FMO DATABASE

FMODB ID: R9598

Calculation Name: 2WB3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WB3

Chain ID: A

ChEMBL ID:

UniProt ID: Q99Z19

Base Structure: X-ray

Registration Date: 2023-06-21

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1012572.781022
FMO2-HF: Nuclear repulsion	954404.203234
FMO2-HF: Total energy	-58168.577788
FMO2-MP2: Total energy	-58337.515137

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:234:THR)

Summations of interaction energy for fragment #1(A:234:THR)

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.
0.314	1.705	-0.007	-0.706	-0.678	0.002

Interaction energy analysis for fragmet #1(A:234:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.010

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	236	ALA	0	0.019	0.014	3.778	0.969	2.234	-0.006	-0.696	-0.563	0.002
4	A	237	VAL	0	0.010	0.003	6.512	0.519	0.519	0.000	0.000	0.000	0.000
5	A	238	ASN	0	0.024	0.017	4.265	-1.637	-1.511	-0.001	-0.010	-0.115	0.000
6	A	239	ILE	0	-0.003	-0.003	8.310	0.026	0.026	0.000	0.000	0.000	0.000
7	A	240	VAL	0	0.002	-0.004	10.398	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	241	MET	0	-0.004	0.018	12.999	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	242	ARG	1	0.933	0.956	16.026	-0.454	-0.454	0.000	0.000	0.000	0.000
10	A	243	GLN	0	0.051	0.028	17.674	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	244	PRO	0	-0.017	0.016	20.656	0.015	0.015	0.000	0.000	0.000	0.000
12	A	245	THR	0	-0.026	-0.033	23.810	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	246	THR	0	0.043	0.029	27.071	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	247	PRO	0	0.013	-0.002	25.910	0.010	0.010	0.000	0.000	0.000	0.000
15	A	248	ASN	0	0.008	0.008	24.935	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	249	PHE	0	0.041	0.002	26.154	0.001	0.001	0.000	0.000	0.000	0.000
17	A	250	SER	0	-0.072	-0.018	23.403	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	251	SER	0	0.042	0.017	20.681	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	252	ALA	0	0.003	-0.001	15.462	0.017	0.017	0.000	0.000	0.000	0.000
20	A	253	LEU	0	-0.008	-0.011	15.470	0.019	0.019	0.000	0.000	0.000	0.000
21	A	254	ASN	0	0.003	0.005	18.340	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	255	ILE	0	0.007	0.005	18.848	0.005	0.005	0.000	0.000	0.000	0.000
23	A	256	THR	0	0.006	-0.005	23.014	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	257	SER	0	0.005	0.006	26.712	0.006	0.006	0.000	0.000	0.000	0.000
25	A	258	ALA	0	-0.009	-0.007	28.558	0.000	0.000	0.000	0.000	0.000	0.000
26	A	259	ASN	0	-0.018	-0.008	29.947	0.003	0.003	0.000	0.000	0.000	0.000
27	A	260	GLU	-1	-0.945	-0.977	31.701	-0.043	-0.043	0.000	0.000	0.000	0.000
28	A	261	GLY	0	0.020	0.016	33.453	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	262	GLY	0	-0.026	-0.015	29.244	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	263	SER	0	-0.041	-0.015	25.074	0.010	0.010	0.000	0.000	0.000	0.000
31	A	264	ALA	0	-0.009	0.002	25.377	0.000	0.000	0.000	0.000	0.000	0.000
32	A	265	MET	0	0.028	0.001	16.717	0.012	0.012	0.000	0.000	0.000	0.000
