FMO DATABASE

FMODB ID: 76M1K

Calculation Name: 1XAO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XAO

Chain ID: A

ChEMBL ID:

UniProt ID: P25491

Base Structure: X-ray

Registration Date: 2023-09-22

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	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-787222.395372
FMO2-HF: Nuclear repulsion	741237.666731
FMO2-HF: Total energy	-45984.72864
FMO2-MP2: Total energy	-46119.799595

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:258:SER)

Summations of interaction energy for fragment #1(A:258: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.
0.68	3.787	0.026	-1.518	-1.615	0.008

Interaction energy analysis for fragmet #1(A:258:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.011

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	260	LYS	1	0.924	0.963	3.744	2.132	4.790	-0.001	-1.357	-1.300	0.007
4	A	261	ARG	1	0.916	0.949	5.856	-0.802	-0.802	0.000	0.000	0.000	0.000
5	A	262	ASP	-1	-0.951	-0.962	9.002	-0.115	-0.115	0.000	0.000	0.000	0.000
6	A	263	GLY	0	0.054	0.028	12.291	-0.038	-0.038	0.000	0.000	0.000	0.000
7	A	264	ASP	-1	-0.896	-0.977	14.142	0.189	0.189	0.000	0.000	0.000	0.000
8	A	265	ASP	-1	-0.804	-0.873	13.615	-0.107	-0.107	0.000	0.000	0.000	0.000
9	A	266	LEU	0	-0.062	-0.034	7.545	0.131	0.131	0.000	0.000	0.000	0.000
10	A	267	VAL	0	-0.026	-0.016	8.408	-0.148	-0.148	0.000	0.000	0.000	0.000
11	A	268	TYR	0	0.023	0.006	3.105	-0.075	0.374	0.027	-0.161	-0.315	0.001
12	A	269	GLU	-1	-0.979	-0.995	5.474	-0.697	-0.697	0.000	0.000	0.000	0.000
13	A	270	ALA	0	-0.002	0.011	6.509	-0.343	-0.343	0.000	0.000	0.000	0.000
14	A	271	GLU	-1	-0.925	-0.973	8.910	-0.364	-0.364	0.000	0.000	0.000	0.000
15	A	272	ILE	0	-0.039	-0.009	11.403	0.031	0.031	0.000	0.000	0.000	0.000
16	A	273	ASP	-1	-0.830	-0.927	14.710	-0.259	-0.259	0.000	0.000	0.000	0.000
17	A	274	LEU	0	0.006	-0.009	18.049	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	275	LEU	0	0.003	0.005	20.940	0.006	0.006	0.000	0.000	0.000	0.000
19	A	276	THR	0	0.015	0.010	17.948	0.008	0.008	0.000	0.000	0.000	0.000
20	A	277	ALA	0	-0.020	-0.008	18.917	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	278	ILE	0	-0.019	-0.020	20.268	0.007	0.007	0.000	0.000	0.000	0.000
22	A	279	ALA	0	-0.020	-0.004	23.764	0.016	0.016	0.000	0.000	0.000	0.000
23	A	280	GLY	0	0.014	0.018	22.336	0.014	0.014	0.000	0.000	0.000	0.000
24	A	281	GLY	0	-0.035	-0.033	20.846	0.006	0.006	0.000	0.000	0.000	0.000
25	A	282	GLU	-1	-0.923	-0.958	17.933	-0.214	-0.214	0.000	0.000	0.000	0.000
26	A	283	PHE	0	-0.009	0.003	11.065	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	284	ALA	0	-0.005	-0.010	12.074	0.040	0.040	0.000	0.000	0.000	0.000
28	A	285	LEU	0	-0.043	-0.011	6.724	-0.086	-0.086	0.000	0.000	0.000	0.000
29	A	286	GLU	-1	-0.900	-0.936	6.667	0.515	0.515	0.000	0.000	0.000	0.000
30	A	287	HIS	0	-0.018	-0.038	6.119	-0.416	-0.416	0.000	0.000	0.000	0.000
31	A	288	VAL	0	0.003	-0.007	5.098	0.208	0.208	0.000	0.000	0.000	0.000
32	A	289	SER	0	-0.058	-0.028	7.449	0.155	0.155	0.000	0.000	0.000	0.000
33	A	290	GLY	0	0.027	0.025	10.018	0.046	0.046	0.000	0.000	0.000	0.000
34	A	291	ASP	-1	-0.947	-0.960	11.255	0.010	0.010	0.000	0.000	0.000	0.000
35	A	292	TRP	0	-0.009	-0.012	9.895	-0.145	-0.145	0.000	0.000	0.000	0.000
