-0.164	-0.164	0.000	0.000	0.000	0.000
130	A	151	ILE	0	-0.044	-0.033	24.906	0.013	0.013	0.000	0.000	0.000	0.000
131	A	152	PHE	0	0.001	0.006	25.942	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	153	LEU	0	0.018	0.023	28.004	0.009	0.009	0.000	0.000	0.000	0.000
133	A	154	VAL	0	-0.005	0.006	30.364	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	155	ARG	1	0.894	0.923	29.727	0.120	0.120	0.000	0.000	0.000	0.000
135	A	156	GLY	0	0.082	0.040	35.503	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	157	GLY	0	0.023	0.007	39.163	0.001	0.001	0.000	0.000	0.000	0.000
137	A	158	MET	0	-0.017	-0.005	42.488	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	159	ARG	1	0.943	0.971	39.529	0.053	0.053	0.000	0.000	0.000	0.000
139	A	160	ALA	0	-0.021	0.012	34.514	0.000	0.000	0.000	0.000	0.000	0.000
140	A	161	VAL	0	0.041	0.034	35.718	0.003	0.003	0.000	0.000	0.000	0.000
141	A	162	GLU	-1	-0.928	-0.967	29.828	-0.099	-0.099	0.000	0.000	0.000	0.000
142	A	163	PHE	0	0.026	0.006	31.466	0.008	0.008	0.000	0.000	0.000	0.000
143	A	164	LYS	1	0.944	0.970	28.237	0.058	0.058	0.000	0.000	0.000	0.000
144	A	165	VAL	0	0.026	0.022	27.378	0.007	0.007	0.000	0.000	0.000	0.000
145	A	166	VAL	0	-0.048	-0.028	28.800	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	167	GLU	-1	-0.832	-0.909	30.352	-0.060	-0.060	0.000	0.000	0.000	0.000
147	A	168	THR	0	-0.036	-0.030	27.320	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	169	ASP	-1	-0.834	-0.865	29.955	-0.062	-0.062	0.000	0.000	0.000	0.000
149	A	170	PRO	0	0.100	0.030	27.609	0.000	0.000	0.000	0.000	0.000	0.000
150	A	171	SER	0	0.001	0.032	27.194	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	172	PRO	0	-0.074	-0.035	22.126	0.001	0.001	0.000	0.000	0.000	0.000
152	A	173	TYR	0	0.049	-0.010	19.118	-0.006	-0.006	0.000	0.000	0.000	0.000
153	A	174	CYS	0	-0.065	-0.002	24.323	0.008	0.008	0.000	0.000	0.000	0.000
154	A	175	ILE	0	0.045	0.027	23.921	-0.011	-0.011	0.000	0.000	0.000	0.000
155	A	176	VAL	0	-0.030	-0.028	27.271	0.012	0.012	0.000	0.000	0.000	0.000
156	A	177	ALA	0	0.022	0.010	30.439	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	178	PRO	0	0.021	0.002	32.757	0.003	0.003	0.000	0.000	0.000	0.000
158	A	179	ASP	-1	-0.921	-0.951	36.231	-0.067	-0.067	0.000	0.000	0.000	0.000
159	A	180	THR	0	-0.109	-0.052	32.182	0.000	0.000	0.000	0.000	0.000	0.000
160	A	181	VAL	0	-0.012	-0.010	35.210	0.002	0.002	0.000	0.000	0.000	0.000
161	A	182	ILE	0	0.011	0.000	34.406	-0.003	-0.003	0.000	0.000	0.000	0.000
162	A	183	HIS	0	-0.062	-0.023	36.448	0.005	0.005	0.000	0.000	0.000	0.000
163	A	184	CYS	0	0.000	-0.022	36.782	-0.005	-0.005	0.000	0.000	0.000	0.000
164	A	185	GLU	-1	-0.874	-0.930	37.830	-0.049	-0.049	0.000	0.000	0.000	0.000
165	A	186	GLY	0	0.034	0.021	40.612	0.001	0.001	0.000	0.000	0.000	0.000
166	A	187	GLU	-1	-0.959	-0.975	41.710	-0.037	-0.037	0.000	0.000	0.000	0.000
167	A	188	PRO	0	0.017	0.018	38.703	-0.002	-0.002	0.000	0.000	0.000	0.000
168	A	189	ILE	0	-0.034	-0.003	33.214	0.003	0.003	0.000	0.000	0.000	0.000
169	A	190	LYS	1	0.917	0.952	35.408	0.034	0.034	0.000	0.000	0.000	0.000
170	A	191	ARG	1	0.919	0.963	28.108	0.041	0.041	0.000	0.000	0.000	0.000

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