FMO DATABASE

FMODB ID: JQLR9

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	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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1844066.524052
FMO2-HF: Nuclear repulsion	1776551.95996
FMO2-HF: Total energy	-67514.564092
FMO2-MP2: Total energy	-67714.684501

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.
20.307	17.299	31.096	-15.218	-12.869	-0.166

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 : 0.875 / q_NPA : 0.924

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	0.841	0.896	1.928	46.267	49.523	8.101	-5.709	-5.649	-0.029
4	D	222	ILE	0	-0.014	0.016	4.195	5.596	5.830	-0.001	-0.076	-0.157	0.000
5	D	223	HIS	0	0.004	0.024	7.368	-1.589	-1.589	0.000	0.000	0.000	0.000
6	D	224	GLN	0	0.058	0.031	7.053	2.604	2.604	0.000	0.000	0.000	0.000
7	D	225	TRP	0	0.015	-0.001	11.257	0.691	0.691	0.000	0.000	0.000	0.000
8	D	226	TYR	0	0.009	-0.005	14.830	-0.170	-0.170	0.000	0.000	0.000	0.000
9	D	227	TYR	0	0.033	0.025	17.558	0.100	0.100	0.000	0.000	0.000	0.000
10	D	228	ARG	1	0.879	0.931	21.349	11.658	11.658	0.000	0.000	0.000	0.000
11	D	229	ALA	0	0.006	-0.018	23.578	0.242	0.242	0.000	0.000	0.000	0.000
12	D	230	ASP	-1	-0.818	-0.890	26.863	-10.584	-10.584	0.000	0.000	0.000	0.000
13	D	231	ASP	-1	-0.871	-0.924	30.341	-9.414	-9.414	0.000	0.000	0.000	0.000
14	D	232	LEU	0	-0.056	-0.046	28.859	-0.432	-0.432	0.000	0.000	0.000	0.000
15	D	233	GLU	-1	-0.879	-0.939	29.818	-9.539	-9.539	0.000	0.000	0.000	0.000
16	D	234	HIS	0	0.094	0.048	27.847	-0.257	-0.257	0.000	0.000	0.000	0.000
17	D	235	LYS	1	0.799	0.906	23.753	12.633	12.633	0.000	0.000	0.000	0.000
18	D	236	THR	0	-0.042	-0.034	26.090	-0.489	-0.489	0.000	0.000	0.000	0.000
19	D	237	ALA	0	0.053	0.031	28.337	-0.020	-0.020	0.000	0.000	0.000	0.000
20	D	238	LEU	0	-0.025	-0.009	24.437	-0.176	-0.176	0.000	0.000	0.000	0.000
21	D	239	LEU	0	-0.017	-0.006	22.225	-0.327	-0.327	0.000	0.000	0.000	0.000
22	D	240	VAL	0	0.030	0.017	24.875	-0.145	-0.145	0.000	0.000	0.000	0.000
23	D	241	HIS	0	-0.006	-0.011	25.840	0.174	0.174	0.000	0.000	0.000	0.000
24	D	242	LEU	0	-0.032	-0.027	20.936	-0.204	-0.204	0.000	0.000	0.000	0.000
25	D	243	LEU	0	-0.058	-0.029	22.425	-0.432	-0.432	0.000	0.000	0.000	0.000
26	D	244	LYS	1	0.830	0.944	24.615	10.016	10.016	0.000	0.000	0.000	0.000
27	D	245	GLN	0	-0.015	-0.023	23.424	0.135	0.135	0.000	0.000	0.000	0.000
28	D	246	PRO	0	0.000	0.008	24.716	-0.213	-0.213	0.000	0.000	0.000	0.000
29	D	247	GLU	-1	-0.890	-0.957	20.046	-13.558	-13.558	0.000	0.000	0.000	0.000
30	D	248	ALA	0	-0.055	0.001	20.527	-0.808	-0.808	0.000	0.000	0.000	0.000
