FMO DATABASE

FMODB ID: 3J94L

Calculation Name: 2YJT-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YJT

Chain ID: D

ChEMBL ID:

UniProt ID: P0A8R0

Base Structure: X-ray

Registration Date: 2023-09-21

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	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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1849756.972141
FMO2-HF: Nuclear repulsion	1782240.615054
FMO2-HF: Total energy	-67516.357087
FMO2-MP2: Total energy	-67716.63105

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(D:219:ARG)

Summations of interaction energy for fragment #1(D:219:ARG)

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.
9.232	0.45299999999996	39.72	-16.718	-14.224	-0.198

Interaction energy analysis for fragmet #1(D:219:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.906

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	D	221	LYS	1	0.833	0.898	1.859	28.098	27.237	14.339	-6.743	-6.735	-0.066
4	D	222	ILE	0	-0.008	0.008	3.703	6.852	7.149	0.003	-0.087	-0.214	-0.001
5	D	223	HIS	0	0.009	0.021	6.867	-1.784	-1.784	0.000	0.000	0.000	0.000
6	D	224	GLN	0	0.045	0.028	6.426	2.046	2.046	0.000	0.000	0.000	0.000
7	D	225	TRP	0	0.035	0.005	10.714	0.957	0.957	0.000	0.000	0.000	0.000
8	D	226	TYR	0	-0.043	-0.032	14.433	-0.198	-0.198	0.000	0.000	0.000	0.000
9	D	227	TYR	0	0.072	0.040	17.206	0.068	0.068	0.000	0.000	0.000	0.000
10	D	228	ARG	1	0.873	0.924	21.019	11.701	11.701	0.000	0.000	0.000	0.000
11	D	229	ALA	0	0.028	0.001	23.283	0.236	0.236	0.000	0.000	0.000	0.000
12	D	230	ASP	-1	-0.788	-0.853	26.561	-10.678	-10.678	0.000	0.000	0.000	0.000
13	D	231	ASP	-1	-0.880	-0.931	30.057	-9.519	-9.519	0.000	0.000	0.000	0.000
14	D	232	LEU	0	-0.047	-0.037	28.515	-0.407	-0.407	0.000	0.000	0.000	0.000
15	D	233	GLU	-1	-0.849	-0.922	29.544	-9.700	-9.700	0.000	0.000	0.000	0.000
16	D	234	HIS	0	0.031	0.013	27.355	-0.300	-0.300	0.000	0.000	0.000	0.000
17	D	235	LYS	1	0.795	0.892	23.552	12.769	12.769	0.000	0.000	0.000	0.000
18	D	236	THR	0	-0.076	-0.044	25.990	-0.444	-0.444	0.000	0.000	0.000	0.000
19	D	237	ALA	0	0.047	0.029	28.029	-0.156	-0.156	0.000	0.000	0.000	0.000
20	D	238	LEU	0	-0.020	-0.011	24.041	-0.203	-0.203	0.000	0.000	0.000	0.000
21	D	239	LEU	0	-0.015	-0.010	22.152	-0.370	-0.370	0.000	0.000	0.000	0.000
22	D	240	VAL	0	0.004	-0.003	24.625	-0.150	-0.150	0.000	0.000	0.000	0.000
23	D	241	HIS	0	0.009	0.008	26.102	0.169	0.169	0.000	0.000	0.000	0.000
24	D	242	LEU	0	-0.035	-0.017	20.638	-0.201	-0.201	0.000	0.000	0.000	0.000
25	D	243	LEU	0	-0.040	-0.030	22.076	-0.390	-0.390	0.000	0.000	0.000	0.000
26	D	244	LYS	1	0.846	0.933	24.277	10.277	10.277	0.000	0.000	0.000	0.000
