FMO DATABASE

FMODB ID: 6NJ9Z

Calculation Name: 1JB2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JB2

Chain ID: A

ChEMBL ID:

UniProt ID: P61972

Base Structure: X-ray

Registration Date: 2023-09-20

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1077377.064256
FMO2-HF: Nuclear repulsion	1027385.721902
FMO2-HF: Total energy	-49991.342354
FMO2-MP2: Total energy	-50135.566364

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:4:LYS)

Summations of interaction energy for fragment #1(A:4:LYS)

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.
-173.644	-173.243	20.882	-8.789	-12.494	-0.082

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.927 / q_NPA : 0.959

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	6	ILE	0	0.078	0.028	3.020	-7.623	-5.706	0.155	-0.946	-1.126	-0.004
4	A	7	TRP	0	0.065	0.020	5.659	0.152	0.152	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.859	-0.941	1.868	-96.704	-101.611	19.763	-6.528	-8.328	-0.072
6	A	9	GLN	0	-0.094	-0.057	2.585	-5.710	-3.312	0.936	-1.061	-2.273	-0.005
7	A	10	ILE	0	0.016	0.026	4.261	1.547	1.689	0.001	-0.023	-0.120	0.000
8	A	11	GLY	0	0.062	0.039	6.993	2.371	2.371	0.000	0.000	0.000	0.000
9	A	12	SER	0	0.003	0.002	3.055	-3.407	-2.844	0.030	-0.205	-0.387	-0.001
10	A	13	SER	0	-0.085	-0.064	5.191	5.492	5.544	-0.001	-0.001	-0.050	0.000
11	A	14	PHE	0	-0.005	0.002	7.947	3.350	3.350	0.000	0.000	0.000	0.000
12	A	15	ILE	0	0.027	0.019	7.778	2.635	2.635	0.000	0.000	0.000	0.000
13	A	16	ASN	0	-0.038	-0.027	8.195	4.265	4.265	0.000	0.000	0.000	0.000
14	A	17	HIS	0	0.025	0.012	9.969	1.740	1.740	0.000	0.000	0.000	0.000
15	A	18	TYR	0	0.034	0.027	12.974	1.968	1.968	0.000	0.000	0.000	0.000
16	A	19	TYR	0	-0.001	-0.055	11.769	1.091	1.091	0.000	0.000	0.000	0.000
17	A	20	GLN	0	0.003	0.026	13.417	2.566	2.566	0.000	0.000	0.000	0.000
18	A	21	LEU	0	0.018	0.001	15.994	1.222	1.222	0.000	0.000	0.000	0.000
19	A	22	PHE	0	-0.060	-0.030	17.957	1.207	1.207	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.777	-0.861	17.603	-16.805	-16.805	0.000	0.000	0.000	0.000
21	A	24	ASN	0	-0.104	-0.046	18.460	1.238	1.238	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.841	-0.917	21.638	-11.928	-11.928	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.940	0.971	22.577	11.848	11.848	0.000	0.000	0.000	0.000
24	A	27	THR	0	-0.080	-0.021	23.593	0.069	0.069	0.000	0.000	0.000	0.000
25	A	28	GLN	0	-0.052	-0.046	22.628	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	29	LEU	0	0.008	0.009	19.162	-0.451	-0.451	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.007	0.004	21.426	-0.326	-0.326	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.047	-0.027	21.791	0.133	0.133	0.000	0.000	0.000	0.000
29	A	32	ILE	0	0.005	0.019	17.109	-0.304	-0.304	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.057	-0.039	19.186	-0.428	-0.428	0.000	0.000	0.000	0.000
31	A	34	ILE	0	0.006	-0.014	21.843	0.482	0.482	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.872	-0.951	24.548	-10.791	-10.791	0.000	0.000	0.000	0.000
33	A	36	ALA	0	-0.042	-0.030	25.845	0.224	0.224	0.000	0.000	0.000	0.000
34	A	37	SER	0	-0.028	-0.033	21.450	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	38	CYS	0	-0.085	-0.033	22.885	0.816	0.816	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.027	0.016	21.633	-0.673	-0.673	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.057	-0.020	22.645	0.820	0.820	0.000	0.000	0.000	0.000
