FMO DATABASE

FMODB ID: 899KY

Calculation Name: 5E3J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E3J

Chain ID: B

ChEMBL ID:

UniProt ID: D0C9D6

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1050192.684364
FMO2-HF: Nuclear repulsion	1002215.750869
FMO2-HF: Total energy	-47976.933495
FMO2-MP2: Total energy	-48116.137647

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:6:LYS)

Summations of interaction energy for fragment #1(B:6: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.
-42.235	-40.323	-0.009	-0.822	-1.082	0.002

Interaction energy analysis for fragmet #1(B:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.935 / 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	B	8	PRO	0	0.016	0.015	3.791	0.380	2.292	-0.009	-0.822	-1.082	0.002
4	B	9	LYS	1	0.979	0.989	5.707	29.027	29.027	0.000	0.000	0.000	0.000
5	B	10	ILE	0	-0.036	-0.026	8.037	1.922	1.922	0.000	0.000	0.000	0.000
6	B	11	LEU	0	0.022	0.015	11.733	-0.051	-0.051	0.000	0.000	0.000	0.000
7	B	12	ILE	0	-0.022	-0.016	14.794	0.477	0.477	0.000	0.000	0.000	0.000
8	B	13	VAL	0	-0.011	-0.014	17.861	0.151	0.151	0.000	0.000	0.000	0.000
9	B	14	GLU	-1	-0.819	-0.913	21.125	-11.405	-11.405	0.000	0.000	0.000	0.000
10	B	15	ASP	-1	-0.890	-0.950	23.899	-10.259	-10.259	0.000	0.000	0.000	0.000
11	B	16	ASP	-1	-0.843	-0.903	27.010	-10.638	-10.638	0.000	0.000	0.000	0.000
12	B	17	GLU	-1	-0.854	-0.945	24.553	-11.192	-11.192	0.000	0.000	0.000	0.000
13	B	18	ARG	1	0.902	0.955	23.845	11.219	11.219	0.000	0.000	0.000	0.000
14	B	19	LEU	0	-0.015	-0.013	24.307	-0.517	-0.517	0.000	0.000	0.000	0.000
15	B	20	ALA	0	0.047	0.026	20.995	-0.662	-0.662	0.000	0.000	0.000	0.000
16	B	21	ARG	1	0.878	0.937	19.781	13.445	13.445	0.000	0.000	0.000	0.000
17	B	22	LEU	0	-0.070	-0.043	19.561	-0.733	-0.733	0.000	0.000	0.000	0.000
18	B	23	THR	0	-0.028	-0.019	18.503	-0.467	-0.467	0.000	0.000	0.000	0.000
19	B	24	GLN	0	0.015	-0.008	14.421	0.000	0.000	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.853	-0.924	15.161	-18.318	-18.318	0.000	0.000	0.000	0.000
21	B	26	TYR	0	-0.062	-0.034	16.042	-0.809	-0.809	0.000	0.000	0.000	0.000
22	B	27	LEU	0	0.018	0.009	13.528	-0.826	-0.826	0.000	0.000	0.000	0.000
23	B	28	ILE	0	0.036	0.038	11.233	-1.794	-1.794	0.000	0.000	0.000	0.000
24	B	29	ARG	1	0.872	0.942	11.085	15.289	15.289	0.000	0.000	0.000	0.000
25	B	30	ASN	0	-0.133	-0.079	11.797	0.094	0.094	0.000	0.000	0.000	0.000
26	B	31	GLY	0	-0.007	0.006	7.505	-0.337	-0.337	0.000	0.000	0.000	0.000
27	B	32	LEU	0	-0.022	-0.012	6.934	-3.137	-3.137	0.000	0.000	0.000	0.000
28	B	33	GLU	-1	-0.924	-0.955	5.460	-33.610	-33.610	0.000	0.000	0.000	0.000
29	B	34	VAL	0	-0.017	-0.003	8.024	1.286	1.286	0.000	0.000	0.000	0.000
30	B	35	GLY	0	0.016	0.019	11.600	0.390	0.390	0.000	0.000	0.000	0.000
31	B	36	VAL	0	0.000	-0.010	14.027	0.219	0.219	0.000	0.000	0.000	0.000
32	B	37	GLU	-1	-0.824	-0.907	17.803	-12.878	-12.878	0.000	0.000	0.000	0.000
33	B	38	THR	0	0.012	0.004	20.493	-0.023	-0.023	0.000	0.000	0.000	0.000
34	B	39	ASP	-1	-0.849	-0.928	24.153	-9.995	-9.995	0.000	0.000	0.000	0.000
35	B	40	GLY	0	0.075	0.041	24.575	-0.460	-0.460	0.000	0.000	0.000	0.000