33	A	266	GLN	0	-0.043	-0.019	20.464	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	267	ILE	0	0.011	-0.002	14.872	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	268	ARG	1	0.966	0.981	16.288	0.283	0.283	0.000	0.000	0.000	0.000
36	A	269	GLY	0	0.017	0.016	14.108	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	270	VAL	0	-0.020	-0.009	13.691	0.058	0.058	0.000	0.000	0.000	0.000
38	A	271	GLU	-1	-0.818	-0.884	11.699	-0.638	-0.638	0.000	0.000	0.000	0.000
39	A	272	LYS	1	0.964	0.989	13.774	0.440	0.440	0.000	0.000	0.000	0.000
40	A	273	ALA	0	-0.047	-0.062	14.200	0.051	0.051	0.000	0.000	0.000	0.000
41	A	274	LEU	0	-0.024	0.003	10.068	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	275	GLY	0	0.018	0.012	14.030	0.042	0.042	0.000	0.000	0.000	0.000
43	A	276	THR	0	-0.008	-0.017	13.118	-0.039	-0.039	0.000	0.000	0.000	0.000
44	A	277	LEU	0	-0.006	0.012	13.222	-0.041	-0.041	0.000	0.000	0.000	0.000
45	A	278	LYS	1	0.903	0.952	12.178	0.497	0.497	0.000	0.000	0.000	0.000
46	A	279	ILE	0	0.034	0.009	13.888	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	280	THR	0	-0.070	-0.049	14.115	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	281	HIS	0	0.007	0.015	16.407	0.018	0.018	0.000	0.000	0.000	0.000
49	A	282	GLU	-1	-0.991	-0.995	16.848	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	283	ASN	0	0.042	0.014	19.807	0.026	0.026	0.000	0.000	0.000	0.000
51	A	284	PRO	0	-0.033	-0.001	22.240	0.007	0.007	0.000	0.000	0.000	0.000
52	A	285	SER	0	0.000	0.007	23.253	0.015	0.015	0.000	0.000	0.000	0.000
53	A	286	VAL	0	-0.012	-0.016	25.642	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	287	ASP	-1	-0.926	-0.956	27.126	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	288	LYS	1	0.920	0.938	28.947	0.024	0.024	0.000	0.000	0.000	0.000
56	A	289	GLU	-1	-0.925	-0.965	30.034	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	290	TYR	0	-0.019	0.005	27.480	0.003	0.003	0.000	0.000	0.000	0.000
58	A	291	ASP	-1	-0.903	-0.965	25.559	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	292	GLU	-1	-0.907	-0.947	28.271	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	293	ASN	0	-0.059	-0.028	30.691	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	294	ALA	0	-0.080	-0.018	25.101	0.001	0.001	0.000	0.000	0.000	0.000
62	A	295	ALA	0	0.015	-0.007	25.134	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	296	ALA	0	-0.030	-0.011	20.459	0.001	0.001	0.000	0.000	0.000	0.000
64	A	297	LEU	0	-0.012	-0.016	21.273	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	298	SER	0	-0.005	0.007	23.417	0.003	0.003	0.000	0.000	0.000	0.000
66	A	299	ILE	0	-0.026	-0.023	26.245	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	300	ASP	-1	-0.854	-0.932	28.568	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	301	ILE	0	-0.053	-0.008	31.478	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	302	VAL	0	0.023	0.022	34.090	0.004	0.004	0.000	0.000	0.000	0.000
70	A	303	LYS	1	0.903	0.963	36.488	0.013	0.013	0.000	0.000	0.000	0.000
71	A	304	LYS	1	1.012	0.991	38.356	0.016	0.016	0.000	0.000	0.000	0.000
72	A	305	GLN	0	0.042	0.008	35.173	0.004	0.004	0.000	0.000	0.000	0.000
