FMO DATABASE

FMODB ID: NNN6Q

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	OptHSide
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	-1050861.951292
FMO2-HF: Nuclear repulsion	1002884.620249
FMO2-HF: Total energy	-47977.331043
FMO2-MP2: Total energy	-48116.522413

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.
-43.945	-41.836	-0.003	-0.89	-1.215	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 : 0.954 / q_NPA : 0.966

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	8	PRO	0	0.014	0.014	3.734	0.834	2.848	-0.002	-0.887	-1.125	0.002
4	B	9	LYS	1	0.878	0.940	5.660	29.831	29.831	0.000	0.000	0.000	0.000
5	B	10	ILE	0	-0.036	-0.032	7.998	2.048	2.048	0.000	0.000	0.000	0.000
6	B	11	LEU	0	0.018	0.016	11.694	-0.049	-0.049	0.000	0.000	0.000	0.000
7	B	12	ILE	0	-0.013	-0.010	14.751	0.500	0.500	0.000	0.000	0.000	0.000
8	B	13	VAL	0	-0.011	-0.014	17.855	0.171	0.171	0.000	0.000	0.000	0.000
9	B	14	GLU	-1	-0.836	-0.921	21.098	-11.743	-11.743	0.000	0.000	0.000	0.000
10	B	15	ASP	-1	-0.870	-0.941	23.893	-10.368	-10.368	0.000	0.000	0.000	0.000
11	B	16	ASP	-1	-0.835	-0.895	26.979	-10.900	-10.900	0.000	0.000	0.000	0.000
12	B	17	GLU	-1	-0.844	-0.940	24.541	-11.360	-11.360	0.000	0.000	0.000	0.000
13	B	18	ARG	1	0.895	0.953	23.838	11.281	11.281	0.000	0.000	0.000	0.000
14	B	19	LEU	0	-0.007	-0.015	24.298	-0.543	-0.543	0.000	0.000	0.000	0.000
15	B	20	ALA	0	0.053	0.032	21.033	-0.695	-0.695	0.000	0.000	0.000	0.000
16	B	21	ARG	1	0.877	0.925	19.772	14.031	14.031	0.000	0.000	0.000	0.000
17	B	22	LEU	0	-0.068	-0.041	19.551	-0.778	-0.778	0.000	0.000	0.000	0.000
18	B	23	THR	0	-0.017	-0.016	18.578	-0.516	-0.516	0.000	0.000	0.000	0.000
19	B	24	GLN	0	-0.006	-0.020	14.360	-0.032	-0.032	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.863	-0.904	15.150	-18.357	-18.357	0.000	0.000	0.000	0.000
21	B	26	TYR	0	-0.036	-0.021	15.465	-0.631	-0.631	0.000	0.000	0.000	0.000
22	B	27	LEU	0	0.025	0.010	13.574	-0.913	-0.913	0.000	0.000	0.000	0.000
23	B	28	ILE	0	0.024	0.031	10.778	-1.836	-1.836	0.000	0.000	0.000	0.000
24	B	29	ARG	1	0.842	0.915	10.437	15.854	15.854	0.000	0.000	0.000	0.000
25	B	30	ASN	0	-0.121	-0.075	11.519	0.387	0.387	0.000	0.000	0.000	0.000
26	B	31	GLY	0	-0.007	0.007	7.118	-0.314	-0.314	0.000	0.000	0.000	0.000
27	B	32	LEU	0	-0.027	-0.014	7.044	-3.456	-3.456	0.000	0.000	0.000	0.000
28	B	33	GLU	-1	-0.919	-0.955	5.127	-36.640	-36.545	-0.001	-0.003	-0.090	0.000
29	B	34	VAL	0	-0.009	-0.002	8.015	1.443	1.443	0.000	0.000	0.000	0.000
30	B	35	GLY	0	0.030	0.031	11.593	0.431	0.431	0.000	0.000	0.000	0.000
31	B	36	VAL	0	-0.008	-0.014	14.023	0.237	0.237	0.000	0.000	0.000	0.000
32	B	37	GLU	-1	-0.810	-0.887	17.798	-13.225	-13.225	0.000	0.000	0.000	0.000
33	B	38	THR	0	0.020	0.003	20.491	0.031	0.031	0.000	0.000	0.000	0.000
34	B	39	ASP	-1	-0.825	-0.910	24.126	-10.192	-10.192	0.000	0.000	0.000	0.000
35	B	40	GLY	0	0.080	0.045	24.533	-0.472	-0.472	0.000	0.000	0.000	0.000
36	B	41	ASN	0	-0.032	-0.025	25.281	-0.225	-0.225	0.000	0.000	0.000	0.000
37	B	42	ARG	1	0.756	0.860	23.267	11.631	11.631	0.000	0.000	0.000	0.000