36	B	41	ASN	0	-0.005	-0.021	25.315	-0.250	-0.250	0.000	0.000	0.000	0.000
37	B	42	ARG	1	0.776	0.880	23.266	11.293	11.293	0.000	0.000	0.000	0.000
38	B	43	ALA	0	0.040	0.029	20.958	-0.498	-0.498	0.000	0.000	0.000	0.000
39	B	44	ILE	0	0.024	0.032	20.549	-0.571	-0.571	0.000	0.000	0.000	0.000
40	B	45	ARG	1	0.930	0.956	21.456	10.616	10.616	0.000	0.000	0.000	0.000
41	B	46	ARG	1	0.841	0.922	15.104	15.791	15.791	0.000	0.000	0.000	0.000
42	B	47	ILE	0	-0.004	-0.001	16.561	-0.898	-0.898	0.000	0.000	0.000	0.000
43	B	48	ILE	0	0.003	0.009	16.343	-0.721	-0.721	0.000	0.000	0.000	0.000
44	B	49	SER	0	-0.013	-0.004	17.000	-0.171	-0.171	0.000	0.000	0.000	0.000
45	B	50	GLU	-1	-0.945	-0.975	12.971	-18.230	-18.230	0.000	0.000	0.000	0.000
46	B	51	GLN	0	-0.132	-0.066	11.883	-1.856	-1.856	0.000	0.000	0.000	0.000
47	B	52	PRO	0	-0.027	-0.001	10.637	-1.574	-1.574	0.000	0.000	0.000	0.000
48	B	53	ASP	-1	-0.811	-0.894	6.756	-29.750	-29.750	0.000	0.000	0.000	0.000
49	B	54	LEU	0	-0.042	-0.021	10.248	0.819	0.819	0.000	0.000	0.000	0.000
50	B	55	VAL	0	0.014	0.012	13.365	-0.423	-0.423	0.000	0.000	0.000	0.000
51	B	56	VAL	0	-0.055	-0.022	16.384	0.379	0.379	0.000	0.000	0.000	0.000
52	B	57	LEU	0	0.007	-0.002	18.705	0.037	0.037	0.000	0.000	0.000	0.000
53	B	58	ASP	-1	-0.711	-0.837	21.942	-10.571	-10.571	0.000	0.000	0.000	0.000
54	B	59	VAL	0	-0.004	-0.011	25.438	0.040	0.040	0.000	0.000	0.000	0.000
55	B	60	MET	0	-0.076	-0.034	28.506	0.341	0.341	0.000	0.000	0.000	0.000
56	B	61	LEU	0	0.000	0.006	25.007	-0.280	-0.280	0.000	0.000	0.000	0.000
57	B	62	PRO	0	0.059	0.040	28.580	0.350	0.350	0.000	0.000	0.000	0.000
58	B	63	GLY	0	-0.015	-0.004	29.461	-0.312	-0.312	0.000	0.000	0.000	0.000
59	B	64	ALA	0	-0.046	-0.036	28.162	0.238	0.238	0.000	0.000	0.000	0.000
60	B	65	ASP	-1	-0.754	-0.857	28.499	-9.748	-9.748	0.000	0.000	0.000	0.000
61	B	66	GLY	0	0.050	0.000	26.212	-0.186	-0.186	0.000	0.000	0.000	0.000
62	B	67	LEU	0	0.006	-0.003	26.295	-0.327	-0.327	0.000	0.000	0.000	0.000
63	B	68	THR	0	-0.055	-0.049	28.357	0.033	0.033	0.000	0.000	0.000	0.000
64	B	69	VAL	0	-0.022	-0.003	22.836	-0.124	-0.124	0.000	0.000	0.000	0.000
65	B	70	CYS	0	-0.023	-0.002	23.554	-0.398	-0.398	0.000	0.000	0.000	0.000
66	B	71	ARG	1	0.901	0.937	24.622	9.218	9.218	0.000	0.000	0.000	0.000
67	B	72	GLU	-1	-0.959	-0.987	26.201	-9.809	-9.809	0.000	0.000	0.000	0.000
68	B	73	VAL	0	-0.056	-0.026	20.583	-0.167	-0.167	0.000	0.000	0.000	0.000
69	B	74	ARG	1	0.836	0.904	18.834	13.222	13.222	0.000	0.000	0.000	0.000
70	B	75	PRO	0	-0.065	-0.018	22.598	-0.187	-0.187	0.000	0.000	0.000	0.000
71	B	76	HIS	0	-0.048	-0.023	21.058	-0.161	-0.161	0.000	0.000	0.000	0.000
72	B	77	TYR	0	-0.021	-0.026	13.640	-0.420	-0.420	0.000	0.000	0.000	0.000
73	B	78	HIS	0	0.020	0.011	17.345	0.396	0.396	0.000	0.000	0.000	0.000
74	B	79	GLN	0	-0.033	0.009	12.672	-0.526	-0.526	0.000	0.000	0.000	0.000
75	B	80	PRO	0	0.010	0.003	14.001	0.800	0.800	0.000	0.000	0.000	0.000
76	B	81	ILE	0	0.006	0.011	16.450	-0.579	-0.579	0.000	0.000	0.000	0.000
77	B	82	LEU	0	-0.046	-0.019	18.798	0.412	0.412	0.000	0.000	0.000	0.000
78	B	83	MET	0	0.005	0.012	20.477	0.023	0.023	0.000	0.000	0.000	0.000
