FMO DATABASE

FMODB ID: 2NLVR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-788020.288191
FMO2-HF: Nuclear repulsion	742034.849699
FMO2-HF: Total energy	-45985.438491
FMO2-MP2: Total energy	-46120.504554

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.
1.647	4.546	0.018	-1.408	-1.509	0.007

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 : 0.013 / q_NPA : 0.009

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	0.813	0.897	3.817	3.031	5.512	-0.011	-1.263	-1.207	0.007
4	A	261	ARG	1	0.865	0.911	6.094	-0.630	-0.630	0.000	0.000	0.000	0.000
5	A	262	ASP	-1	-0.932	-0.956	9.146	-0.215	-0.215	0.000	0.000	0.000	0.000
6	A	263	GLY	0	0.051	0.030	12.494	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	264	ASP	-1	-0.861	-0.954	14.234	0.190	0.190	0.000	0.000	0.000	0.000
8	A	265	ASP	-1	-0.780	-0.860	13.647	-0.152	-0.152	0.000	0.000	0.000	0.000
9	A	266	LEU	0	-0.061	-0.026	7.729	0.111	0.111	0.000	0.000	0.000	0.000
10	A	267	VAL	0	-0.015	-0.013	8.439	-0.124	-0.124	0.000	0.000	0.000	0.000
11	A	268	TYR	0	0.032	0.011	3.029	-0.381	0.037	0.029	-0.145	-0.302	0.000
12	A	269	GLU	-1	-0.821	-0.900	5.538	-0.899	-0.899	0.000	0.000	0.000	0.000
13	A	270	ALA	0	0.018	0.019	6.558	-0.332	-0.332	0.000	0.000	0.000	0.000
14	A	271	GLU	-1	-0.911	-0.968	8.970	-0.409	-0.409	0.000	0.000	0.000	0.000
15	A	272	ILE	0	-0.031	-0.005	11.439	0.043	0.043	0.000	0.000	0.000	0.000
16	A	273	ASP	-1	-0.786	-0.888	14.754	-0.272	-0.272	0.000	0.000	0.000	0.000
17	A	274	LEU	0	0.027	0.005	18.083	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	275	LEU	0	0.006	0.004	20.977	0.006	0.006	0.000	0.000	0.000	0.000
19	A	276	THR	0	0.008	0.009	17.977	0.008	0.008	0.000	0.000	0.000	0.000
20	A	277	ALA	0	-0.018	-0.006	18.885	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	278	ILE	0	-0.014	-0.014	20.326	0.006	0.006	0.000	0.000	0.000	0.000
22	A	279	ALA	0	-0.020	-0.005	23.815	0.017	0.017	0.000	0.000	0.000	0.000
23	A	280	GLY	0	0.008	0.017	22.292	0.016	0.016	0.000	0.000	0.000	0.000
24	A	281	GLY	0	-0.025	-0.030	20.798	0.007	0.007	0.000	0.000	0.000	0.000
25	A	282	GLU	-1	-0.869	-0.911	17.890	-0.194	-0.194	0.000	0.000	0.000	0.000
26	A	283	PHE	0	-0.002	0.002	10.911	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	284	ALA	0	-0.005	-0.007	12.041	0.038	0.038	0.000	0.000	0.000	0.000
28	A	285	LEU	0	-0.026	-0.003	6.652	-0.086	-0.086	0.000	0.000	0.000	0.000
29	A	286	GLU	-1	-0.870	-0.906	6.696	0.702	0.702	0.000	0.000	0.000	0.000
30	A	287	HIS	0	-0.010	-0.037	6.128	-0.350	-0.350	0.000	0.000	0.000	0.000
31	A	288	VAL	0	-0.006	-0.011	5.032	0.255	0.255	0.000	0.000	0.000	0.000
32	A	289	SER	0	-0.068	-0.057	7.429	0.167	0.167	0.000	0.000	0.000	0.000
33	A	290	GLY	0	0.027	0.019	10.040	0.037	0.037	0.000	0.000	0.000	0.000
34	A	291	ASP	-1	-0.917	-0.922	11.308	0.068	0.068	0.000	0.000	0.000	0.000
35	A	292	TRP	0	-0.060	-0.044	9.996	-0.159	-0.159	0.000	0.000	0.000	0.000
36	A	293	LEU	0	-0.066	-0.028	10.606	0.040	0.040	0.000	0.000	0.000	0.000
37	A	294	LYS	1	0.857	0.901	12.490	0.098	0.098	0.000	0.000	0.000	0.000
38	A	295	VAL	0	-0.022	-0.020	13.332	0.025	0.025	0.000	0.000	0.000	0.000