38	A	41	TRP	0	0.001	-0.012	21.011	-0.668	-0.668	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.871	-0.954	23.851	-11.934	-11.934	0.000	0.000	0.000	0.000
40	A	43	GLY	0	-0.067	-0.035	25.452	0.458	0.458	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.010	0.006	27.356	0.426	0.426	0.000	0.000	0.000	0.000
42	A	45	GLN	0	-0.016	-0.013	27.403	-0.238	-0.238	0.000	0.000	0.000	0.000
43	A	46	PHE	0	0.034	0.009	26.983	0.443	0.443	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.003	-0.007	26.841	-0.441	-0.441	0.000	0.000	0.000	0.000
45	A	48	GLY	0	0.052	0.032	27.383	0.446	0.446	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.910	0.963	25.201	12.437	12.437	0.000	0.000	0.000	0.000
47	A	50	ALA	0	0.001	0.001	27.397	-0.105	-0.105	0.000	0.000	0.000	0.000
48	A	51	ALA	0	0.058	0.032	29.909	0.077	0.077	0.000	0.000	0.000	0.000
49	A	52	ILE	0	-0.028	-0.002	23.385	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.009	-0.012	26.503	-0.175	-0.175	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.952	-0.965	27.681	-9.288	-9.288	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.926	0.979	27.156	11.178	11.178	0.000	0.000	0.000	0.000
53	A	56	LEU	0	-0.009	-0.011	22.761	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	57	SER	0	-0.049	-0.028	26.493	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	58	SER	0	-0.095	-0.044	29.419	0.261	0.261	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.060	-0.019	24.729	0.195	0.195	0.000	0.000	0.000	0.000
57	A	60	PRO	0	0.010	-0.006	29.035	0.060	0.060	0.000	0.000	0.000	0.000
58	A	61	PHE	0	0.040	0.037	24.052	0.116	0.116	0.000	0.000	0.000	0.000
59	A	62	GLN	0	-0.036	-0.026	29.013	0.173	0.173	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.937	0.958	24.992	11.612	11.612	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.031	-0.007	21.173	0.130	0.130	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.045	-0.008	18.429	-0.916	-0.916	0.000	0.000	0.000	0.000
63	A	66	HIS	1	0.812	0.872	15.336	17.819	17.819	0.000	0.000	0.000	0.000
64	A	67	SER	0	-0.008	-0.006	13.839	-0.184	-0.184	0.000	0.000	0.000	0.000
65	A	68	ILE	0	-0.029	-0.012	8.383	0.740	0.740	0.000	0.000	0.000	0.000
66	A	69	THR	0	-0.071	-0.051	10.529	-0.139	-0.139	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.006	-0.003	8.034	-1.220	-1.220	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.012	0.003	4.509	-2.548	-2.461	-0.001	-0.004	-0.082	0.000
69	A	72	ASP	-1	-0.877	-0.902	6.309	-38.690	-38.690	0.000	0.000	0.000	0.000
70	A	73	HIS	0	-0.008	-0.041	3.992	5.808	5.957	-0.001	-0.021	-0.128	0.000
71	A	74	GLN	0	-0.024	-0.005	7.618	0.585	0.585	0.000	0.000	0.000	0.000
72	A	75	PRO	0	0.005	0.018	9.631	0.431	0.431	0.000	0.000	0.000	0.000
73	A	76	THR	0	0.013	-0.004	11.690	0.927	0.927	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.027	-0.009	15.527	-0.084	-0.084	0.000	0.000	0.000	0.000
75	A	78	ASP	-1	-0.952	-0.954	18.304	-13.787	-13.787	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.056	-0.035	15.159	0.078	0.078	0.000	0.000	0.000	0.000
77	A	80	CYS	0	-0.068	-0.017	15.038	-0.066	-0.066	0.000	0.000	0.000	0.000
78	A	81	ILE	0	-0.011	-0.013	9.151	-0.939	-0.939	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.012	0.008	11.963	1.240	1.240	0.000	0.000	0.000	0.000
