FMO DATABASE

FMODB ID: NN97Q

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	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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1843462.444023
FMO2-HF: Nuclear repulsion	1775951.651738
FMO2-HF: Total energy	-67510.792285
FMO2-MP2: Total energy	-67711.160553

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.
43.856	53.321	4.118	-7.027	-6.556	-0.077

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 : 0.929 / q_NPA : 0.949

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	0.981	0.975	2.442	44.582	47.683	0.845	-1.647	-2.298	0.002
4	D	222	ILE	0	-0.009	0.018	5.431	4.615	4.615	0.000	0.000	0.000	0.000
5	D	223	HIS	0	-0.005	0.019	8.339	-1.930	-1.930	0.000	0.000	0.000	0.000
6	D	224	GLN	0	0.135	0.132	7.225	2.642	2.642	0.000	0.000	0.000	0.000
7	D	225	TRP	0	-0.016	-0.009	11.598	0.446	0.446	0.000	0.000	0.000	0.000
8	D	226	TYR	0	0.001	0.000	15.014	-0.186	-0.186	0.000	0.000	0.000	0.000
9	D	227	TYR	0	0.036	0.028	17.700	0.106	0.106	0.000	0.000	0.000	0.000
10	D	228	ARG	1	0.874	0.929	21.495	11.375	11.375	0.000	0.000	0.000	0.000
11	D	229	ALA	0	-0.019	-0.032	23.738	0.239	0.239	0.000	0.000	0.000	0.000
12	D	230	ASP	-1	-0.804	-0.851	26.990	-10.460	-10.460	0.000	0.000	0.000	0.000
13	D	231	ASP	-1	-0.831	-0.903	30.474	-9.293	-9.293	0.000	0.000	0.000	0.000
14	D	232	LEU	0	-0.071	-0.056	29.062	-0.431	-0.431	0.000	0.000	0.000	0.000
15	D	233	GLU	-1	-0.866	-0.948	29.868	-9.284	-9.284	0.000	0.000	0.000	0.000
16	D	234	HIS	0	0.105	0.063	28.489	-0.150	-0.150	0.000	0.000	0.000	0.000
17	D	235	LYS	1	0.856	0.935	23.789	12.156	12.156	0.000	0.000	0.000	0.000
18	D	236	THR	0	-0.037	-0.026	26.040	-0.412	-0.412	0.000	0.000	0.000	0.000
19	D	237	ALA	0	0.056	0.037	28.294	-0.005	-0.005	0.000	0.000	0.000	0.000
20	D	238	LEU	0	-0.033	-0.012	24.702	-0.143	-0.143	0.000	0.000	0.000	0.000
21	D	239	LEU	0	-0.019	-0.003	22.312	-0.304	-0.304	0.000	0.000	0.000	0.000
22	D	240	VAL	0	0.044	0.024	25.019	-0.127	-0.127	0.000	0.000	0.000	0.000
23	D	241	HIS	0	0.000	-0.014	26.090	0.206	0.206	0.000	0.000	0.000	0.000
24	D	242	LEU	0	-0.024	-0.030	21.083	-0.174	-0.174	0.000	0.000	0.000	0.000
25	D	243	LEU	0	-0.055	-0.028	22.757	-0.394	-0.394	0.000	0.000	0.000	0.000
26	D	244	LYS	1	0.867	0.969	25.013	9.852	9.852	0.000	0.000	0.000	0.000
27	D	245	GLN	0	0.033	0.001	24.176	0.186	0.186	0.000	0.000	0.000	0.000
28	D	246	PRO	0	-0.044	-0.012	25.470	-0.224	-0.224	0.000	0.000	0.000	0.000
29	D	247	GLU	-1	-0.896	-0.958	21.133	-12.829	-12.829	0.000	0.000	0.000	0.000
30	D	248	ALA	0	-0.048	0.003	21.188	-0.690	-0.690	0.000	0.000	0.000	0.000