31	D	249	THR	0	0.019	0.006	20.408	0.135	0.135	0.000	0.000	0.000	0.000
32	D	250	ARG	1	0.892	0.969	19.615	14.516	14.516	0.000	0.000	0.000	0.000
33	D	251	SER	0	-0.027	-0.008	18.587	-1.162	-1.162	0.000	0.000	0.000	0.000
34	D	252	ILE	0	-0.012	-0.001	16.302	0.679	0.679	0.000	0.000	0.000	0.000
35	D	253	VAL	0	0.003	0.002	18.105	-0.779	-0.779	0.000	0.000	0.000	0.000
36	D	254	PHE	0	-0.007	-0.014	14.699	0.456	0.456	0.000	0.000	0.000	0.000
37	D	255	VAL	0	0.012	0.002	19.008	0.067	0.067	0.000	0.000	0.000	0.000
38	D	256	ARG	1	0.795	0.880	20.587	13.569	13.569	0.000	0.000	0.000	0.000
39	D	257	LYS	1	0.781	0.878	22.261	10.855	10.855	0.000	0.000	0.000	0.000
40	D	258	ARG	1	0.922	0.954	25.725	10.862	10.862	0.000	0.000	0.000	0.000
41	D	259	GLU	-1	-0.751	-0.878	27.472	-10.487	-10.487	0.000	0.000	0.000	0.000
42	D	260	ARG	1	0.872	0.920	26.604	10.646	10.646	0.000	0.000	0.000	0.000
43	D	261	VAL	0	-0.014	-0.003	24.755	-0.150	-0.150	0.000	0.000	0.000	0.000
44	D	262	HIS	0	0.005	0.015	27.271	-0.146	-0.146	0.000	0.000	0.000	0.000
45	D	263	GLU	-1	-0.790	-0.895	30.862	-9.874	-9.874	0.000	0.000	0.000	0.000
46	D	264	LEU	0	0.000	0.020	24.763	0.027	0.027	0.000	0.000	0.000	0.000
47	D	265	ALA	0	0.028	-0.008	28.772	-0.101	-0.101	0.000	0.000	0.000	0.000
48	D	266	ASN	0	0.007	0.016	29.768	0.194	0.194	0.000	0.000	0.000	0.000
49	D	267	TRP	0	0.077	0.036	29.608	-0.246	-0.246	0.000	0.000	0.000	0.000
50	D	268	LEU	0	-0.005	-0.009	26.086	-0.009	-0.009	0.000	0.000	0.000	0.000
51	D	269	ARG	1	0.865	0.932	30.813	9.220	9.220	0.000	0.000	0.000	0.000
52	D	270	GLU	-1	-0.902	-0.938	33.473	-8.828	-8.828	0.000	0.000	0.000	0.000
53	D	271	ALA	0	-0.019	-0.010	31.875	0.146	0.146	0.000	0.000	0.000	0.000
54	D	272	GLY	0	0.018	0.016	33.442	0.091	0.091	0.000	0.000	0.000	0.000
55	D	273	ILE	0	-0.068	-0.031	27.465	-0.164	-0.164	0.000	0.000	0.000	0.000
56	D	274	ASN	0	-0.025	-0.003	30.512	0.211	0.211	0.000	0.000	0.000	0.000
57	D	275	ASN	0	-0.025	-0.006	27.290	-0.464	-0.464	0.000	0.000	0.000	0.000
58	D	276	CYS	0	-0.086	-0.044	26.119	0.404	0.404	0.000	0.000	0.000	0.000
59	D	277	TYR	0	0.036	0.034	25.905	-0.504	-0.504	0.000	0.000	0.000	0.000
60	D	278	LEU	0	0.023	-0.015	22.890	0.317	0.317	0.000	0.000	0.000	0.000
61	D	279	GLH	0	0.020	-0.048	24.548	-0.484	-0.484	0.000	0.000	0.000	0.000
62	D	280	GLY	0	0.010	0.008	25.327	0.286	0.286	0.000	0.000	0.000	0.000
63	D	281	GLU	-1	-0.828	-0.902	26.112	-9.813	-9.813	0.000	0.000	0.000	0.000
64	D	282	MET	0	-0.099	-0.002	28.456	0.159	0.159	0.000	0.000	0.000	0.000
65	D	283	VAL	0	0.053	0.015	29.463	-0.216	-0.216	0.000	0.000	0.000	0.000