39	A	296	GLY	0	0.082	0.051	16.018	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	297	ILE	0	-0.079	-0.042	16.495	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	298	VAL	0	0.053	0.012	20.322	0.019	0.019	0.000	0.000	0.000	0.000
42	A	299	PRO	0	0.022	0.013	24.073	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	300	GLY	0	0.010	0.007	26.384	0.012	0.012	0.000	0.000	0.000	0.000
44	A	301	GLU	-1	-0.962	-0.982	23.453	-0.219	-0.219	0.000	0.000	0.000	0.000
45	A	302	VAL	0	-0.034	-0.014	22.913	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	303	ILE	0	-0.011	-0.008	16.726	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	304	ALA	0	0.009	-0.010	20.085	0.011	0.011	0.000	0.000	0.000	0.000
48	A	305	PRO	0	0.045	-0.001	17.763	-0.047	-0.047	0.000	0.000	0.000	0.000
49	A	306	GLY	0	0.004	0.015	15.444	0.030	0.030	0.000	0.000	0.000	0.000
50	A	307	MET	0	-0.093	-0.014	16.476	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	308	ARG	1	0.938	0.958	14.625	0.384	0.384	0.000	0.000	0.000	0.000
52	A	309	LYS	1	0.900	0.958	15.157	0.360	0.360	0.000	0.000	0.000	0.000
53	A	310	VAL	0	-0.004	-0.005	15.048	-0.072	-0.072	0.000	0.000	0.000	0.000
54	A	311	ILE	0	-0.002	0.009	12.157	0.028	0.028	0.000	0.000	0.000	0.000
55	A	312	GLU	-1	-0.870	-0.948	15.494	-0.161	-0.161	0.000	0.000	0.000	0.000
56	A	313	GLY	0	0.026	0.006	17.590	0.007	0.007	0.000	0.000	0.000	0.000
57	A	314	LYS	1	0.893	0.957	12.265	0.114	0.114	0.000	0.000	0.000	0.000
58	A	315	GLY	0	0.024	0.028	11.761	-0.055	-0.055	0.000	0.000	0.000	0.000
59	A	316	MET	0	-0.060	-0.039	10.510	0.137	0.137	0.000	0.000	0.000	0.000
60	A	317	PRO	0	0.042	0.024	13.966	-0.045	-0.045	0.000	0.000	0.000	0.000
61	A	318	ILE	0	0.049	0.041	17.388	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	319	PRO	0	-0.055	-0.031	18.845	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	320	LYS	1	0.862	0.916	20.431	-0.068	-0.068	0.000	0.000	0.000	0.000
64	A	321	TYR	0	-0.001	-0.002	23.043	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	322	GLY	0	0.013	0.014	22.123	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	323	GLY	0	-0.006	0.016	21.889	0.000	0.000	0.000	0.000	0.000	0.000
67	A	324	TYR	0	-0.046	-0.040	15.540	0.042	0.042	0.000	0.000	0.000	0.000
68	A	325	GLY	0	0.021	0.026	16.345	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	326	ASN	0	-0.035	-0.025	15.609	0.014	0.014	0.000	0.000	0.000	0.000
70	A	327	LEU	0	-0.028	-0.007	8.541	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	328	ILE	0	0.001	-0.004	11.737	0.007	0.007	0.000	0.000	0.000	0.000
72	A	329	ILE	0	0.001	-0.002	9.512	-0.226	-0.226	0.000	0.000	0.000	0.000
73	A	330	LYS	1	0.856	0.922	10.063	1.147	1.147	0.000	0.000	0.000	0.000
74	A	331	PHE	0	0.044	0.006	10.734	-0.189	-0.189	0.000	0.000	0.000	0.000
75	A	332	THR	0	-0.002	0.010	11.372	0.094	0.094	0.000	0.000	0.000	0.000
76	A	333	ILE	0	-0.018	-0.015	13.705	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	334	LYS	1	0.874	0.943	15.545	0.322	0.322	0.000	0.000	0.000	0.000
78	A	335	PHE	0	-0.018	-0.026	17.389	0.024	0.024	0.000	0.000	0.000	0.000
79	A	336	PRO	0	-0.023	-0.006	21.158	0.001	0.001	0.000	0.000	0.000	0.000
80	A	337	GLU	-1	-0.883	-0.932	22.524	-0.171	-0.171	0.000	0.000	0.000	0.000