38	B	43	ALA	0	0.036	0.025	20.920	-0.516	-0.516	0.000	0.000	0.000	0.000
39	B	44	ILE	0	0.019	0.029	20.518	-0.556	-0.556	0.000	0.000	0.000	0.000
40	B	45	ARG	1	0.930	0.955	21.432	10.699	10.699	0.000	0.000	0.000	0.000
41	B	46	ARG	1	0.810	0.891	15.214	16.113	16.113	0.000	0.000	0.000	0.000
42	B	47	ILE	0	0.002	0.000	16.532	-0.914	-0.914	0.000	0.000	0.000	0.000
43	B	48	ILE	0	-0.010	0.004	16.324	-0.718	-0.718	0.000	0.000	0.000	0.000
44	B	49	SER	0	-0.013	-0.006	17.147	-0.121	-0.121	0.000	0.000	0.000	0.000
45	B	50	GLU	-1	-0.912	-0.950	12.892	-18.525	-18.525	0.000	0.000	0.000	0.000
46	B	51	GLN	0	-0.105	-0.051	11.860	-1.862	-1.862	0.000	0.000	0.000	0.000
47	B	52	PRO	0	-0.022	-0.002	10.612	-1.729	-1.729	0.000	0.000	0.000	0.000
48	B	53	ASP	-1	-0.792	-0.871	6.733	-30.316	-30.316	0.000	0.000	0.000	0.000
49	B	54	LEU	0	-0.019	-0.009	10.243	0.806	0.806	0.000	0.000	0.000	0.000
50	B	55	VAL	0	0.020	0.015	13.352	-0.496	-0.496	0.000	0.000	0.000	0.000
51	B	56	VAL	0	-0.051	-0.020	16.360	0.400	0.400	0.000	0.000	0.000	0.000
52	B	57	LEU	0	0.010	0.002	18.675	0.037	0.037	0.000	0.000	0.000	0.000
53	B	58	ASP	-1	-0.694	-0.805	21.912	-10.657	-10.657	0.000	0.000	0.000	0.000
54	B	59	VAL	0	-0.006	-0.014	25.405	0.031	0.031	0.000	0.000	0.000	0.000
55	B	60	MET	0	-0.046	-0.017	28.476	0.334	0.334	0.000	0.000	0.000	0.000
56	B	61	LEU	0	-0.002	0.004	24.882	-0.300	-0.300	0.000	0.000	0.000	0.000
57	B	62	PRO	0	0.056	0.038	28.627	0.355	0.355	0.000	0.000	0.000	0.000
58	B	63	GLY	0	-0.027	-0.016	29.420	-0.321	-0.321	0.000	0.000	0.000	0.000
59	B	64	ALA	0	-0.047	-0.040	28.113	0.248	0.248	0.000	0.000	0.000	0.000
60	B	65	ASP	-1	-0.740	-0.841	28.465	-9.931	-9.931	0.000	0.000	0.000	0.000
61	B	66	GLY	0	0.055	0.002	26.184	-0.188	-0.188	0.000	0.000	0.000	0.000
62	B	67	LEU	0	0.011	-0.005	26.274	-0.335	-0.335	0.000	0.000	0.000	0.000
63	B	68	THR	0	-0.049	-0.047	28.342	0.020	0.020	0.000	0.000	0.000	0.000
64	B	69	VAL	0	-0.035	-0.014	22.786	-0.143	-0.143	0.000	0.000	0.000	0.000
65	B	70	CYS	0	-0.027	-0.006	23.542	-0.413	-0.413	0.000	0.000	0.000	0.000
66	B	71	ARG	1	0.828	0.909	24.614	9.373	9.373	0.000	0.000	0.000	0.000
67	B	72	GLU	-1	-0.848	-0.929	26.148	-9.786	-9.786	0.000	0.000	0.000	0.000
68	B	73	VAL	0	-0.052	-0.030	20.585	-0.155	-0.155	0.000	0.000	0.000	0.000
69	B	74	ARG	1	0.828	0.905	18.951	13.344	13.344	0.000	0.000	0.000	0.000
70	B	75	PRO	0	-0.054	-0.016	22.606	-0.171	-0.171	0.000	0.000	0.000	0.000
71	B	76	HIS	0	-0.061	-0.031	21.216	-0.123	-0.123	0.000	0.000	0.000	0.000
72	B	77	TYR	0	-0.030	-0.033	13.582	-0.451	-0.451	0.000	0.000	0.000	0.000
73	B	78	HIS	0	0.021	0.007	17.321	0.370	0.370	0.000	0.000	0.000	0.000
74	B	79	GLN	0	-0.027	0.010	12.639	-0.215	-0.215	0.000	0.000	0.000	0.000
75	B	80	PRO	0	-0.008	-0.003	14.050	0.789	0.789	0.000	0.000	0.000	0.000
76	B	81	ILE	0	-0.002	0.000	16.443	-0.635	-0.635	0.000	0.000	0.000	0.000
77	B	82	LEU	0	-0.038	-0.016	18.940	0.425	0.425	0.000	0.000	0.000	0.000
78	B	83	MET	0	0.000	0.011	20.463	0.019	0.019	0.000	0.000	0.000	0.000
79	B	84	LEU	0	-0.045	-0.026	22.040	0.020	0.020	0.000	0.000	0.000	0.000