66	D	284	GLN	0	0.029	-0.005	28.249	0.024	0.024	0.000	0.000	0.000	0.000
67	D	285	GLY	0	0.075	0.044	29.193	-0.188	-0.188	0.000	0.000	0.000	0.000
68	D	286	LYS	1	0.997	0.999	30.919	9.081	9.081	0.000	0.000	0.000	0.000
69	D	287	ARG	1	0.930	0.964	23.900	11.279	11.279	0.000	0.000	0.000	0.000
70	D	288	ASN	0	0.009	0.000	26.179	-0.748	-0.748	0.000	0.000	0.000	0.000
71	D	289	GLU	-1	-0.902	-0.946	27.849	-9.059	-9.059	0.000	0.000	0.000	0.000
72	D	290	ALA	0	-0.083	-0.047	27.164	0.016	0.016	0.000	0.000	0.000	0.000
73	D	291	ILE	0	0.014	0.009	21.488	-0.140	-0.140	0.000	0.000	0.000	0.000
74	D	292	LYS	1	0.885	0.924	24.929	10.007	10.007	0.000	0.000	0.000	0.000
75	D	293	ARG	1	0.934	0.951	27.408	9.992	9.992	0.000	0.000	0.000	0.000
76	D	294	LEU	0	0.051	0.040	21.047	-0.011	-0.011	0.000	0.000	0.000	0.000
77	D	295	THR	0	-0.037	-0.027	22.059	-0.384	-0.384	0.000	0.000	0.000	0.000
78	D	296	GLU	-1	-0.798	-0.873	24.380	-10.645	-10.645	0.000	0.000	0.000	0.000
79	D	297	GLY	0	-0.004	0.047	27.584	0.026	0.026	0.000	0.000	0.000	0.000
80	D	298	ARG	1	0.912	0.927	28.624	9.332	9.332	0.000	0.000	0.000	0.000
81	D	299	VAL	0	-0.071	-0.057	26.332	0.160	0.160	0.000	0.000	0.000	0.000
82	D	300	ASN	0	0.030	0.028	24.158	0.059	0.059	0.000	0.000	0.000	0.000
83	D	301	VAL	0	0.022	0.005	23.221	-0.464	-0.464	0.000	0.000	0.000	0.000
84	D	302	LEU	0	0.013	0.014	20.672	0.435	0.435	0.000	0.000	0.000	0.000
85	D	303	VAL	0	0.008	0.012	21.858	-0.566	-0.566	0.000	0.000	0.000	0.000
86	D	304	ALA	0	0.037	0.017	20.484	0.434	0.434	0.000	0.000	0.000	0.000
87	D	305	THR	0	0.004	-0.009	20.627	-0.164	-0.164	0.000	0.000	0.000	0.000
88	D	306	ASP	-1	-0.772	-0.866	15.935	-17.468	-17.468	0.000	0.000	0.000	0.000
89	D	307	VAL	0	-0.015	-0.012	18.189	-0.177	-0.177	0.000	0.000	0.000	0.000
90	D	308	ALA	0	-0.037	-0.022	20.710	0.009	0.009	0.000	0.000	0.000	0.000
91	D	309	ALA	0	0.047	0.034	18.547	0.369	0.369	0.000	0.000	0.000	0.000
92	D	310	ARG	1	0.939	0.970	15.926	15.124	15.124	0.000	0.000	0.000	0.000
93	D	311	GLY	0	-0.035	-0.015	17.052	-0.637	-0.637	0.000	0.000	0.000	0.000
94	D	312	ILE	0	-0.035	-0.010	18.357	0.315	0.315	0.000	0.000	0.000	0.000
95	D	313	ASP	-1	-0.871	-0.922	14.494	-18.902	-18.902	0.000	0.000	0.000	0.000
96	D	314	ILE	0	-0.036	-0.020	16.325	0.969	0.969	0.000	0.000	0.000	0.000
97	D	315	PRO	0	0.063	0.039	16.106	-0.946	-0.946	0.000	0.000	0.000	0.000
98	D	316	ASP	-1	-0.895	-0.954	16.486	-15.740	-15.740	0.000	0.000	0.000	0.000
99	D	317	VAL	0	-0.059	-0.037	14.892	0.665	0.665	0.000	0.000	0.000	0.000
100	D	318	SER	0	-0.013	-0.040	15.131	-1.068	-1.068	0.000	0.000	0.000	0.000
101	D	319	HIS	0	-0.026	-0.008	15.390	-0.796	-0.796	0.000	0.000	0.000	0.000