31	D	249	THR	0	0.026	0.003	20.554	0.520	0.520	0.000	0.000	0.000	0.000
32	D	250	ARG	1	0.918	0.974	19.387	13.698	13.698	0.000	0.000	0.000	0.000
33	D	251	SER	0	-0.028	-0.019	18.802	-1.091	-1.091	0.000	0.000	0.000	0.000
34	D	252	ILE	0	-0.011	0.003	16.261	0.603	0.603	0.000	0.000	0.000	0.000
35	D	253	VAL	0	0.003	0.004	18.469	-0.740	-0.740	0.000	0.000	0.000	0.000
36	D	254	PHE	0	-0.015	-0.017	15.047	0.405	0.405	0.000	0.000	0.000	0.000
37	D	255	VAL	0	0.035	0.012	19.291	0.023	0.023	0.000	0.000	0.000	0.000
38	D	256	ARG	1	0.818	0.909	20.787	13.224	13.224	0.000	0.000	0.000	0.000
39	D	257	LYS	1	0.891	0.944	22.408	11.429	11.429	0.000	0.000	0.000	0.000
40	D	258	ARG	1	0.949	0.973	24.244	11.146	11.146	0.000	0.000	0.000	0.000
41	D	259	GLU	-1	-0.877	-0.946	27.676	-9.990	-9.990	0.000	0.000	0.000	0.000
42	D	260	ARG	1	0.936	0.968	26.835	10.525	10.525	0.000	0.000	0.000	0.000
43	D	261	VAL	0	-0.009	0.000	25.137	-0.155	-0.155	0.000	0.000	0.000	0.000
44	D	262	HIS	0	-0.003	0.009	27.556	-0.163	-0.163	0.000	0.000	0.000	0.000
45	D	263	GLU	-1	-0.815	-0.930	31.149	-9.564	-9.564	0.000	0.000	0.000	0.000
46	D	264	LEU	0	-0.018	0.000	25.281	0.030	0.030	0.000	0.000	0.000	0.000
47	D	265	ALA	0	0.008	-0.018	29.204	-0.084	-0.084	0.000	0.000	0.000	0.000
48	D	266	ASN	0	0.007	-0.018	30.116	0.115	0.115	0.000	0.000	0.000	0.000
49	D	267	TRP	0	0.065	0.050	29.929	-0.206	-0.206	0.000	0.000	0.000	0.000
50	D	268	LEU	0	-0.017	-0.006	26.529	0.002	0.002	0.000	0.000	0.000	0.000
51	D	269	ARG	1	0.910	0.968	31.045	9.063	9.063	0.000	0.000	0.000	0.000
52	D	270	GLU	-1	-0.931	-0.955	33.778	-8.533	-8.533	0.000	0.000	0.000	0.000
53	D	271	ALA	0	-0.030	-0.024	32.174	0.140	0.140	0.000	0.000	0.000	0.000
54	D	272	GLY	0	-0.015	0.009	33.719	0.097	0.097	0.000	0.000	0.000	0.000
55	D	273	ILE	0	-0.069	-0.032	27.872	-0.161	-0.161	0.000	0.000	0.000	0.000
56	D	274	ASN	0	-0.047	-0.017	30.549	0.211	0.211	0.000	0.000	0.000	0.000
57	D	275	ASN	0	0.014	0.026	27.680	-0.499	-0.499	0.000	0.000	0.000	0.000
58	D	276	CYS	0	-0.089	-0.058	26.839	0.293	0.293	0.000	0.000	0.000	0.000
59	D	277	TYR	0	0.019	0.034	26.140	-0.475	-0.475	0.000	0.000	0.000	0.000
60	D	278	LEU	0	0.018	-0.012	22.762	0.285	0.285	0.000	0.000	0.000	0.000
61	D	279	GLH	0	-0.050	-0.101	24.900	-0.388	-0.388	0.000	0.000	0.000	0.000
62	D	280	GLY	0	-0.020	-0.020	25.607	0.237	0.237	0.000	0.000	0.000	0.000
63	D	281	GLU	-1	-0.763	-0.831	26.401	-9.898	-9.898	0.000	0.000	0.000	0.000
64	D	282	MET	0	-0.099	-0.026	28.583	0.238	0.238	0.000	0.000	0.000	0.000
65	D	283	VAL	0	0.032	0.006	29.731	-0.193	-0.193	0.000	0.000	0.000	0.000