80	B	85	THR	0	0.008	-0.023	24.670	0.195	0.195	0.000	0.000	0.000	0.000
81	B	86	ALA	0	0.007	0.003	28.197	0.020	0.020	0.000	0.000	0.000	0.000
82	B	87	ARG	1	0.843	0.918	31.333	9.047	9.047	0.000	0.000	0.000	0.000
83	B	88	THR	0	0.038	0.009	31.733	-0.245	-0.245	0.000	0.000	0.000	0.000
84	B	89	GLU	-1	-0.919	-0.938	33.674	-8.007	-8.007	0.000	0.000	0.000	0.000
85	B	90	ASP	-1	-0.894	-0.951	35.059	-8.507	-8.507	0.000	0.000	0.000	0.000
86	B	91	MET	0	-0.032	-0.025	35.336	-0.208	-0.208	0.000	0.000	0.000	0.000
87	B	92	ASP	-1	-0.830	-0.909	33.096	-8.844	-8.844	0.000	0.000	0.000	0.000
88	B	93	GLN	0	-0.020	-0.011	30.233	-0.439	-0.439	0.000	0.000	0.000	0.000
89	B	94	VAL	0	-0.004	-0.005	30.734	-0.255	-0.255	0.000	0.000	0.000	0.000
90	B	95	LEU	0	0.008	0.008	31.986	-0.117	-0.117	0.000	0.000	0.000	0.000
91	B	96	GLY	0	0.022	-0.006	28.869	-0.150	-0.150	0.000	0.000	0.000	0.000
92	B	97	LEU	0	-0.054	-0.032	26.196	-0.342	-0.342	0.000	0.000	0.000	0.000
93	B	98	GLU	-1	-0.949	-0.968	27.838	-9.517	-9.517	0.000	0.000	0.000	0.000
94	B	99	MET	0	-0.092	-0.026	28.256	0.095	0.095	0.000	0.000	0.000	0.000
95	B	100	GLY	0	0.004	-0.003	25.290	-0.139	-0.139	0.000	0.000	0.000	0.000
96	B	101	ALA	0	-0.015	-0.001	23.017	-0.624	-0.624	0.000	0.000	0.000	0.000
97	B	102	ASP	-1	-0.827	-0.912	20.161	-13.985	-13.985	0.000	0.000	0.000	0.000
98	B	103	ASP	-1	-0.856	-0.934	21.813	-13.170	-13.170	0.000	0.000	0.000	0.000
99	B	104	TYR	0	0.003	-0.013	23.532	-0.074	-0.074	0.000	0.000	0.000	0.000
100	B	105	VAL	0	-0.071	-0.039	23.257	0.175	0.175	0.000	0.000	0.000	0.000
101	B	106	ALA	0	0.048	0.025	26.307	0.018	0.018	0.000	0.000	0.000	0.000
102	B	107	LYS	1	0.728	0.867	25.925	11.199	11.199	0.000	0.000	0.000	0.000
103	B	108	PRO	0	-0.003	-0.009	28.366	0.315	0.315	0.000	0.000	0.000	0.000
104	B	109	VAL	0	0.060	0.021	23.353	0.083	0.083	0.000	0.000	0.000	0.000
105	B	110	GLN	0	0.000	-0.006	24.900	-0.250	-0.250	0.000	0.000	0.000	0.000
106	B	111	PRO	0	0.069	0.023	20.323	-0.397	-0.397	0.000	0.000	0.000	0.000
107	B	112	ARG	1	0.950	0.975	17.315	16.226	16.226	0.000	0.000	0.000	0.000
108	B	113	VAL	0	0.012	0.000	19.524	-0.572	-0.572	0.000	0.000	0.000	0.000
109	B	114	LEU	0	0.064	0.040	18.622	-0.273	-0.273	0.000	0.000	0.000	0.000
110	B	115	LEU	0	0.009	0.013	12.824	-0.466	-0.466	0.000	0.000	0.000	0.000
111	B	116	ALA	0	-0.079	-0.048	15.697	-1.009	-1.009	0.000	0.000	0.000	0.000
112	B	117	ARG	1	0.890	0.934	17.653	12.561	12.561	0.000	0.000	0.000	0.000
113	B	118	ILE	0	0.070	0.046	13.409	-0.137	-0.137	0.000	0.000	0.000	0.000
114	B	119	ARG	1	0.938	0.963	10.230	23.516	23.516	0.000	0.000	0.000	0.000
115	B	120	ALA	0	-0.062	-0.035	13.977	-0.264	-0.264	0.000	0.000	0.000	0.000
116	B	121	LEU	0	0.044	0.018	16.504	0.125	0.125	0.000	0.000	0.000	0.000
117	B	122	LEU	0	0.033	0.018	10.123	-0.064	-0.064	0.000	0.000	0.000	0.000
118	B	123	ARG	1	0.874	0.955	12.350	16.271	16.271	0.000	0.000	0.000	0.000
119	B	124	ARG	1	0.880	0.942	13.882	14.477	14.477	0.000	0.000	0.000	0.000
120	B	125	THR	0	0.019	0.030	11.962	0.516	0.516	0.000	0.000	0.000	0.000

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