79	B	84	LEU	0	-0.038	-0.021	22.093	0.025	0.025	0.000	0.000	0.000	0.000
80	B	85	THR	0	0.041	0.017	24.698	0.209	0.209	0.000	0.000	0.000	0.000
81	B	86	ALA	0	0.010	0.001	28.227	0.012	0.012	0.000	0.000	0.000	0.000
82	B	87	ARG	1	0.931	0.968	31.351	8.924	8.924	0.000	0.000	0.000	0.000
83	B	88	THR	0	0.027	0.006	31.841	-0.216	-0.216	0.000	0.000	0.000	0.000
84	B	89	GLU	-1	-0.933	-0.936	33.695	-7.840	-7.840	0.000	0.000	0.000	0.000
85	B	90	ASP	-1	-0.895	-0.950	35.073	-8.410	-8.410	0.000	0.000	0.000	0.000
86	B	91	MET	0	-0.036	-0.025	35.345	-0.210	-0.210	0.000	0.000	0.000	0.000
87	B	92	ASP	-1	-0.875	-0.945	33.137	-8.711	-8.711	0.000	0.000	0.000	0.000
88	B	93	GLN	0	-0.028	-0.018	30.166	-0.514	-0.514	0.000	0.000	0.000	0.000
89	B	94	VAL	0	-0.004	-0.004	30.740	-0.254	-0.254	0.000	0.000	0.000	0.000
90	B	95	LEU	0	0.009	0.009	31.988	-0.118	-0.118	0.000	0.000	0.000	0.000
91	B	96	GLY	0	0.017	-0.013	28.879	-0.150	-0.150	0.000	0.000	0.000	0.000
92	B	97	LEU	0	-0.045	-0.027	26.274	-0.331	-0.331	0.000	0.000	0.000	0.000
93	B	98	GLU	-1	-0.948	-0.969	27.834	-9.435	-9.435	0.000	0.000	0.000	0.000
94	B	99	MET	0	-0.081	-0.011	28.297	0.108	0.108	0.000	0.000	0.000	0.000
95	B	100	GLY	0	0.004	-0.005	25.289	-0.132	-0.132	0.000	0.000	0.000	0.000
96	B	101	ALA	0	-0.025	-0.008	23.020	-0.596	-0.596	0.000	0.000	0.000	0.000
97	B	102	ASP	-1	-0.840	-0.929	20.028	-13.772	-13.772	0.000	0.000	0.000	0.000
98	B	103	ASP	-1	-0.869	-0.935	21.845	-12.977	-12.977	0.000	0.000	0.000	0.000
99	B	104	TYR	0	-0.007	-0.028	23.535	-0.054	-0.054	0.000	0.000	0.000	0.000
100	B	105	VAL	0	-0.056	-0.033	23.190	0.155	0.155	0.000	0.000	0.000	0.000
101	B	106	ALA	0	0.042	0.020	26.325	0.020	0.020	0.000	0.000	0.000	0.000
102	B	107	LYS	1	0.726	0.873	26.119	10.945	10.945	0.000	0.000	0.000	0.000
103	B	108	PRO	0	0.009	-0.004	28.374	0.301	0.301	0.000	0.000	0.000	0.000
104	B	109	VAL	0	0.065	0.027	23.527	0.088	0.088	0.000	0.000	0.000	0.000
105	B	110	GLN	0	-0.016	-0.017	24.863	-0.109	-0.109	0.000	0.000	0.000	0.000
106	B	111	PRO	0	0.071	0.026	20.449	-0.391	-0.391	0.000	0.000	0.000	0.000
107	B	112	ARG	1	0.957	0.978	17.230	16.154	16.154	0.000	0.000	0.000	0.000
108	B	113	VAL	0	0.012	0.000	19.665	-0.555	-0.555	0.000	0.000	0.000	0.000
109	B	114	LEU	0	0.069	0.040	18.572	-0.253	-0.253	0.000	0.000	0.000	0.000
110	B	115	LEU	0	0.012	0.011	12.904	-0.399	-0.399	0.000	0.000	0.000	0.000
111	B	116	ALA	0	-0.079	-0.044	15.551	-0.977	-0.977	0.000	0.000	0.000	0.000
112	B	117	ARG	1	0.892	0.941	17.275	12.477	12.477	0.000	0.000	0.000	0.000
113	B	118	ILE	0	0.077	0.050	12.951	-0.095	-0.095	0.000	0.000	0.000	0.000
114	B	119	ARG	1	0.936	0.961	10.722	22.495	22.495	0.000	0.000	0.000	0.000
115	B	120	ALA	0	-0.069	-0.038	13.609	-0.293	-0.293	0.000	0.000	0.000	0.000
116	B	121	LEU	0	0.035	0.015	16.246	0.081	0.081	0.000	0.000	0.000	0.000
117	B	122	LEU	0	0.026	0.011	9.537	-0.055	-0.055	0.000	0.000	0.000	0.000
118	B	123	ARG	1	0.880	0.949	12.266	16.305	16.305	0.000	0.000	0.000	0.000
119	B	124	ARG	1	0.879	0.942	13.670	14.482	14.482	0.000	0.000	0.000	0.000
120	B	125	THR	0	0.042	0.050	11.480	0.772	0.772	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:6:LYS)