FMO DATABASE

FMODB ID: YZ952

Calculation Name: 1JFI-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JFI

Chain ID: B

ChEMBL ID:

UniProt ID: Q14919

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-906074.168021
FMO2-HF: Nuclear repulsion	851898.66525
FMO2-HF: Total energy	-54175.502771
FMO2-MP2: Total energy	-54332.236704

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(B:109:ASP)

Summations of interaction energy for fragment #1(B:109:ASP)

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.
-15.345	-10.922	1.401	-2.49	-3.334	0.013

Interaction energy analysis for fragmet #1(B:109:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.943 / q_NPA : -0.979

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	B	111	LEU	0	-0.065	-0.031	2.323	-12.192	-7.791	1.401	-2.472	-3.330	0.013
4	B	112	THR	0	0.007	-0.003	4.180	-3.904	-3.882	0.000	-0.018	-0.004	0.000
5	B	113	ILE	0	-0.001	0.002	7.846	-0.282	-0.282	0.000	0.000	0.000	0.000
6	B	114	PRO	0	0.039	0.011	11.129	-1.108	-1.108	0.000	0.000	0.000	0.000
7	B	115	ARG	1	0.879	0.899	13.293	-18.342	-18.342	0.000	0.000	0.000	0.000
8	B	116	ALA	0	-0.029	-0.007	16.115	-0.863	-0.863	0.000	0.000	0.000	0.000
9	B	117	ALA	0	0.028	0.021	16.079	-0.866	-0.866	0.000	0.000	0.000	0.000
10	B	118	ILE	0	0.064	0.034	14.706	-0.832	-0.832	0.000	0.000	0.000	0.000
11	B	119	ASN	0	-0.010	-0.011	18.443	-0.818	-0.818	0.000	0.000	0.000	0.000
12	B	120	LYS	1	0.802	0.889	21.295	-12.774	-12.774	0.000	0.000	0.000	0.000
13	B	121	MET	0	0.059	0.034	20.831	-0.419	-0.419	0.000	0.000	0.000	0.000
14	B	122	ILE	0	0.003	0.009	20.979	-0.551	-0.551	0.000	0.000	0.000	0.000
15	B	123	LYS	1	0.867	0.940	24.116	-10.234	-10.234	0.000	0.000	0.000	0.000
16	B	124	GLU	-1	-0.796	-0.891	25.186	11.215	11.215	0.000	0.000	0.000	0.000
17	B	125	THR	0	-0.007	-0.006	24.948	-0.328	-0.328	0.000	0.000	0.000	0.000
18	B	126	LEU	0	-0.031	-0.016	26.042	-0.321	-0.321	0.000	0.000	0.000	0.000
19	B	127	PRO	0	0.012	0.003	29.128	-0.026	-0.026	0.000	0.000	0.000	0.000
20	B	128	ASN	0	-0.052	-0.031	30.988	-0.105	-0.105	0.000	0.000	0.000	0.000
21	B	129	VAL	0	0.052	0.041	29.069	-0.209	-0.209	0.000	0.000	0.000	0.000
22	B	130	ARG	1	0.930	0.960	28.940	-8.542	-8.542	0.000	0.000	0.000	0.000
23	B	131	VAL	0	0.026	0.019	23.396	-0.028	-0.028	0.000	0.000	0.000	0.000
24	B	132	ALA	0	0.067	0.033	24.988	0.166	0.166	0.000	0.000	0.000	0.000
25	B	133	ASN	0	0.024	-0.011	20.022	0.697	0.697	0.000	0.000	0.000	0.000
26	B	134	ASP	-1	-0.870	-0.919	19.861	14.474	14.474	0.000	0.000	0.000	0.000
27	B	135	ALA	0	0.053	0.021	19.356	0.541	0.541	0.000	0.000	0.000	0.000
28	B	136	ARG	1	0.802	0.890	19.077	-12.303	-12.303	0.000	0.000	0.000	0.000