27	D	245	GLN	0	-0.024	-0.001	22.987	0.429	0.429	0.000	0.000	0.000	0.000
28	D	246	PRO	0	0.021	0.007	24.275	-0.264	-0.264	0.000	0.000	0.000	0.000
29	D	247	GLU	-1	-0.872	-0.944	19.482	-14.036	-14.036	0.000	0.000	0.000	0.000
30	D	248	ALA	0	-0.035	0.008	20.078	-0.863	-0.863	0.000	0.000	0.000	0.000
31	D	249	THR	0	0.001	-0.005	20.291	0.062	0.062	0.000	0.000	0.000	0.000
32	D	250	ARG	1	0.826	0.918	19.422	14.624	14.624	0.000	0.000	0.000	0.000
33	D	251	SER	0	-0.015	0.005	18.414	-1.291	-1.291	0.000	0.000	0.000	0.000
34	D	252	ILE	0	-0.012	-0.003	16.057	0.707	0.707	0.000	0.000	0.000	0.000
35	D	253	VAL	0	0.000	0.005	17.922	-0.817	-0.817	0.000	0.000	0.000	0.000
36	D	254	PHE	0	0.012	0.004	14.387	0.590	0.590	0.000	0.000	0.000	0.000
37	D	255	VAL	0	-0.001	0.003	18.629	-0.056	-0.056	0.000	0.000	0.000	0.000
38	D	256	ARG	1	0.749	0.825	20.364	13.907	13.907	0.000	0.000	0.000	0.000
39	D	257	LYS	1	0.781	0.873	22.158	11.001	11.001	0.000	0.000	0.000	0.000
40	D	258	ARG	1	0.903	0.939	25.741	10.868	10.868	0.000	0.000	0.000	0.000
41	D	259	GLU	-1	-0.760	-0.875	27.167	-10.533	-10.533	0.000	0.000	0.000	0.000
42	D	260	ARG	1	0.910	0.940	26.571	10.633	10.633	0.000	0.000	0.000	0.000
43	D	261	VAL	0	-0.049	-0.015	24.143	-0.094	-0.094	0.000	0.000	0.000	0.000
44	D	262	HIS	0	0.011	0.012	26.746	-0.192	-0.192	0.000	0.000	0.000	0.000
45	D	263	GLU	-1	-0.846	-0.918	30.379	-9.945	-9.945	0.000	0.000	0.000	0.000
46	D	264	LEU	0	0.027	0.013	24.570	0.094	0.094	0.000	0.000	0.000	0.000
47	D	265	ALA	0	0.028	0.009	28.226	-0.033	-0.033	0.000	0.000	0.000	0.000
48	D	266	ASN	0	-0.012	0.010	29.402	0.250	0.250	0.000	0.000	0.000	0.000
49	D	267	TRP	0	0.099	0.046	29.627	-0.221	-0.221	0.000	0.000	0.000	0.000
50	D	268	LEU	0	-0.023	-0.006	25.890	0.004	0.004	0.000	0.000	0.000	0.000
51	D	269	ARG	1	0.858	0.932	30.457	9.368	9.368	0.000	0.000	0.000	0.000
52	D	270	GLU	-1	-0.894	-0.951	33.274	-8.780	-8.780	0.000	0.000	0.000	0.000
53	D	271	ALA	0	-0.018	0.001	31.713	0.165	0.165	0.000	0.000	0.000	0.000
54	D	272	GLY	0	0.008	0.012	33.437	-0.041	-0.041	0.000	0.000	0.000	0.000
55	D	273	ILE	0	-0.039	-0.021	27.243	-0.185	-0.185	0.000	0.000	0.000	0.000
56	D	274	ASN	0	-0.006	-0.005	30.303	0.169	0.169	0.000	0.000	0.000	0.000
57	D	275	ASN	0	-0.061	-0.039	26.880	-0.530	-0.530	0.000	0.000	0.000	0.000
58	D	276	CYS	0	-0.049	-0.019	25.463	0.417	0.417	0.000	0.000	0.000	0.000
59	D	277	TYR	0	0.037	0.022	25.748	-0.492	-0.492	0.000	0.000	0.000	0.000
60	D	278	LEU	0	0.015	-0.010	22.247	0.281	0.281	0.000	0.000	0.000	0.000
61	D	279	GLH	0	0.006	-0.043	24.141	-0.513	-0.513	0.000	0.000	0.000	0.000
62	D	280	GLY	0	0.039	0.009	25.127	0.160	0.160	0.000	0.000	0.000	0.000