66	D	284	GLN	0	0.033	-0.014	28.539	0.108	0.108	0.000	0.000	0.000	0.000
67	D	285	GLY	0	0.068	0.056	29.369	-0.171	-0.171	0.000	0.000	0.000	0.000
68	D	286	LYS	1	0.993	0.999	31.130	8.804	8.804	0.000	0.000	0.000	0.000
69	D	287	ARG	1	0.933	0.960	24.104	11.239	11.239	0.000	0.000	0.000	0.000
70	D	288	ASN	0	0.040	-0.002	26.357	-0.706	-0.706	0.000	0.000	0.000	0.000
71	D	289	GLU	-1	-0.926	-0.957	28.062	-8.795	-8.795	0.000	0.000	0.000	0.000
72	D	290	ALA	0	-0.077	-0.039	27.237	0.019	0.019	0.000	0.000	0.000	0.000
73	D	291	ILE	0	0.006	0.009	21.718	-0.102	-0.102	0.000	0.000	0.000	0.000
74	D	292	LYS	1	0.967	0.985	25.053	9.385	9.385	0.000	0.000	0.000	0.000
75	D	293	ARG	1	0.930	0.949	27.561	9.718	9.718	0.000	0.000	0.000	0.000
76	D	294	LEU	0	0.063	0.029	21.208	0.006	0.006	0.000	0.000	0.000	0.000
77	D	295	THR	0	-0.075	-0.044	22.184	-0.304	-0.304	0.000	0.000	0.000	0.000
78	D	296	GLU	-1	-0.744	-0.840	24.475	-10.423	-10.423	0.000	0.000	0.000	0.000
79	D	297	GLY	0	-0.075	0.015	27.570	0.030	0.030	0.000	0.000	0.000	0.000
80	D	298	ARG	1	0.858	0.878	28.618	9.094	9.094	0.000	0.000	0.000	0.000
81	D	299	VAL	0	-0.088	-0.037	25.864	0.152	0.152	0.000	0.000	0.000	0.000
82	D	300	ASN	0	0.062	0.028	24.414	-0.107	-0.107	0.000	0.000	0.000	0.000
83	D	301	VAL	0	0.003	0.006	23.384	-0.424	-0.424	0.000	0.000	0.000	0.000
84	D	302	LEU	0	0.031	0.017	20.923	0.370	0.370	0.000	0.000	0.000	0.000
85	D	303	VAL	0	0.009	0.012	22.194	-0.543	-0.543	0.000	0.000	0.000	0.000
86	D	304	ALA	0	0.035	0.015	20.872	0.384	0.384	0.000	0.000	0.000	0.000
87	D	305	THR	0	-0.006	-0.013	20.932	-0.122	-0.122	0.000	0.000	0.000	0.000
88	D	306	ASP	-1	-0.759	-0.880	15.898	-17.398	-17.398	0.000	0.000	0.000	0.000
89	D	307	VAL	0	-0.011	-0.001	18.448	-0.223	-0.223	0.000	0.000	0.000	0.000
90	D	308	ALA	0	-0.054	-0.031	20.954	0.002	0.002	0.000	0.000	0.000	0.000
91	D	309	ALA	0	0.049	0.036	18.727	0.368	0.368	0.000	0.000	0.000	0.000
92	D	310	ARG	1	0.928	0.959	16.436	15.060	15.060	0.000	0.000	0.000	0.000
93	D	311	GLY	0	-0.043	-0.016	17.019	-0.611	-0.611	0.000	0.000	0.000	0.000
94	D	312	ILE	0	0.003	0.004	18.443	0.279	0.279	0.000	0.000	0.000	0.000
95	D	313	ASP	-1	-0.831	-0.893	16.255	-16.688	-16.688	0.000	0.000	0.000	0.000
96	D	314	ILE	0	-0.116	-0.053	16.507	0.895	0.895	0.000	0.000	0.000	0.000
97	D	315	PRO	0	0.094	0.047	16.273	-0.889	-0.889	0.000	0.000	0.000	0.000
98	D	316	ASP	-1	-0.928	-0.950	16.640	-14.773	-14.773	0.000	0.000	0.000	0.000
99	D	317	VAL	0	-0.054	-0.035	14.938	0.499	0.499	0.000	0.000	0.000	0.000
100	D	318	SER	0	-0.004	-0.003	15.183	-0.812	-0.812	0.000	0.000	0.000	0.000
101	D	319	HIS	0	-0.052	-0.036	15.819	-0.326	-0.326	0.000	0.000	0.000	0.000