29	B	137	GLU	-1	-0.776	-0.863	13.548	20.465	20.465	0.000	0.000	0.000	0.000
30	B	138	LEU	0	0.017	0.036	15.045	1.027	1.027	0.000	0.000	0.000	0.000
31	B	139	VAL	0	0.011	0.002	16.001	0.547	0.547	0.000	0.000	0.000	0.000
32	B	140	VAL	0	0.012	-0.002	11.538	0.282	0.282	0.000	0.000	0.000	0.000
33	B	141	ASN	0	-0.023	-0.027	10.776	2.778	2.778	0.000	0.000	0.000	0.000
34	B	142	CYS	0	0.004	-0.002	11.843	0.660	0.660	0.000	0.000	0.000	0.000
35	B	143	CYS	0	-0.087	-0.042	12.581	-0.367	-0.367	0.000	0.000	0.000	0.000
36	B	144	THR	0	0.009	0.004	6.511	0.101	0.101	0.000	0.000	0.000	0.000
37	B	145	GLU	-1	-0.943	-0.966	9.622	19.331	19.331	0.000	0.000	0.000	0.000
38	B	146	PHE	0	0.009	0.001	11.336	-0.200	-0.200	0.000	0.000	0.000	0.000
39	B	147	ILE	0	0.012	0.006	9.527	-0.625	-0.625	0.000	0.000	0.000	0.000
40	B	148	HIS	0	0.038	0.035	5.240	-1.549	-1.549	0.000	0.000	0.000	0.000
41	B	149	LEU	0	0.001	0.021	10.342	-0.783	-0.783	0.000	0.000	0.000	0.000
42	B	150	ILE	0	-0.010	-0.007	14.077	-0.759	-0.759	0.000	0.000	0.000	0.000
43	B	151	SER	0	-0.040	-0.043	11.395	-0.599	-0.599	0.000	0.000	0.000	0.000
44	B	152	SER	0	-0.044	-0.028	12.543	-0.068	-0.068	0.000	0.000	0.000	0.000
45	B	153	GLU	-1	-0.828	-0.882	14.375	13.308	13.308	0.000	0.000	0.000	0.000
46	B	154	ALA	0	-0.011	-0.009	16.438	-0.677	-0.677	0.000	0.000	0.000	0.000
47	B	155	ASN	0	-0.013	-0.014	14.753	0.023	0.023	0.000	0.000	0.000	0.000
48	B	156	GLU	-1	-0.820	-0.904	16.907	13.769	13.769	0.000	0.000	0.000	0.000
49	B	157	ILE	0	-0.043	-0.020	19.588	-0.774	-0.774	0.000	0.000	0.000	0.000
50	B	158	CYS	0	-0.057	-0.019	19.296	-0.552	-0.552	0.000	0.000	0.000	0.000
51	B	159	ASN	0	-0.024	-0.013	18.628	-0.337	-0.337	0.000	0.000	0.000	0.000
52	B	160	LYS	1	0.855	0.928	22.079	-13.829	-13.829	0.000	0.000	0.000	0.000
53	B	161	SER	0	-0.085	-0.032	24.118	-0.521	-0.521	0.000	0.000	0.000	0.000
54	B	162	GLU	-1	-0.838	-0.923	26.372	10.740	10.740	0.000	0.000	0.000	0.000
55	B	163	LYS	1	0.792	0.901	23.852	-11.390	-11.390	0.000	0.000	0.000	0.000
56	B	164	LYS	1	0.971	0.981	19.660	-15.011	-15.011	0.000	0.000	0.000	0.000
57	B	165	THR	0	-0.033	-0.025	18.461	0.929	0.929	0.000	0.000	0.000	0.000
58	B	166	ILE	0	0.037	0.031	14.426	-0.875	-0.875	0.000	0.000	0.000	0.000
59	B	167	SER	0	-0.027	-0.019	18.505	0.036	0.036	0.000	0.000	0.000	0.000
60	B	168	PRO	0	0.023	-0.025	20.685	0.137	0.137	0.000	0.000	0.000	0.000
61	B	169	GLU	-1	-0.872	-0.916	21.800	11.170	11.170	0.000	0.000	0.000	0.000
62	B	170	HIS	0	0.065	0.046	20.379	0.342	0.342	0.000	0.000	0.000	0.000
63	B	171	VAL	0	0.028	0.016	17.511	0.121	0.121	0.000	0.000	0.000	0.000
64	B	172	ILE	0	-0.027	-0.017	20.114	-0.172	-0.172	0.000	0.000	0.000	0.000