36	A	293	LEU	0	-0.068	-0.030	10.471	0.054	0.054	0.000	0.000	0.000	0.000
37	A	294	LYS	1	0.932	0.962	12.517	0.097	0.097	0.000	0.000	0.000	0.000
38	A	295	VAL	0	-0.031	-0.024	13.304	0.027	0.027	0.000	0.000	0.000	0.000
39	A	296	GLY	0	0.099	0.058	16.072	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	297	ILE	0	-0.093	-0.052	16.639	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	298	VAL	0	0.059	0.016	20.395	0.017	0.017	0.000	0.000	0.000	0.000
42	A	299	PRO	0	0.000	0.003	24.146	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	300	GLY	0	0.011	0.008	26.460	0.011	0.011	0.000	0.000	0.000	0.000
44	A	301	GLU	-1	-1.014	-1.005	23.763	-0.180	-0.180	0.000	0.000	0.000	0.000
45	A	302	VAL	0	-0.021	-0.007	22.836	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	303	ILE	0	-0.029	-0.010	16.642	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	304	ALA	0	0.005	-0.020	20.018	0.010	0.010	0.000	0.000	0.000	0.000
48	A	305	PRO	0	0.035	-0.007	17.731	-0.043	-0.043	0.000	0.000	0.000	0.000
49	A	306	GLY	0	0.015	0.020	15.403	0.030	0.030	0.000	0.000	0.000	0.000
50	A	307	MET	0	-0.092	-0.006	16.425	0.002	0.002	0.000	0.000	0.000	0.000
51	A	308	ARG	1	0.965	0.963	14.659	0.318	0.318	0.000	0.000	0.000	0.000
52	A	309	LYS	1	0.944	0.975	15.073	0.346	0.346	0.000	0.000	0.000	0.000
53	A	310	VAL	0	0.009	0.000	15.023	-0.063	-0.063	0.000	0.000	0.000	0.000
54	A	311	ILE	0	-0.009	0.011	12.345	0.022	0.022	0.000	0.000	0.000	0.000
55	A	312	GLU	-1	-0.893	-0.976	15.558	-0.133	-0.133	0.000	0.000	0.000	0.000
56	A	313	GLY	0	0.020	0.001	17.603	0.001	0.001	0.000	0.000	0.000	0.000
57	A	314	LYS	1	0.883	0.953	12.268	0.167	0.167	0.000	0.000	0.000	0.000
58	A	315	GLY	0	0.030	0.032	11.773	-0.050	-0.050	0.000	0.000	0.000	0.000
59	A	316	MET	0	-0.057	-0.036	10.335	0.132	0.132	0.000	0.000	0.000	0.000
60	A	317	PRO	0	0.027	0.017	13.959	-0.043	-0.043	0.000	0.000	0.000	0.000
61	A	318	ILE	0	0.034	0.043	17.394	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	319	PRO	0	-0.071	-0.050	19.170	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	320	LYS	1	0.927	0.950	21.605	-0.073	-0.073	0.000	0.000	0.000	0.000
64	A	321	TYR	0	-0.002	-0.002	23.200	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	322	GLY	0	0.011	0.016	21.646	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	323	GLY	0	-0.001	0.017	21.872	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	324	TYR	0	-0.045	-0.042	16.117	0.038	0.038	0.000	0.000	0.000	0.000
68	A	325	GLY	0	0.034	0.032	16.341	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	326	ASN	0	-0.007	0.005	15.615	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	327	LEU	0	-0.017	0.000	8.565	0.013	0.013	0.000	0.000	0.000	0.000
71	A	328	ILE	0	-0.008	-0.010	11.733	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	329	ILE	0	0.008	0.001	9.699	-0.188	-0.188	0.000	0.000	0.000	0.000
73	A	330	LYS	1	0.889	0.942	10.233	0.835	0.835	0.000	0.000	0.000	0.000
74	A	331	PHE	0	0.050	0.014	10.675	-0.177	-0.177	0.000	0.000	0.000	0.000
75	A	332	THR	0	0.020	0.023	11.511	0.108	0.108	0.000	0.000	0.000	0.000
76	A	333	ILE	0	-0.026	-0.019	13.674	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	334	LYS	1	0.984	1.014	15.499	0.271	0.271	0.000	0.000	0.000	0.000
78	A	335	PHE	0	-0.027	-0.030	17.376	0.021	0.021	0.000	0.000	0.000	0.000