102	D	320	VAL	0	0.012	0.012	12.910	0.713	0.713	0.000	0.000	0.000	0.000
103	D	321	PHE	0	0.034	0.009	15.075	-0.744	-0.744	0.000	0.000	0.000	0.000
104	D	322	ASN	0	-0.035	-0.010	13.110	0.692	0.692	0.000	0.000	0.000	0.000
105	D	323	PHE	0	0.069	0.029	17.409	0.134	0.134	0.000	0.000	0.000	0.000
106	D	324	ASP	-1	-0.822	-0.916	20.200	-12.576	-12.576	0.000	0.000	0.000	0.000
107	D	325	MET	0	0.031	0.010	14.994	-0.930	-0.930	0.000	0.000	0.000	0.000
108	D	326	PRO	0	-0.046	-0.011	13.850	1.141	1.141	0.000	0.000	0.000	0.000
109	D	327	ARG	1	0.964	0.962	16.217	13.396	13.396	0.000	0.000	0.000	0.000
110	D	328	SER	0	0.026	0.026	13.339	-0.517	-0.517	0.000	0.000	0.000	0.000
111	D	329	GLY	0	0.089	0.038	10.275	0.018	0.018	0.000	0.000	0.000	0.000
112	D	330	ASP	-1	-0.882	-0.930	8.772	-26.716	-26.716	0.000	0.000	0.000	0.000
113	D	331	THR	0	-0.001	-0.016	9.497	-0.340	-0.340	0.000	0.000	0.000	0.000
114	D	332	TYR	0	-0.057	-0.045	8.569	1.786	1.786	0.000	0.000	0.000	0.000
115	D	333	LEU	0	0.011	-0.001	3.773	-0.902	-0.697	0.001	-0.027	-0.178	0.000
116	D	334	HIS	0	-0.038	-0.005	6.991	-1.610	-1.610	0.000	0.000	0.000	0.000
117	D	335	ARG	1	0.707	0.827	9.244	19.159	19.159	0.000	0.000	0.000	0.000
118	D	336	ILE	0	0.008	-0.006	6.592	1.057	1.057	0.000	0.000	0.000	0.000
119	D	337	GLY	0	0.015	0.018	7.467	-1.565	-1.565	0.000	0.000	0.000	0.000
120	D	338	ARG	1	0.799	0.890	8.223	20.455	20.455	0.000	0.000	0.000	0.000
121	D	339	THR	0	-0.030	-0.002	9.944	0.930	0.930	0.000	0.000	0.000	0.000
122	D	340	ALA	0	0.034	0.022	10.909	-1.560	-1.560	0.000	0.000	0.000	0.000
123	D	341	ARG	1	0.960	0.980	8.526	21.950	21.950	0.000	0.000	0.000	0.000
124	D	342	ALA	0	0.004	0.012	10.264	0.581	0.581	0.000	0.000	0.000	0.000
125	D	343	GLY	0	-0.048	-0.027	11.458	1.107	1.107	0.000	0.000	0.000	0.000
126	D	344	ARG	1	0.931	0.955	11.813	16.607	16.607	0.000	0.000	0.000	0.000
127	D	345	LYS	1	0.967	0.993	9.175	28.881	28.881	0.000	0.000	0.000	0.000
128	D	346	GLY	0	0.088	0.047	10.858	1.437	1.437	0.000	0.000	0.000	0.000
129	D	347	THR	0	-0.027	-0.018	11.058	-1.828	-1.828	0.000	0.000	0.000	0.000
130	D	348	ALA	0	-0.020	-0.009	10.834	1.007	1.007	0.000	0.000	0.000	0.000
131	D	349	ILE	0	0.024	0.012	12.718	-0.433	-0.433	0.000	0.000	0.000	0.000
132	D	350	SER	0	0.002	0.000	14.634	0.351	0.351	0.000	0.000	0.000	0.000
133	D	351	LEU	0	-0.012	-0.007	17.215	0.325	0.325	0.000	0.000	0.000	0.000
134	D	352	VAL	0	-0.028	-0.020	18.979	0.000	0.000	0.000	0.000	0.000	0.000
135	D	353	GLU	-1	-0.693	-0.833	22.032	-11.286	-11.286	0.000	0.000	0.000	0.000
136	D	354	ALA	0	0.048	0.030	24.525	-0.440	-0.440	0.000	0.000	0.000	0.000