65	B	173	GLN	0	-0.045	-0.042	23.652	-0.067	-0.067	0.000	0.000	0.000	0.000
66	B	174	ALA	0	0.036	0.014	19.245	-0.228	-0.228	0.000	0.000	0.000	0.000
67	B	175	LEU	0	-0.024	-0.020	19.747	0.020	0.020	0.000	0.000	0.000	0.000
68	B	176	GLU	-1	-0.942	-0.982	22.419	10.252	10.252	0.000	0.000	0.000	0.000
69	B	177	SER	0	-0.097	-0.060	23.131	-0.407	-0.407	0.000	0.000	0.000	0.000
70	B	178	LEU	0	-0.020	-0.018	18.438	-0.105	-0.105	0.000	0.000	0.000	0.000
71	B	179	GLY	0	-0.012	0.012	22.899	-0.018	-0.018	0.000	0.000	0.000	0.000
72	B	180	PHE	0	-0.027	-0.021	19.582	-0.158	-0.158	0.000	0.000	0.000	0.000
73	B	181	GLY	0	0.081	0.036	24.374	0.018	0.018	0.000	0.000	0.000	0.000
74	B	182	SER	0	-0.038	-0.017	27.088	-0.149	-0.149	0.000	0.000	0.000	0.000
75	B	183	TYR	0	-0.002	-0.003	22.167	-0.078	-0.078	0.000	0.000	0.000	0.000
76	B	184	ILE	0	-0.006	-0.005	25.710	0.137	0.137	0.000	0.000	0.000	0.000
77	B	185	SER	0	-0.057	-0.024	27.232	-0.178	-0.178	0.000	0.000	0.000	0.000
78	B	186	GLU	-1	-0.861	-0.932	26.544	11.083	11.083	0.000	0.000	0.000	0.000
79	B	187	VAL	0	-0.006	-0.003	22.598	0.227	0.227	0.000	0.000	0.000	0.000
80	B	188	LYS	1	0.917	0.964	25.039	-10.218	-10.218	0.000	0.000	0.000	0.000
81	B	189	GLU	-1	-0.902	-0.944	27.893	9.720	9.720	0.000	0.000	0.000	0.000
82	B	190	VAL	0	0.048	0.022	22.613	-0.043	-0.043	0.000	0.000	0.000	0.000
83	B	191	LEU	0	-0.009	0.002	24.010	0.101	0.101	0.000	0.000	0.000	0.000
84	B	192	GLN	0	0.048	0.022	25.826	0.135	0.135	0.000	0.000	0.000	0.000
85	B	193	GLU	-1	-0.890	-0.936	26.304	11.189	11.189	0.000	0.000	0.000	0.000
86	B	194	CYS	0	-0.023	-0.009	23.516	0.151	0.151	0.000	0.000	0.000	0.000
87	B	195	LYS	1	0.890	0.943	25.847	-10.767	-10.767	0.000	0.000	0.000	0.000
88	B	196	THR	0	-0.042	-0.033	28.568	-0.371	-0.371	0.000	0.000	0.000	0.000
89	B	197	VAL	0	0.005	0.000	26.218	-0.335	-0.335	0.000	0.000	0.000	0.000
90	B	198	ALA	0	0.016	0.012	26.250	-0.133	-0.133	0.000	0.000	0.000	0.000
91	B	199	LEU	0	-0.013	-0.014	28.010	-0.164	-0.164	0.000	0.000	0.000	0.000
92	B	200	LYS	1	0.940	0.959	31.794	-9.683	-9.683	0.000	0.000	0.000	0.000
93	B	201	ARG	1	0.945	0.978	25.044	-12.255	-12.255	0.000	0.000	0.000	0.000
94	B	202	ARG	1	0.955	0.984	29.996	-10.119	-10.119	0.000	0.000	0.000	0.000
95	B	203	LYS	1	0.974	0.983	32.244	-8.931	-8.931	0.000	0.000	0.000	0.000
96	B	204	ALA	0	-0.027	-0.003	32.957	-0.263	-0.263	0.000	0.000	0.000	0.000
97	B	205	SER	0	0.025	0.019	31.317	-0.095	-0.095	0.000	0.000	0.000	0.000
98	B	206	SER	0	0.005	0.014	33.907	-0.262	-0.262	0.000	0.000	0.000	0.000
99	B	207	ARG	1	0.955	0.961	36.990	-8.290	-8.290	0.000	0.000	0.000	0.000
100	B	208	LEU	0	-0.004	0.000	34.293	-0.193	-0.193	0.000	0.000	0.000	0.000