73	A	306	LYS	1	0.968	0.977	39.668	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	307	GLY	0	0.002	-0.010	42.930	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	308	GLY	0	-0.024	0.015	42.798	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	309	LYS	1	0.965	0.963	43.839	0.016	0.016	0.000	0.000	0.000	0.000
77	A	310	GLY	0	0.018	0.012	43.002	0.000	0.000	0.000	0.000	0.000	0.000
78	A	311	THR	0	-0.014	-0.013	37.296	0.000	0.000	0.000	0.000	0.000	0.000
79	A	312	ALA	0	0.051	0.029	39.653	0.001	0.001	0.000	0.000	0.000	0.000
80	A	313	ALA	0	-0.024	0.005	34.269	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	314	GLN	0	0.021	0.002	33.463	0.000	0.000	0.000	0.000	0.000	0.000
82	A	315	GLY	0	0.030	0.011	31.648	0.000	0.000	0.000	0.000	0.000	0.000
83	A	316	ILE	0	-0.001	-0.005	26.488	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	317	TYR	0	-0.024	0.001	28.689	0.002	0.002	0.000	0.000	0.000	0.000
85	A	318	ILE	0	0.002	-0.009	26.338	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	319	ASN	0	0.039	0.014	27.590	0.009	0.009	0.000	0.000	0.000	0.000
87	A	320	SER	0	-0.021	-0.015	27.199	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	321	THR	0	-0.013	-0.008	28.305	0.003	0.003	0.000	0.000	0.000	0.000
89	A	322	SER	0	0.011	0.005	27.869	0.005	0.005	0.000	0.000	0.000	0.000
90	A	323	GLY	0	0.063	0.053	29.614	0.007	0.007	0.000	0.000	0.000	0.000
91	A	324	THR	0	-0.064	-0.040	25.632	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	325	ALA	0	0.060	0.035	28.088	0.010	0.010	0.000	0.000	0.000	0.000
93	A	326	GLY	0	-0.056	-0.026	25.987	0.002	0.002	0.000	0.000	0.000	0.000
94	A	327	LYS	1	0.935	0.946	26.873	0.179	0.179	0.000	0.000	0.000	0.000
95	A	328	MET	0	0.047	0.043	26.353	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	329	LEU	0	0.033	0.029	26.594	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	330	ARG	1	0.829	0.891	23.722	0.204	0.204	0.000	0.000	0.000	0.000
98	A	331	ILE	0	0.051	0.032	25.175	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	332	ARG	1	0.877	0.927	22.348	0.200	0.200	0.000	0.000	0.000	0.000
100	A	333	ASN	0	0.048	0.020	25.430	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	334	LYS	1	0.971	0.972	24.314	0.100	0.100	0.000	0.000	0.000	0.000
102	A	335	ASN	0	0.021	0.005	20.399	0.019	0.019	0.000	0.000	0.000	0.000
103	A	336	LYS	1	0.935	0.979	23.983	0.108	0.108	0.000	0.000	0.000	0.000
104	A	337	ASP	-1	-0.781	-0.870	27.130	-0.163	-0.163	0.000	0.000	0.000	0.000
105	A	338	LYS	1	0.873	0.930	28.842	0.106	0.106	0.000	0.000	0.000	0.000
106	A	339	PHE	0	0.087	0.045	30.211	0.007	0.007	0.000	0.000	0.000	0.000
107	A	340	TYR	0	-0.058	-0.028	29.711	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	341	VAL	0	0.056	0.037	30.519	0.009	0.009	0.000	0.000	0.000	0.000
109	A	342	GLY	0	0.020	-0.005	30.639	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	343	PRO	0	-0.047	-0.032	30.582	0.003	0.003	0.000	0.000	0.000	0.000
111	A	344	ASP	-1	-0.883	-0.928	32.191	-0.106	-0.106	0.000	0.000	0.000	0.000
112	A	345	GLY	0	-0.061	-0.025	34.675	0.006	0.006	0.000	0.000	0.000	0.000
113	A	346	ASP	-1	-0.916	-0.944	36.029	-0.102	-0.102	0.000	0.000	0.000	0.000
