FMO DATABASE

FMODB ID: 5349Z

Calculation Name: 2J4B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J4B

Chain ID: A

ChEMBL ID:

UniProt ID: Q8SQS4

Base Structure: X-ray

Registration Date: 2023-06-19

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1310394.087538
FMO2-HF: Nuclear repulsion	1255501.95035
FMO2-HF: Total energy	-54892.137188
FMO2-MP2: Total energy	-55055.731459

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:18:GLN)

Summations of interaction energy for fragment #1(A:18:GLN)

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.
1.429	5.128	0.125	-1.304	-2.522	-0.001

Interaction energy analysis for fragmet #1(A:18:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.007

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

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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	20	GLU	-1	-0.839	-0.918	3.535	-0.595	1.292	-0.008	-0.733	-1.147	0.001
4	A	21	THR	0	0.014	0.001	2.940	-1.565	-0.372	0.125	-0.367	-0.952	-0.002
5	A	22	SER	0	-0.016	-0.020	3.049	0.768	1.387	0.008	-0.204	-0.423	0.000
6	A	23	TYR	0	0.023	0.019	5.530	0.488	0.488	0.000	0.000	0.000	0.000
7	A	24	VAL	0	0.036	0.026	8.048	0.083	0.083	0.000	0.000	0.000	0.000
8	A	25	SER	0	-0.008	0.002	7.719	0.088	0.088	0.000	0.000	0.000	0.000
9	A	26	LEU	0	0.008	0.003	9.568	0.110	0.110	0.000	0.000	0.000	0.000
10	A	27	LYS	1	0.829	0.913	11.452	0.083	0.083	0.000	0.000	0.000	0.000
11	A	28	THR	0	-0.017	-0.027	12.764	0.033	0.033	0.000	0.000	0.000	0.000
12	A	29	TRP	0	0.008	0.023	13.918	0.039	0.039	0.000	0.000	0.000	0.000
13	A	30	ILE	0	-0.003	-0.013	15.469	0.043	0.043	0.000	0.000	0.000	0.000
14	A	31	GLU	-1	-1.002	-0.995	17.527	-0.094	-0.094	0.000	0.000	0.000	0.000
15	A	32	ASP	-1	-0.874	-0.930	18.772	-0.265	-0.265	0.000	0.000	0.000	0.000
16	A	33	SER	0	-0.140	-0.065	20.188	0.019	0.019	0.000	0.000	0.000	0.000
17	A	34	LEU	0	0.028	-0.005	21.754	0.011	0.011	0.000	0.000	0.000	0.000
18	A	35	ASP	-1	-0.836	-0.921	25.024	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	36	LEU	0	-0.081	-0.034	26.915	0.013	0.013	0.000	0.000	0.000	0.000
20	A	37	PHE	0	0.007	-0.016	23.183	0.012	0.012	0.000	0.000	0.000	0.000
21	A	38	LYS	1	0.923	0.965	21.718	0.085	0.085	0.000	0.000	0.000	0.000
22	A	39	ASN	0	0.009	0.001	22.670	0.018	0.018	0.000	0.000	0.000	0.000
23	A	40	ASP	-1	-0.839	-0.922	23.754	0.060	0.060	0.000	0.000	0.000	0.000
24	A	41	LEU	0	-0.041	-0.019	18.282	0.019	0.019	0.000	0.000	0.000	0.000
25	A	42	LEU	0	0.020	0.012	18.697	0.016	0.016	0.000	0.000	0.000	0.000
26	A	43	PRO	0	-0.044	-0.017	19.307	0.028	0.028	0.000	0.000	0.000	0.000
27	A	44	LEU	0	0.016	0.008	14.729	0.040	0.040	0.000	0.000	0.000	0.000
28	A	45	LEU	0	0.035	0.003	13.538	0.051	0.051	0.000	0.000	0.000	0.000
29	A	46	TYR	0	0.000	0.007	15.022	0.059	0.059	0.000	0.000	0.000	0.000
30	A	47	PRO	0	0.020	0.002	16.482	0.054	0.054	0.000	0.000	0.000	0.000
31	A	48	LEU	0	-0.001	0.014	9.423	0.075	0.075	0.000	0.000	0.000	0.000
32	A	49	PHE	0	-0.012	-0.003	11.685	0.108	0.108	0.000	0.000	0.000	0.000
33	A	50	ILE	0	0.006	0.020	12.599	0.120	0.120	0.000	0.000	0.000	0.000
34	A	51	HIS	0	0.006	-0.006	11.909	0.141	0.141	0.000	0.000	0.000	0.000
35	A	52	ILE	0	0.010	0.010	7.344	0.138	0.138	0.000	0.000	0.000	0.000
36	A	53	TYR	0	-0.036	-0.018	9.658	0.290	0.290	0.000	0.000	0.000	0.000
37	A	54	PHE	0	-0.004	-0.026	12.012	0.050	0.050	0.000	0.000	0.000	0.000
38	A	55	ASP	-1	-0.825	-0.881	8.662	1.367	1.367	0.000	0.000	0.000	0.000
39	A	56	LEU	0	-0.056	-0.023	6.019	0.166	0.166	0.000	0.000	0.000	0.000