101	B	209	GLU	-1	-0.923	-0.968	34.012	9.278	9.278	0.000	0.000	0.000	0.000
102	B	210	ASN	0	-0.080	-0.041	38.427	-0.236	-0.236	0.000	0.000	0.000	0.000
103	B	211	LEU	0	-0.073	-0.037	41.629	-0.180	-0.180	0.000	0.000	0.000	0.000
104	B	212	GLY	0	0.015	0.024	42.336	-0.060	-0.060	0.000	0.000	0.000	0.000
105	B	213	ILE	0	-0.011	-0.010	43.178	-0.137	-0.137	0.000	0.000	0.000	0.000
106	B	214	PRO	0	0.036	0.021	44.518	0.147	0.147	0.000	0.000	0.000	0.000
107	B	215	GLU	-1	-0.902	-0.968	41.680	7.566	7.566	0.000	0.000	0.000	0.000
108	B	216	GLU	-1	-0.934	-0.958	44.845	6.250	6.250	0.000	0.000	0.000	0.000
109	B	217	GLU	-1	-0.816	-0.894	48.383	6.228	6.228	0.000	0.000	0.000	0.000
110	B	218	LEU	0	-0.033	-0.011	41.919	0.015	0.015	0.000	0.000	0.000	0.000
111	B	219	LEU	0	0.020	0.013	44.118	0.043	0.043	0.000	0.000	0.000	0.000
112	B	220	ARG	1	0.795	0.863	45.819	-6.153	-6.153	0.000	0.000	0.000	0.000
113	B	221	GLN	0	0.014	-0.006	46.711	0.032	0.032	0.000	0.000	0.000	0.000
114	B	222	GLN	0	-0.029	-0.010	40.030	-0.056	-0.056	0.000	0.000	0.000	0.000
115	B	223	GLN	0	-0.008	-0.017	45.336	-0.006	-0.006	0.000	0.000	0.000	0.000
116	B	224	GLU	-1	-0.843	-0.885	47.759	6.002	6.002	0.000	0.000	0.000	0.000
117	B	225	LEU	0	-0.047	-0.042	44.843	-0.076	-0.076	0.000	0.000	0.000	0.000
118	B	226	PHE	0	0.020	-0.002	41.306	-0.022	-0.022	0.000	0.000	0.000	0.000
119	B	227	ALA	0	-0.053	-0.020	47.159	-0.035	-0.035	0.000	0.000	0.000	0.000
120	B	228	LYS	1	0.972	1.005	48.451	-6.591	-6.591	0.000	0.000	0.000	0.000
121	B	229	ALA	0	-0.014	-0.001	46.903	-0.049	-0.049	0.000	0.000	0.000	0.000
122	B	230	ARG	1	0.960	0.968	47.260	-6.668	-6.668	0.000	0.000	0.000	0.000
123	B	231	GLN	0	-0.018	-0.002	50.315	0.004	0.004	0.000	0.000	0.000	0.000
124	B	232	GLN	0	0.075	0.051	49.620	0.051	0.051	0.000	0.000	0.000	0.000
125	B	233	GLN	0	-0.048	-0.044	47.750	-0.059	-0.059	0.000	0.000	0.000	0.000
126	B	234	ALA	0	-0.017	0.008	51.232	-0.017	-0.017	0.000	0.000	0.000	0.000
127	B	235	GLU	-1	-0.945	-0.978	54.057	5.560	5.560	0.000	0.000	0.000	0.000
128	B	236	LEU	0	0.009	0.010	51.226	-0.071	-0.071	0.000	0.000	0.000	0.000
129	B	237	ALA	0	0.031	0.015	52.333	-0.048	-0.048	0.000	0.000	0.000	0.000
130	B	238	GLN	0	-0.023	-0.026	54.245	-0.029	-0.029	0.000	0.000	0.000	0.000
131	B	239	GLN	0	-0.033	-0.023	57.767	-0.036	-0.036	0.000	0.000	0.000	0.000
132	B	240	GLU	-1	-0.958	-0.967	53.151	6.029	6.029	0.000	0.000	0.000	0.000
133	B	241	TRP	0	-0.051	-0.032	52.846	-0.053	-0.053	0.000	0.000	0.000	0.000
134	B	242	LEU	0	-0.078	-0.014	58.753	-0.086	-0.086	0.000	0.000	0.000	0.000
135	B	243	GLN	0	-0.072	-0.038	59.328	-0.129	-0.129	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:109:ASP)