114	A	347	PHE	0	0.003	-0.012	35.190	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	348	TRP	0	-0.008	0.001	31.968	0.002	0.002	0.000	0.000	0.000	0.000
116	A	349	SER	0	0.026	0.002	34.461	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	350	CYS	0	-0.086	-0.044	34.113	0.001	0.001	0.000	0.000	0.000	0.000
118	A	351	ALA	0	-0.023	-0.008	36.175	0.003	0.003	0.000	0.000	0.000	0.000
119	A	352	SER	0	0.028	0.017	38.820	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	353	SER	0	-0.024	-0.014	39.861	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	354	ILE	0	0.003	-0.011	41.878	0.002	0.002	0.000	0.000	0.000	0.000
122	A	355	VAL	0	-0.015	-0.001	43.049	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	356	ASP	-1	-0.941	-0.946	45.435	-0.034	-0.034	0.000	0.000	0.000	0.000
124	A	357	GLY	0	0.037	0.006	47.764	0.001	0.001	0.000	0.000	0.000	0.000
125	A	358	ASN	0	-0.061	-0.029	49.812	0.000	0.000	0.000	0.000	0.000	0.000
126	A	359	LEU	0	0.035	0.022	44.806	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	360	THR	0	-0.029	-0.015	48.261	0.002	0.002	0.000	0.000	0.000	0.000
128	A	361	VAL	0	-0.019	-0.013	47.111	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	362	LYS	1	0.963	0.969	48.128	0.060	0.060	0.000	0.000	0.000	0.000
130	A	363	ASP	-1	-0.803	-0.878	51.002	-0.043	-0.043	0.000	0.000	0.000	0.000
131	A	364	PRO	0	-0.053	-0.007	51.865	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	365	THR	0	-0.009	-0.011	51.142	0.001	0.001	0.000	0.000	0.000	0.000
133	A	366	SER	0	-0.002	-0.018	49.879	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	367	GLY	0	0.017	0.013	51.967	0.001	0.001	0.000	0.000	0.000	0.000
135	A	368	LYS	1	0.916	0.945	47.857	0.049	0.049	0.000	0.000	0.000	0.000
136	A	369	HIS	0	0.020	0.032	46.987	0.000	0.000	0.000	0.000	0.000	0.000
137	A	370	ALA	0	0.019	0.008	48.832	0.002	0.002	0.000	0.000	0.000	0.000
138	A	371	ALA	0	-0.009	-0.002	50.538	0.000	0.000	0.000	0.000	0.000	0.000
139	A	372	THR	0	0.027	-0.003	53.311	0.001	0.001	0.000	0.000	0.000	0.000
140	A	373	LYS	1	0.817	0.875	55.228	0.033	0.033	0.000	0.000	0.000	0.000
141	A	374	ASP	-1	-0.815	-0.897	58.095	-0.036	-0.036	0.000	0.000	0.000	0.000
142	A	375	TYR	0	0.035	0.017	57.447	0.001	0.001	0.000	0.000	0.000	0.000
143	A	376	VAL	0	-0.059	-0.037	58.237	0.001	0.001	0.000	0.000	0.000	0.000
144	A	377	ASP	-1	-0.803	-0.897	60.835	-0.030	-0.030	0.000	0.000	0.000	0.000
145	A	378	GLU	-1	-0.924	-0.960	61.486	-0.035	-0.035	0.000	0.000	0.000	0.000
146	A	379	LYS	1	0.919	0.958	61.274	0.036	0.036	0.000	0.000	0.000	0.000
147	A	380	ILE	0	-0.022	0.004	64.625	0.001	0.001	0.000	0.000	0.000	0.000
148	A	381	ALA	0	-0.025	-0.022	66.825	0.001	0.001	0.000	0.000	0.000	0.000
149	A	382	GLU	-1	-0.940	-0.981	66.366	-0.031	-0.031	0.000	0.000	0.000	0.000
150	A	383	LEU	0	-0.015	-0.005	68.188	0.001	0.001	0.000	0.000	0.000	0.000
151	A	384	LYS	1	0.921	0.961	70.560	0.024	0.024	0.000	0.000	0.000	0.000
152	A	385	LYS	1	0.943	0.966	72.750	0.025	0.025	0.000	0.000	0.000	0.000
153	A	386	LEU	0	0.007	0.018	72.180	0.001	0.001	0.000	0.000	0.000	0.000
154	A	387	ILE	0	-0.014	-0.003	73.866	0.000	0.000	0.000	0.000	0.000	0.000
155	A	388	LEU	0	-0.091	-0.029	77.109	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:234:THR)