79	A	336	PRO	0	-0.026	-0.010	21.147	0.001	0.001	0.000	0.000	0.000	0.000
80	A	337	GLU	-1	-0.887	-0.934	22.421	-0.158	-0.158	0.000	0.000	0.000	0.000
81	A	338	ASN	0	0.020	-0.015	25.390	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	339	HIS	0	-0.025	-0.019	29.053	0.003	0.003	0.000	0.000	0.000	0.000
83	A	340	PHE	0	0.020	0.034	27.466	0.004	0.004	0.000	0.000	0.000	0.000
84	A	341	THR	0	-0.071	-0.033	29.433	0.000	0.000	0.000	0.000	0.000	0.000
85	A	342	SER	0	0.023	0.010	32.498	0.001	0.001	0.000	0.000	0.000	0.000
86	A	343	GLU	-1	-0.775	-0.924	35.979	-0.080	-0.080	0.000	0.000	0.000	0.000
87	A	344	GLU	-1	-0.940	-0.966	38.080	-0.062	-0.062	0.000	0.000	0.000	0.000
88	A	345	ASN	0	0.006	-0.025	34.218	0.000	0.000	0.000	0.000	0.000	0.000
89	A	346	LEU	0	0.006	0.006	31.940	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	347	LYS	1	0.881	0.950	35.139	0.067	0.067	0.000	0.000	0.000	0.000
91	A	348	LYS	1	0.950	0.984	36.352	0.070	0.070	0.000	0.000	0.000	0.000
92	A	349	LEU	0	-0.007	0.006	30.682	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	350	GLU	-1	-0.907	-0.932	34.343	-0.086	-0.086	0.000	0.000	0.000	0.000
94	A	351	GLU	-1	-0.971	-0.976	36.806	-0.070	-0.070	0.000	0.000	0.000	0.000
95	A	352	ILE	0	-0.070	-0.021	32.073	0.000	0.000	0.000	0.000	0.000	0.000
96	A	353	LEU	0	-0.052	-0.025	29.263	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	354	PRO	0	-0.010	-0.013	31.850	0.006	0.006	0.000	0.000	0.000	0.000
98	A	355	PRO	0	0.005	0.000	34.825	0.000	0.000	0.000	0.000	0.000	0.000
99	A	356	ARG	1	0.899	0.929	36.046	0.087	0.087	0.000	0.000	0.000	0.000
100	A	357	ILE	0	-0.004	0.010	34.040	0.004	0.004	0.000	0.000	0.000	0.000
101	A	358	VAL	0	-0.021	-0.013	37.255	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	359	PRO	0	-0.002	-0.005	38.996	0.001	0.001	0.000	0.000	0.000	0.000
103	A	360	ALA	0	0.014	0.012	41.145	0.003	0.003	0.000	0.000	0.000	0.000
104	A	361	ILE	0	0.016	0.005	43.338	0.000	0.000	0.000	0.000	0.000	0.000
105	A	362	PRO	0	-0.018	-0.004	45.416	0.003	0.003	0.000	0.000	0.000	0.000
106	A	363	LYS	1	1.008	0.989	48.656	0.049	0.049	0.000	0.000	0.000	0.000
107	A	364	LYS	1	0.941	0.962	51.959	0.044	0.044	0.000	0.000	0.000	0.000
108	A	365	ALA	0	-0.016	0.018	48.415	0.001	0.001	0.000	0.000	0.000	0.000
109	A	366	THR	0	0.018	-0.003	48.443	0.001	0.001	0.000	0.000	0.000	0.000
110	A	367	VAL	0	-0.054	-0.029	46.164	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	368	ASP	-1	-0.872	-0.927	44.082	-0.054	-0.054	0.000	0.000	0.000	0.000
112	A	369	GLU	-1	-0.986	-0.992	43.423	-0.059	-0.059	0.000	0.000	0.000	0.000
113	A	370	CYS	0	-0.059	-0.031	39.526	0.001	0.001	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.002	-0.006	37.546	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	372	LEU	0	-0.038	-0.017	31.928	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	373	ALA	0	-0.003	-0.002	33.977	0.003	0.003	0.000	0.000	0.000	0.000
117	A	374	ASP	-1	-0.923	-0.959	29.336	-0.108	-0.108	0.000	0.000	0.000	0.000
118	A	375	PHE	0	-0.037	-0.017	24.466	0.005	0.005	0.000	0.000	0.000	0.000
119	A	376	ASP	-1	-0.887	-0.945	27.131	-0.094	-0.094	0.000	0.000	0.000	0.000
120	A	377	PRO	0	-0.068	-0.044	22.445	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	378	ALA	0	-0.041	-0.005	24.151	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:258:SER)