102	D	320	VAL	0	0.022	0.018	12.815	0.625	0.625	0.000	0.000	0.000	0.000
103	D	321	PHE	0	0.039	0.017	15.218	-0.692	-0.692	0.000	0.000	0.000	0.000
104	D	322	ASN	0	-0.047	-0.019	13.383	0.419	0.419	0.000	0.000	0.000	0.000
105	D	323	PHE	0	0.063	0.024	17.617	0.100	0.100	0.000	0.000	0.000	0.000
106	D	324	ASP	-1	-0.821	-0.913	20.363	-12.378	-12.378	0.000	0.000	0.000	0.000
107	D	325	MET	0	0.026	-0.001	15.102	-0.939	-0.939	0.000	0.000	0.000	0.000
108	D	326	PRO	0	-0.057	-0.022	14.120	1.042	1.042	0.000	0.000	0.000	0.000
109	D	327	ARG	1	0.949	0.953	16.149	13.625	13.625	0.000	0.000	0.000	0.000
110	D	328	SER	0	0.028	0.024	13.162	-0.524	-0.524	0.000	0.000	0.000	0.000
111	D	329	GLY	0	0.090	0.041	10.066	0.159	0.159	0.000	0.000	0.000	0.000
112	D	330	ASP	-1	-0.894	-0.943	8.687	-27.710	-27.710	0.000	0.000	0.000	0.000
113	D	331	THR	0	-0.019	-0.024	9.542	-0.240	-0.240	0.000	0.000	0.000	0.000
114	D	332	TYR	0	-0.139	-0.138	8.486	1.090	1.090	0.000	0.000	0.000	0.000
115	D	333	LEU	0	0.021	-0.003	3.759	-0.697	-0.456	0.001	-0.040	-0.203	0.000
116	D	334	HIS	0	-0.018	0.019	7.307	-1.123	-1.123	0.000	0.000	0.000	0.000
117	D	335	ARG	1	0.722	0.848	9.527	19.025	19.025	0.000	0.000	0.000	0.000
118	D	336	ILE	0	0.017	-0.005	6.492	1.155	1.155	0.000	0.000	0.000	0.000
119	D	337	GLY	0	0.016	0.020	7.416	-1.190	-1.190	0.000	0.000	0.000	0.000
120	D	338	ARG	1	0.789	0.879	8.306	19.517	19.517	0.000	0.000	0.000	0.000
121	D	339	THR	0	-0.014	-0.020	9.948	0.799	0.799	0.000	0.000	0.000	0.000
122	D	340	ALA	0	0.014	0.045	10.839	-1.272	-1.272	0.000	0.000	0.000	0.000
123	D	341	ARG	1	0.995	0.989	8.564	21.075	21.075	0.000	0.000	0.000	0.000
124	D	342	ALA	0	0.010	0.012	10.238	0.490	0.490	0.000	0.000	0.000	0.000
125	D	343	GLY	0	-0.022	-0.016	11.452	0.894	0.894	0.000	0.000	0.000	0.000
126	D	344	ARG	1	0.895	0.938	11.786	15.940	15.940	0.000	0.000	0.000	0.000
127	D	345	LYS	1	0.985	1.004	10.391	23.800	23.800	0.000	0.000	0.000	0.000
128	D	346	GLY	0	0.073	0.042	11.623	1.175	1.175	0.000	0.000	0.000	0.000
129	D	347	THR	0	-0.009	-0.011	12.017	-1.487	-1.487	0.000	0.000	0.000	0.000
130	D	348	ALA	0	-0.024	-0.011	11.132	0.836	0.836	0.000	0.000	0.000	0.000
131	D	349	ILE	0	0.029	0.020	12.969	-0.401	-0.401	0.000	0.000	0.000	0.000
132	D	350	SER	0	-0.014	-0.016	14.696	0.153	0.153	0.000	0.000	0.000	0.000
133	D	351	LEU	0	-0.008	-0.006	17.117	0.337	0.337	0.000	0.000	0.000	0.000
134	D	352	VAL	0	-0.010	-0.018	19.433	-0.007	-0.007	0.000	0.000	0.000	0.000
135	D	353	GLU	-1	-0.767	-0.882	21.977	-10.719	-10.719	0.000	0.000	0.000	0.000
136	D	354	ALA	0	0.073	0.038	24.473	-0.449	-0.449	0.000	0.000	0.000	0.000