81	A	338	ASN	0	0.009	-0.019	25.381	0.001	0.001	0.000	0.000	0.000	0.000
82	A	339	HIS	0	-0.026	-0.020	29.043	0.003	0.003	0.000	0.000	0.000	0.000
83	A	340	PHE	0	0.029	0.035	27.460	0.005	0.005	0.000	0.000	0.000	0.000
84	A	341	THR	0	-0.054	-0.033	29.436	0.001	0.001	0.000	0.000	0.000	0.000
85	A	342	SER	0	0.022	0.014	32.509	0.000	0.000	0.000	0.000	0.000	0.000
86	A	343	GLU	-1	-0.747	-0.883	35.994	-0.085	-0.085	0.000	0.000	0.000	0.000
87	A	344	GLU	-1	-0.908	-0.941	38.092	-0.067	-0.067	0.000	0.000	0.000	0.000
88	A	345	ASN	0	0.020	-0.010	34.385	0.000	0.000	0.000	0.000	0.000	0.000
89	A	346	LEU	0	0.025	0.018	32.055	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	347	LYS	1	0.855	0.910	35.161	0.074	0.074	0.000	0.000	0.000	0.000
91	A	348	LYS	1	0.884	0.936	36.463	0.074	0.074	0.000	0.000	0.000	0.000
92	A	349	LEU	0	-0.017	0.001	30.892	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	350	GLU	-1	-0.897	-0.923	34.380	-0.094	-0.094	0.000	0.000	0.000	0.000
94	A	351	GLU	-1	-0.962	-0.973	36.844	-0.076	-0.076	0.000	0.000	0.000	0.000
95	A	352	ILE	0	-0.078	-0.027	32.172	0.000	0.000	0.000	0.000	0.000	0.000
96	A	353	LEU	0	-0.051	-0.023	29.471	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	354	PRO	0	0.000	-0.008	32.003	0.007	0.007	0.000	0.000	0.000	0.000
98	A	355	PRO	0	0.007	0.002	34.875	0.000	0.000	0.000	0.000	0.000	0.000
99	A	356	ARG	1	0.866	0.912	35.901	0.096	0.096	0.000	0.000	0.000	0.000
100	A	357	ILE	0	-0.011	0.003	34.022	0.004	0.004	0.000	0.000	0.000	0.000
101	A	358	VAL	0	-0.018	-0.010	37.279	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	359	PRO	0	0.015	0.001	39.071	0.000	0.000	0.000	0.000	0.000	0.000
103	A	360	ALA	0	0.006	0.007	41.163	0.004	0.004	0.000	0.000	0.000	0.000
104	A	361	ILE	0	0.014	0.004	43.379	0.000	0.000	0.000	0.000	0.000	0.000
105	A	362	PRO	0	-0.008	0.001	45.498	0.003	0.003	0.000	0.000	0.000	0.000
106	A	363	LYS	1	1.002	0.990	48.669	0.056	0.056	0.000	0.000	0.000	0.000
107	A	364	LYS	1	0.933	0.957	51.970	0.051	0.051	0.000	0.000	0.000	0.000
108	A	365	ALA	0	-0.014	0.020	48.439	0.001	0.001	0.000	0.000	0.000	0.000
109	A	366	THR	0	0.010	-0.001	48.570	0.001	0.001	0.000	0.000	0.000	0.000
110	A	367	VAL	0	-0.041	-0.030	46.183	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	368	ASP	-1	-0.882	-0.930	44.164	-0.063	-0.063	0.000	0.000	0.000	0.000
112	A	369	GLU	-1	-0.977	-0.985	43.412	-0.068	-0.068	0.000	0.000	0.000	0.000
113	A	370	CYS	0	-0.063	-0.034	39.462	0.002	0.002	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.009	-0.012	37.607	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	372	LEU	0	-0.037	-0.015	32.088	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	373	ALA	0	0.001	0.000	33.946	0.003	0.003	0.000	0.000	0.000	0.000
117	A	374	ASP	-1	-0.921	-0.958	29.313	-0.124	-0.124	0.000	0.000	0.000	0.000
118	A	375	PHE	0	-0.046	-0.018	24.974	0.005	0.005	0.000	0.000	0.000	0.000
119	A	376	ASP	-1	-0.873	-0.940	27.177	-0.110	-0.110	0.000	0.000	0.000	0.000
120	A	377	PRO	0	-0.077	-0.053	22.475	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	378	ALA	0	-0.036	0.001	24.237	-0.006	-0.006	0.000	0.000	0.000	0.000

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