40	A	57	ILE	0	0.007	0.019	9.918	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	58	GLN	0	-0.037	-0.011	12.574	-0.184	-0.184	0.000	0.000	0.000	0.000
42	A	59	GLN	0	-0.080	-0.045	6.471	0.318	0.318	0.000	0.000	0.000	0.000
43	A	60	ASN	0	-0.047	-0.022	11.909	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	61	LYS	1	0.904	0.962	6.819	-2.825	-2.825	0.000	0.000	0.000	0.000
45	A	62	THR	0	0.040	0.011	11.450	0.072	0.072	0.000	0.000	0.000	0.000
46	A	63	ASP	-1	-0.901	-0.955	12.764	0.790	0.790	0.000	0.000	0.000	0.000
47	A	64	GLU	-1	-0.907	-0.959	6.237	4.659	4.659	0.000	0.000	0.000	0.000
48	A	65	ALA	0	-0.019	-0.010	10.083	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	66	LYS	1	0.941	0.963	11.684	-0.810	-0.810	0.000	0.000	0.000	0.000
50	A	67	GLU	-1	-0.925	-0.954	11.345	0.807	0.807	0.000	0.000	0.000	0.000
51	A	68	PHE	0	-0.047	-0.020	8.632	-0.183	-0.183	0.000	0.000	0.000	0.000
52	A	69	PHE	0	-0.029	-0.027	11.151	-0.197	-0.197	0.000	0.000	0.000	0.000
53	A	70	GLU	-1	-0.874	-0.964	14.263	0.315	0.315	0.000	0.000	0.000	0.000
54	A	71	LYS	1	0.881	0.971	11.597	-0.663	-0.663	0.000	0.000	0.000	0.000
55	A	72	TYR	0	-0.015	-0.018	9.596	-0.193	-0.193	0.000	0.000	0.000	0.000
56	A	73	ARG	1	0.863	0.949	15.083	-0.373	-0.373	0.000	0.000	0.000	0.000
57	A	74	GLY	0	-0.028	-0.014	17.881	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	75	ASP	-1	-0.807	-0.894	16.009	0.069	0.069	0.000	0.000	0.000	0.000
59	A	76	HIS	1	0.795	0.883	15.637	-0.285	-0.285	0.000	0.000	0.000	0.000
60	A	77	TYR	0	0.065	0.033	20.921	0.039	0.039	0.000	0.000	0.000	0.000
61	A	78	ASN	0	0.042	0.037	23.654	0.004	0.004	0.000	0.000	0.000	0.000
62	A	79	LYS	1	0.956	0.969	22.709	-0.207	-0.207	0.000	0.000	0.000	0.000
63	A	80	SER	0	-0.011	-0.001	24.155	0.024	0.024	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.930	-0.954	25.209	0.188	0.188	0.000	0.000	0.000	0.000
65	A	82	GLU	-1	-0.890	-0.959	23.640	0.232	0.232	0.000	0.000	0.000	0.000
66	A	83	ILE	0	-0.048	-0.017	19.135	0.034	0.034	0.000	0.000	0.000	0.000
67	A	84	LYS	1	0.973	0.980	21.751	-0.212	-0.212	0.000	0.000	0.000	0.000
68	A	85	GLN	0	-0.014	-0.005	24.336	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	86	PHE	0	0.006	-0.026	19.097	0.019	0.019	0.000	0.000	0.000	0.000
70	A	87	GLU	-1	-0.898	-0.937	20.111	0.355	0.355	0.000	0.000	0.000	0.000
71	A	88	SER	0	-0.080	-0.024	20.934	0.023	0.023	0.000	0.000	0.000	0.000
72	A	89	ILE	0	-0.038	-0.009	19.188	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	90	TYR	0	0.026	0.013	17.952	0.049	0.049	0.000	0.000	0.000	0.000
74	A	91	THR	0	0.008	-0.010	17.384	0.079	0.079	0.000	0.000	0.000	0.000
75	A	92	VAL	0	0.087	0.024	17.290	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	93	GLN	0	-0.014	-0.012	19.488	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	94	HIS	0	0.030	0.025	21.424	0.008	0.008	0.000	0.000	0.000	0.000
78	A	95	ILE	0	0.021	0.027	16.868	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	96	HIS	0	-0.082	-0.049	21.005	-0.041	-0.041	0.000	0.000	0.000	0.000
80	A	97	GLU	-1	-0.896	-0.929	24.043	0.323	0.323	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.030	-0.018	24.467	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	99	ASN	0	0.062	0.009	24.714	0.039	0.039	0.000	0.000	0.000	0.000
83	A	100	PHE	0	0.006	0.002	22.737	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	101	ALA	0	0.028	0.016	20.754	0.013	0.013	0.000	0.000	0.000	0.000
85	A	102	TYR	0	0.007	0.000	20.679	0.034	0.034	0.000	0.000	0.000	0.000
86	A	103	THR	0	-0.032	-0.034	22.069	0.008	0.008	0.000	0.000	0.000	0.000