137	D	355	HIS	1	0.832	0.919	24.742	11.922	11.922	0.000	0.000	0.000	0.000
138	D	356	ASP	-1	-0.840	-0.932	20.736	-14.301	-14.301	0.000	0.000	0.000	0.000
139	D	357	HIS	0	0.036	0.019	20.743	-0.860	-0.860	0.000	0.000	0.000	0.000
140	D	358	LEU	0	0.043	0.006	20.377	-0.785	-0.785	0.000	0.000	0.000	0.000
141	D	359	LEU	0	-0.072	-0.031	18.318	-0.775	-0.775	0.000	0.000	0.000	0.000
142	D	360	LEU	0	0.022	0.012	15.539	-1.081	-1.081	0.000	0.000	0.000	0.000
143	D	361	GLY	0	0.016	0.010	15.485	-1.171	-1.171	0.000	0.000	0.000	0.000
144	D	362	LYS	1	0.904	0.934	15.505	14.495	14.495	0.000	0.000	0.000	0.000
145	D	363	VAL	0	-0.002	0.011	11.233	-0.904	-0.904	0.000	0.000	0.000	0.000
146	D	364	GLY	0	0.015	0.004	11.144	-2.232	-2.232	0.000	0.000	0.000	0.000
147	D	365	ARG	1	0.994	0.991	10.593	17.020	17.020	0.000	0.000	0.000	0.000
148	D	366	TYR	0	-0.045	-0.008	7.027	0.513	0.513	0.000	0.000	0.000	0.000
149	D	367	ILE	0	-0.067	-0.038	6.284	-2.633	-2.633	0.000	0.000	0.000	0.000
150	D	368	GLU	-1	-0.898	-0.914	2.139	-97.331	-91.208	3.272	-5.340	-4.055	-0.079
151	D	369	GLU	-1	-0.863	-0.952	6.255	-38.594	-38.594	0.000	0.000	0.000	0.000
152	D	370	PRO	0	-0.067	-0.041	8.833	0.220	0.220	0.000	0.000	0.000	0.000
153	D	371	ILE	0	0.021	0.020	10.618	-0.857	-0.857	0.000	0.000	0.000	0.000
154	D	372	LYS	1	0.970	0.977	11.924	23.860	23.860	0.000	0.000	0.000	0.000
155	D	373	ALA	0	0.021	0.011	15.117	0.015	0.015	0.000	0.000	0.000	0.000
156	D	374	ARG	1	0.937	0.963	17.905	16.364	16.364	0.000	0.000	0.000	0.000
157	D	375	VAL	0	-0.031	-0.021	20.882	0.173	0.173	0.000	0.000	0.000	0.000
158	D	376	ILE	0	-0.042	-0.005	24.609	-0.144	-0.144	0.000	0.000	0.000	0.000
159	D	377	ASP	-1	-0.878	-0.925	26.677	-9.599	-9.599	0.000	0.000	0.000	0.000
160	D	378	GLU	-1	-0.833	-0.923	29.873	-9.958	-9.958	0.000	0.000	0.000	0.000
161	D	379	LEU	0	-0.063	-0.030	29.126	0.159	0.159	0.000	0.000	0.000	0.000
162	D	380	ARG	1	0.885	0.935	28.907	9.770	9.770	0.000	0.000	0.000	0.000
163	D	381	PRO	0	-0.050	-0.035	26.979	0.252	0.252	0.000	0.000	0.000	0.000
164	D	382	LYS	1	0.975	1.005	30.012	8.640	8.640	0.000	0.000	0.000	0.000
165	D	383	THR	0	-0.031	-0.050	31.760	0.261	0.261	0.000	0.000	0.000	0.000
166	D	384	ARG	1	0.986	0.989	30.654	9.385	9.385	0.000	0.000	0.000	0.000
167	D	385	ALA	0	-0.018	-0.008	25.475	-0.131	-0.131	0.000	0.000	0.000	0.000
168	D	386	PRO	0	-0.044	-0.045	25.456	0.298	0.298	0.000	0.000	0.000	0.000
169	D	387	SER	0	0.008	0.006	26.442	-0.161	-0.161	0.000	0.000	0.000	0.000
170	D	388	GLU	-1	-0.952	-0.947	22.974	-12.910	-12.910	0.000	0.000	0.000	0.000

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