63	D	281	GLU	-1	-0.790	-0.877	25.730	-9.853	-9.853	0.000	0.000	0.000	0.000
64	D	282	MET	0	-0.101	0.001	27.674	0.178	0.178	0.000	0.000	0.000	0.000
65	D	283	VAL	0	0.074	0.026	28.522	-0.340	-0.340	0.000	0.000	0.000	0.000
66	D	284	GLN	0	0.036	0.010	28.155	0.009	0.009	0.000	0.000	0.000	0.000
67	D	285	GLY	0	0.057	0.037	28.960	-0.206	-0.206	0.000	0.000	0.000	0.000
68	D	286	LYS	1	0.965	0.984	30.734	9.213	9.213	0.000	0.000	0.000	0.000
69	D	287	ARG	1	0.894	0.957	23.818	11.392	11.392	0.000	0.000	0.000	0.000
70	D	288	ASN	0	0.016	0.001	26.215	-0.719	-0.719	0.000	0.000	0.000	0.000
71	D	289	GLU	-1	-0.888	-0.946	27.639	-9.208	-9.208	0.000	0.000	0.000	0.000
72	D	290	ALA	0	-0.066	-0.019	26.568	0.045	0.045	0.000	0.000	0.000	0.000
73	D	291	ILE	0	0.013	0.009	21.172	-0.130	-0.130	0.000	0.000	0.000	0.000
74	D	292	LYS	1	0.880	0.924	24.506	10.262	10.262	0.000	0.000	0.000	0.000
75	D	293	ARG	1	0.877	0.916	26.787	10.149	10.149	0.000	0.000	0.000	0.000
76	D	294	LEU	0	0.011	0.023	20.526	0.053	0.053	0.000	0.000	0.000	0.000
77	D	295	THR	0	0.002	-0.022	22.044	-0.415	-0.415	0.000	0.000	0.000	0.000
78	D	296	GLU	-1	-0.829	-0.887	24.273	-10.673	-10.673	0.000	0.000	0.000	0.000
79	D	297	GLY	0	0.038	0.022	27.181	-0.212	-0.212	0.000	0.000	0.000	0.000
80	D	298	ARG	1	0.886	0.946	28.585	9.615	9.615	0.000	0.000	0.000	0.000
81	D	299	VAL	0	-0.013	-0.007	25.907	0.242	0.242	0.000	0.000	0.000	0.000
82	D	300	ASN	0	0.037	0.035	23.895	0.148	0.148	0.000	0.000	0.000	0.000
83	D	301	VAL	0	0.030	0.011	22.812	-0.705	-0.705	0.000	0.000	0.000	0.000
84	D	302	LEU	0	0.018	0.011	20.380	0.551	0.551	0.000	0.000	0.000	0.000
85	D	303	VAL	0	0.005	0.009	21.686	-0.671	-0.671	0.000	0.000	0.000	0.000
86	D	304	ALA	0	0.033	0.006	20.160	0.490	0.490	0.000	0.000	0.000	0.000
87	D	305	THR	0	0.024	0.002	20.323	-0.095	-0.095	0.000	0.000	0.000	0.000
88	D	306	ASP	-1	-0.782	-0.868	15.442	-17.602	-17.602	0.000	0.000	0.000	0.000
89	D	307	VAL	0	-0.016	-0.021	17.783	-0.185	-0.185	0.000	0.000	0.000	0.000
90	D	308	ALA	0	-0.015	-0.004	20.313	0.240	0.240	0.000	0.000	0.000	0.000
91	D	309	ALA	0	0.051	0.024	17.962	0.356	0.356	0.000	0.000	0.000	0.000
92	D	310	ARG	1	0.925	0.969	15.430	15.413	15.413	0.000	0.000	0.000	0.000
93	D	311	GLY	0	-0.024	0.002	16.577	-0.630	-0.630	0.000	0.000	0.000	0.000
94	D	312	ILE	0	-0.011	-0.005	17.603	0.716	0.716	0.000	0.000	0.000	0.000
95	D	313	ASP	-1	-0.833	-0.906	13.944	-19.994	-19.994	0.000	0.000	0.000	0.000
96	D	314	ILE	0	-0.027	-0.024	15.598	1.077	1.077	0.000	0.000	0.000	0.000
97	D	315	PRO	0	0.047	0.027	15.978	-0.957	-0.957	0.000	0.000	0.000	0.000
98	D	316	ASP	-1	-0.916	-0.961	16.375	-15.808	-15.808	0.000	0.000	0.000	0.000
99	D	317	VAL	0	-0.032	-0.008	14.687	0.567	0.567	0.000	0.000	0.000	0.000