87	A	104	PHE	0	-0.018	-0.008	16.854	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	105	LYS	1	0.912	0.971	16.308	-0.584	-0.584	0.000	0.000	0.000	0.000
89	A	106	ASN	0	-0.066	-0.030	18.214	0.061	0.061	0.000	0.000	0.000	0.000
90	A	107	SER	0	-0.018	0.006	20.938	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	108	LYS	1	0.871	0.940	20.285	-0.327	-0.327	0.000	0.000	0.000	0.000
92	A	109	TYR	0	0.026	0.019	19.723	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	110	HIS	0	0.018	0.015	21.485	0.007	0.007	0.000	0.000	0.000	0.000
94	A	111	LEU	0	-0.043	-0.016	19.077	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	112	SER	0	-0.039	-0.023	23.732	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	113	MET	0	0.010	0.022	18.968	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	114	GLY	0	0.027	0.026	25.133	0.002	0.002	0.000	0.000	0.000	0.000
98	A	115	ARG	1	0.953	0.955	25.349	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	116	TYR	0	-0.004	-0.004	25.230	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	117	ALA	0	0.056	0.043	22.453	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	118	PHE	0	0.029	0.006	20.323	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	119	ASP	-1	-0.888	-0.937	20.108	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	120	LEU	0	0.005	-0.007	20.106	-0.013	-0.013	0.000	0.000	0.000	0.000
104	A	121	LEU	0	-0.012	-0.006	14.880	-0.027	-0.027	0.000	0.000	0.000	0.000
105	A	122	ILE	0	-0.032	-0.020	15.445	0.005	0.005	0.000	0.000	0.000	0.000
106	A	123	ASN	0	0.036	0.019	15.761	0.007	0.007	0.000	0.000	0.000	0.000
107	A	124	PHE	0	-0.008	0.002	11.288	-0.054	-0.054	0.000	0.000	0.000	0.000
108	A	125	LEU	0	-0.042	-0.040	10.425	-0.061	-0.061	0.000	0.000	0.000	0.000
109	A	126	GLU	-1	-0.953	-0.983	11.112	0.084	0.084	0.000	0.000	0.000	0.000
110	A	127	GLU	-1	-0.987	-0.972	13.425	-0.343	-0.343	0.000	0.000	0.000	0.000
111	A	128	ARG	1	0.894	0.952	9.266	0.690	0.690	0.000	0.000	0.000	0.000
112	A	129	ASN	0	-0.010	0.001	8.358	-0.175	-0.175	0.000	0.000	0.000	0.000
113	A	130	LEU	0	0.018	0.016	5.824	0.235	0.235	0.000	0.000	0.000	0.000
114	A	131	THR	0	-0.013	-0.031	6.157	0.185	0.185	0.000	0.000	0.000	0.000
115	A	132	TYR	0	-0.083	-0.086	5.574	0.014	0.014	0.000	0.000	0.000	0.000
116	A	133	ILE	0	0.037	0.012	7.505	-0.249	-0.249	0.000	0.000	0.000	0.000
117	A	134	LEU	0	0.061	0.031	9.641	-0.076	-0.076	0.000	0.000	0.000	0.000
118	A	135	LYS	1	0.924	0.983	8.600	-1.668	-1.668	0.000	0.000	0.000	0.000
119	A	136	ILE	0	-0.005	-0.002	10.206	-0.104	-0.104	0.000	0.000	0.000	0.000
120	A	137	LEU	0	-0.004	-0.002	12.930	-0.074	-0.074	0.000	0.000	0.000	0.000
121	A	138	ASN	0	0.004	0.003	15.309	-0.081	-0.081	0.000	0.000	0.000	0.000
122	A	139	GLN	0	-0.037	-0.030	14.748	0.012	0.012	0.000	0.000	0.000	0.000
123	A	140	HIS	0	-0.003	0.001	13.737	-0.082	-0.082	0.000	0.000	0.000	0.000
124	A	141	LEU	0	-0.069	-0.020	15.800	-0.031	-0.031	0.000	0.000	0.000	0.000
125	A	142	ASP	-1	-0.932	-0.959	19.149	0.203	0.203	0.000	0.000	0.000	0.000
126	A	143	ILE	0	0.017	-0.001	18.567	-0.017	-0.017	0.000	0.000	0.000	0.000
127	A	144	LYS	1	0.985	0.994	23.174	-0.103	-0.103	0.000	0.000	0.000	0.000
128	A	145	VAL	0	0.015	0.003	24.089	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	146	TYR	0	-0.061	-0.030	26.762	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	147	VAL	0	0.010	-0.008	29.591	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	148	GLY	0	-0.009	0.002	31.684	-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:18:GLN)