80	A	83	SER	0	-0.034	-0.038	8.508	-1.500	-1.500	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.866	-0.914	9.414	-20.247	-20.247	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.028	-0.010	9.357	-3.853	-3.853	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.061	0.040	10.948	2.683	2.683	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.009	-0.005	11.856	-2.214	-2.214	0.000	0.000	0.000	0.000
85	A	88	GLN	0	-0.044	-0.011	14.261	2.035	2.035	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.017	0.006	17.110	-0.869	-0.869	0.000	0.000	0.000	0.000
87	A	90	LYS	1	0.878	0.942	19.772	12.506	12.506	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.026	0.013	23.039	-0.330	-0.330	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.795	-0.888	25.615	-10.552	-10.552	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.916	-0.974	28.310	-10.344	-10.344	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.952	-0.956	27.535	-10.668	-10.668	0.000	0.000	0.000	0.000
92	A	95	PRO	0	-0.061	-0.037	27.542	-0.297	-0.297	0.000	0.000	0.000	0.000
93	A	96	ILE	0	-0.014	-0.015	21.407	-0.230	-0.230	0.000	0.000	0.000	0.000
94	A	97	MET	0	-0.005	0.002	22.348	0.470	0.470	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.062	0.037	19.171	-0.784	-0.784	0.000	0.000	0.000	0.000
96	A	99	PHE	0	-0.067	-0.021	13.998	0.859	0.859	0.000	0.000	0.000	0.000
97	A	100	HIS	0	-0.037	-0.039	14.889	-0.451	-0.451	0.000	0.000	0.000	0.000
98	A	101	GLN	0	-0.004	-0.013	14.574	0.686	0.686	0.000	0.000	0.000	0.000
99	A	102	MET	0	-0.006	0.008	13.774	-1.511	-1.511	0.000	0.000	0.000	0.000
100	A	103	PHE	0	0.017	-0.012	12.132	1.004	1.004	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.034	0.004	13.632	-1.198	-1.198	0.000	0.000	0.000	0.000
102	A	105	LEU	0	0.000	-0.010	10.751	0.905	0.905	0.000	0.000	0.000	0.000
103	A	106	LYS	1	0.998	0.980	14.895	14.251	14.251	0.000	0.000	0.000	0.000
104	A	107	ASN	0	-0.009	0.020	15.517	1.129	1.129	0.000	0.000	0.000	0.000
105	A	108	ILE	0	-0.002	-0.021	17.499	0.871	0.871	0.000	0.000	0.000	0.000
106	A	109	ASN	0	-0.071	-0.040	21.254	0.192	0.192	0.000	0.000	0.000	0.000
107	A	110	ASP	-1	-0.895	-0.960	18.536	-15.457	-15.457	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.035	0.040	18.033	-0.381	-0.381	0.000	0.000	0.000	0.000
109	A	112	TRP	0	-0.048	-0.022	12.704	-0.057	-0.057	0.000	0.000	0.000	0.000
110	A	113	VAL	0	0.005	0.014	16.095	0.085	0.085	0.000	0.000	0.000	0.000
111	A	114	CYS	0	-0.033	-0.003	16.229	-0.590	-0.590	0.000	0.000	0.000	0.000
112	A	115	THR	0	-0.006	-0.008	17.517	0.844	0.844	0.000	0.000	0.000	0.000
113	A	116	ASN	0	0.001	0.015	18.607	0.653	0.653	0.000	0.000	0.000	0.000
114	A	117	ASP	-1	-0.723	-0.834	17.675	-18.214	-18.214	0.000	0.000	0.000	0.000
115	A	118	MET	0	-0.050	-0.019	18.028	1.065	1.065	0.000	0.000	0.000	0.000
116	A	119	PHE	0	0.057	0.037	18.314	-1.012	-1.012	0.000	0.000	0.000	0.000
117	A	120	ARG	1	0.952	0.964	19.819	13.934	13.934	0.000	0.000	0.000	0.000
118	A	121	LEU	0	0.050	0.046	20.376	-0.710	-0.710	0.000	0.000	0.000	0.000
119	A	122	ALA	0	-0.046	-0.039	19.964	0.201	0.201	0.000	0.000	0.000	0.000
120	A	123	LEU	0	-0.010	-0.013	21.959	0.070	0.070	0.000	0.000	0.000	0.000
121	A	124	HIS	0	-0.043	-0.016	22.148	0.071	0.071	0.000	0.000	0.000	0.000
122	A	125	ASN	0	-0.017	-0.004	16.978	-1.203	-1.203	0.000	0.000	0.000	0.000
123	A	126	PHE	0	0.065	0.032	13.683	0.352	0.352	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)