100	D	318	SER	0	0.002	-0.012	14.598	-1.481	-1.481	0.000	0.000	0.000	0.000
101	D	319	HIS	0	-0.016	-0.011	14.840	-1.432	-1.432	0.000	0.000	0.000	0.000
102	D	320	VAL	0	-0.004	-0.003	12.603	0.649	0.649	0.000	0.000	0.000	0.000
103	D	321	PHE	0	0.049	0.015	15.029	-0.736	-0.736	0.000	0.000	0.000	0.000
104	D	322	ASN	0	-0.028	-0.020	13.067	0.822	0.822	0.000	0.000	0.000	0.000
105	D	323	PHE	0	0.075	0.033	17.238	0.242	0.242	0.000	0.000	0.000	0.000
106	D	324	ASP	-1	-0.797	-0.901	19.976	-12.675	-12.675	0.000	0.000	0.000	0.000
107	D	325	MET	0	-0.006	0.009	14.705	-0.811	-0.811	0.000	0.000	0.000	0.000
108	D	326	PRO	0	0.010	0.022	13.430	1.148	1.148	0.000	0.000	0.000	0.000
109	D	327	ARG	1	0.948	0.950	16.209	13.493	13.493	0.000	0.000	0.000	0.000
110	D	328	SER	0	0.021	0.016	13.070	-0.307	-0.307	0.000	0.000	0.000	0.000
111	D	329	GLY	0	0.076	0.023	9.971	0.058	0.058	0.000	0.000	0.000	0.000
112	D	330	ASP	-1	-0.831	-0.902	8.459	-26.229	-26.229	0.000	0.000	0.000	0.000
113	D	331	THR	0	-0.018	-0.017	8.983	-0.592	-0.592	0.000	0.000	0.000	0.000
114	D	332	TYR	0	-0.041	-0.034	8.349	2.284	2.284	0.000	0.000	0.000	0.000
115	D	333	LEU	0	0.013	0.011	3.438	-1.261	-0.946	0.007	-0.048	-0.275	0.000
116	D	334	HIS	0	-0.051	-0.026	6.858	-1.102	-1.102	0.000	0.000	0.000	0.000
117	D	335	ARG	1	0.721	0.834	9.259	20.037	20.037	0.000	0.000	0.000	0.000
118	D	336	ILE	0	0.014	-0.011	6.412	0.862	0.862	0.000	0.000	0.000	0.000
119	D	337	GLY	0	-0.009	0.004	7.073	-0.628	-0.628	0.000	0.000	0.000	0.000
120	D	338	ARG	1	0.825	0.903	7.799	21.478	21.478	0.000	0.000	0.000	0.000
121	D	339	THR	0	-0.026	-0.003	9.605	1.101	1.101	0.000	0.000	0.000	0.000
122	D	340	ALA	0	0.020	0.014	10.704	-1.577	-1.577	0.000	0.000	0.000	0.000
123	D	341	ARG	1	0.898	0.926	8.696	21.647	21.647	0.000	0.000	0.000	0.000
124	D	342	ALA	0	0.072	0.059	10.206	0.238	0.238	0.000	0.000	0.000	0.000
125	D	343	GLY	0	-0.038	-0.023	11.003	1.288	1.288	0.000	0.000	0.000	0.000
126	D	344	ARG	1	0.899	0.932	11.977	17.061	17.061	0.000	0.000	0.000	0.000
127	D	345	LYS	1	0.932	0.973	8.543	29.891	29.891	0.000	0.000	0.000	0.000
128	D	346	GLY	0	0.082	0.042	11.064	1.486	1.486	0.000	0.000	0.000	0.000
129	D	347	THR	0	-0.071	-0.042	11.011	-2.460	-2.460	0.000	0.000	0.000	0.000
130	D	348	ALA	0	0.005	0.018	10.290	1.210	1.210	0.000	0.000	0.000	0.000
131	D	349	ILE	0	0.011	-0.005	12.146	0.038	0.038	0.000	0.000	0.000	0.000
132	D	350	SER	0	-0.017	-0.008	14.487	-0.035	-0.035	0.000	0.000	0.000	0.000
133	D	351	LEU	0	0.010	0.011	17.088	0.301	0.301	0.000	0.000	0.000	0.000
134	D	352	VAL	0	-0.026	-0.017	18.748	0.082	0.082	0.000	0.000	0.000	0.000
135	D	353	GLU	-1	-0.707	-0.834	21.971	-11.503	-11.503	0.000	0.000	0.000	0.000