137	D	355	HIS	1	0.821	0.871	24.653	12.130	12.130	0.000	0.000	0.000	0.000
138	D	356	ASP	-1	-0.820	-0.894	20.840	-14.303	-14.303	0.000	0.000	0.000	0.000
139	D	357	HIS	0	0.041	0.023	20.836	-0.894	-0.894	0.000	0.000	0.000	0.000
140	D	358	LEU	0	0.057	0.021	20.176	-0.775	-0.775	0.000	0.000	0.000	0.000
141	D	359	LEU	0	-0.074	-0.035	18.375	-0.803	-0.803	0.000	0.000	0.000	0.000
142	D	360	LEU	0	0.026	0.015	15.074	-1.078	-1.078	0.000	0.000	0.000	0.000
143	D	361	GLY	0	0.068	0.024	15.305	-1.228	-1.228	0.000	0.000	0.000	0.000
144	D	362	LYS	1	0.910	0.945	14.906	14.389	14.389	0.000	0.000	0.000	0.000
145	D	363	VAL	0	-0.001	0.013	11.321	-0.911	-0.911	0.000	0.000	0.000	0.000
146	D	364	GLY	0	0.012	0.002	10.916	-2.302	-2.302	0.000	0.000	0.000	0.000
147	D	365	ARG	1	0.940	0.965	9.982	16.721	16.721	0.000	0.000	0.000	0.000
148	D	366	TYR	0	-0.029	-0.004	7.661	0.283	0.283	0.000	0.000	0.000	0.000
149	D	367	ILE	0	-0.054	-0.030	6.135	-2.735	-2.735	0.000	0.000	0.000	0.000
150	D	368	GLU	-1	-0.715	-0.801	1.755	-124.768	-131.471	22.995	-9.406	-6.885	-0.137
151	D	369	GLU	-1	-0.908	-0.967	5.636	-41.638	-41.638	0.000	0.000	0.000	0.000
152	D	370	PRO	0	0.007	-0.010	8.578	-0.109	-0.109	0.000	0.000	0.000	0.000
153	D	371	ILE	0	-0.020	0.013	10.143	-1.191	-1.191	0.000	0.000	0.000	0.000
154	D	372	LYS	1	0.971	0.975	11.408	25.636	25.636	0.000	0.000	0.000	0.000
155	D	373	ALA	0	0.027	0.016	14.834	-0.018	-0.018	0.000	0.000	0.000	0.000
156	D	374	ARG	1	0.901	0.956	16.868	17.184	17.184	0.000	0.000	0.000	0.000
157	D	375	VAL	0	-0.024	-0.024	20.668	0.202	0.202	0.000	0.000	0.000	0.000
158	D	376	ILE	0	-0.042	-0.007	24.380	-0.161	-0.161	0.000	0.000	0.000	0.000
159	D	377	ASP	-1	-0.832	-0.887	26.378	-9.979	-9.979	0.000	0.000	0.000	0.000
160	D	378	GLU	-1	-0.833	-0.919	29.611	-10.336	-10.336	0.000	0.000	0.000	0.000
161	D	379	LEU	0	-0.049	-0.021	28.531	0.192	0.192	0.000	0.000	0.000	0.000
162	D	380	ARG	1	0.845	0.890	28.701	9.984	9.984	0.000	0.000	0.000	0.000
163	D	381	PRO	0	-0.059	-0.037	26.605	0.289	0.289	0.000	0.000	0.000	0.000
164	D	382	LYS	1	0.975	1.005	29.825	8.937	8.937	0.000	0.000	0.000	0.000
165	D	383	THR	0	-0.028	-0.015	31.363	0.266	0.266	0.000	0.000	0.000	0.000
166	D	384	ARG	1	0.998	1.003	30.422	9.537	9.537	0.000	0.000	0.000	0.000
167	D	385	ALA	0	-0.002	-0.007	25.252	-0.139	-0.139	0.000	0.000	0.000	0.000
168	D	386	PRO	0	-0.038	-0.039	25.105	0.360	0.360	0.000	0.000	0.000	0.000
169	D	387	SER	0	-0.010	-0.003	26.167	-0.153	-0.153	0.000	0.000	0.000	0.000
170	D	388	GLU	-1	-0.946	-0.946	22.921	-13.927	-13.927	0.000	0.000	0.000	0.000

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