136	D	354	ALA	0	0.055	0.024	24.473	-0.482	-0.482	0.000	0.000	0.000	0.000
137	D	355	HIS	1	0.792	0.864	24.922	11.945	11.945	0.000	0.000	0.000	0.000
138	D	356	ASP	-1	-0.774	-0.848	21.030	-14.377	-14.377	0.000	0.000	0.000	0.000
139	D	357	HIS	0	0.045	0.019	20.406	-1.090	-1.090	0.000	0.000	0.000	0.000
140	D	358	LEU	0	0.049	0.022	19.700	-0.738	-0.738	0.000	0.000	0.000	0.000
141	D	359	LEU	0	-0.058	-0.026	17.962	-0.580	-0.580	0.000	0.000	0.000	0.000
142	D	360	LEU	0	0.008	0.010	14.956	-1.310	-1.310	0.000	0.000	0.000	0.000
143	D	361	GLY	0	0.067	0.026	14.726	-1.392	-1.392	0.000	0.000	0.000	0.000
144	D	362	LYS	1	0.922	0.972	15.252	15.129	15.129	0.000	0.000	0.000	0.000
145	D	363	VAL	0	0.037	0.008	10.967	-1.207	-1.207	0.000	0.000	0.000	0.000
146	D	364	GLY	0	-0.013	-0.011	10.310	-2.617	-2.617	0.000	0.000	0.000	0.000
147	D	365	ARG	1	0.894	0.933	11.119	18.698	18.698	0.000	0.000	0.000	0.000
148	D	366	TYR	0	-0.029	0.014	7.578	0.076	0.076	0.000	0.000	0.000	0.000
149	D	367	ILE	0	-0.044	-0.024	5.359	-3.254	-3.254	0.000	0.000	0.000	0.000
150	D	368	GLU	-1	-0.777	-0.860	1.753	-122.257	-130.787	25.371	-9.840	-7.000	-0.131
151	D	369	GLU	-1	-0.844	-0.923	5.506	-45.065	-45.065	0.000	0.000	0.000	0.000
152	D	370	PRO	0	0.030	0.008	8.489	0.075	0.075	0.000	0.000	0.000	0.000
153	D	371	ILE	0	-0.033	-0.003	10.091	-0.626	-0.626	0.000	0.000	0.000	0.000
154	D	372	LYS	1	0.961	0.983	10.717	27.267	27.267	0.000	0.000	0.000	0.000
155	D	373	ALA	0	0.031	0.013	14.505	0.187	0.187	0.000	0.000	0.000	0.000
156	D	374	ARG	1	0.873	0.952	16.704	17.423	17.423	0.000	0.000	0.000	0.000
157	D	375	VAL	0	-0.013	-0.014	20.496	0.230	0.230	0.000	0.000	0.000	0.000
158	D	376	ILE	0	-0.004	0.012	23.967	-0.259	-0.259	0.000	0.000	0.000	0.000
159	D	377	ASP	-1	-0.820	-0.876	26.279	-10.108	-10.108	0.000	0.000	0.000	0.000
160	D	378	GLU	-1	-0.806	-0.926	29.386	-10.511	-10.511	0.000	0.000	0.000	0.000
161	D	379	LEU	0	-0.044	-0.023	28.437	0.223	0.223	0.000	0.000	0.000	0.000
162	D	380	ARG	1	0.820	0.890	28.748	9.935	9.935	0.000	0.000	0.000	0.000
163	D	381	PRO	0	-0.056	-0.026	26.383	0.258	0.258	0.000	0.000	0.000	0.000
164	D	382	LYS	1	0.945	0.964	29.581	9.162	9.162	0.000	0.000	0.000	0.000
165	D	383	THR	0	-0.041	-0.022	30.837	0.222	0.222	0.000	0.000	0.000	0.000
166	D	384	ARG	1	0.954	0.971	30.471	9.774	9.774	0.000	0.000	0.000	0.000
167	D	385	ALA	0	0.020	0.011	25.471	-0.176	-0.176	0.000	0.000	0.000	0.000
168	D	386	PRO	0	-0.034	-0.040	24.837	0.471	0.471	0.000	0.000	0.000	0.000
169	D	387	SER	0	0.001	0.001	26.302	0.000	0.000	0.000	0.000	0.000	0.000
170	D	388	GLU	-1	-0.942	-0.946	21.873	-14.210	-14.210	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:219:ARG)