FMO DATABASE

FMODB ID: JQQK9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1053316.932055
FMO2-HF: Nuclear repulsion	1005339.438576
FMO2-HF: Total energy	-47977.493479
FMO2-MP2: Total energy	-48116.689345

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.
-48.891	-46.91	-0.018	-0.834	-1.128	0.001

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 : 0.936 / 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	0.009	3.869	2.089	3.911	-0.017	-0.821	-0.984	0.001
4	B	9	LYS	1	0.874	0.940	5.831	31.018	31.018	0.000	0.000	0.000	0.000
5	B	10	ILE	0	-0.036	-0.018	8.022	2.211	2.211	0.000	0.000	0.000	0.000
6	B	11	LEU	0	0.003	0.005	11.664	-0.088	-0.088	0.000	0.000	0.000	0.000
7	B	12	ILE	0	-0.013	-0.007	14.721	0.718	0.718	0.000	0.000	0.000	0.000
8	B	13	VAL	0	-0.009	-0.011	17.904	0.072	0.072	0.000	0.000	0.000	0.000
9	B	14	GLU	-1	-0.842	-0.915	21.125	-11.950	-11.950	0.000	0.000	0.000	0.000
10	B	15	ASP	-1	-0.870	-0.942	23.992	-10.437	-10.437	0.000	0.000	0.000	0.000
11	B	16	ASP	-1	-0.824	-0.896	27.146	-11.185	-11.185	0.000	0.000	0.000	0.000
12	B	17	GLU	-1	-0.843	-0.942	24.190	-11.668	-11.668	0.000	0.000	0.000	0.000
13	B	18	ARG	1	0.887	0.960	23.514	11.385	11.385	0.000	0.000	0.000	0.000
14	B	19	LEU	0	0.007	-0.011	23.981	-0.559	-0.559	0.000	0.000	0.000	0.000
15	B	20	ALA	0	0.041	0.031	21.062	-0.736	-0.736	0.000	0.000	0.000	0.000
16	B	21	ARG	1	0.900	0.929	19.297	14.325	14.325	0.000	0.000	0.000	0.000
17	B	22	LEU	0	-0.063	-0.045	19.304	-0.719	-0.719	0.000	0.000	0.000	0.000
18	B	23	THR	0	-0.021	-0.014	18.285	-0.472	-0.472	0.000	0.000	0.000	0.000
19	B	24	GLN	0	-0.022	-0.031	14.295	0.022	0.022	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.837	-0.883	14.922	-18.276	-18.276	0.000	0.000	0.000	0.000
21	B	26	TYR	0	-0.059	-0.037	15.609	-0.333	-0.333	0.000	0.000	0.000	0.000
22	B	27	LEU	0	0.017	0.006	13.384	-1.021	-1.021	0.000	0.000	0.000	0.000
23	B	28	ILE	0	0.036	0.031	10.266	-1.884	-1.884	0.000	0.000	0.000	0.000
24	B	29	ARG	1	0.817	0.891	10.095	16.029	16.029	0.000	0.000	0.000	0.000
25	B	30	ASN	0	-0.074	-0.042	11.576	1.229	1.229	0.000	0.000	0.000	0.000
26	B	31	GLY	0	-0.025	0.003	7.147	-0.081	-0.081	0.000	0.000	0.000	0.000
27	B	32	LEU	0	-0.032	-0.020	6.819	-3.837	-3.837	0.000	0.000	0.000	0.000
28	B	33	GLU	-1	-0.915	-0.961	4.521	-43.271	-43.112	-0.001	-0.013	-0.144	0.000
29	B	34	VAL	0	-0.019	-0.005	7.772	1.876	1.876	0.000	0.000	0.000	0.000
30	B	35	GLY	0	0.042	0.034	11.504	0.779	0.779	0.000	0.000	0.000	0.000
31	B	36	VAL	0	-0.006	-0.013	14.006	0.269	0.269	0.000	0.000	0.000	0.000
32	B	37	GLU	-1	-0.795	-0.864	17.826	-13.673	-13.673	0.000	0.000	0.000	0.000
33	B	38	THR	0	0.008	-0.001	20.639	0.022	0.022	0.000	0.000	0.000	0.000
34	B	39	ASP	-1	-0.794	-0.903	24.194	-10.294	-10.294	0.000	0.000	0.000	0.000
35	B	40	GLY	0	0.095	0.046	24.467	-0.520	-0.520	0.000	0.000	0.000	0.000
36	B	41	ASN	0	-0.053	-0.027	25.180	-0.203	-0.203	0.000	0.000	0.000	0.000
37	B	42	ARG	1	0.734	0.849	23.023	11.944	11.944	0.000	0.000	0.000	0.000
38	B	43	ALA	0	0.026	0.010	20.757	-0.453	-0.453	0.000	0.000	0.000	0.000
39	B	44	ILE	0	0.026	0.021	20.566	-0.548	-0.548	0.000	0.000	0.000	0.000
40	B	45	ARG	1	0.928	0.958	21.422	10.846	10.846	0.000	0.000	0.000	0.000
41	B	46	ARG	1	0.800	0.880	15.411	16.498	16.498	0.000	0.000	0.000	0.000
42	B	47	ILE	0	0.009	0.004	16.414	-0.970	-0.970	0.000	0.000	0.000	0.000
43	B	48	ILE	0	-0.012	0.004	16.204	-0.781	-0.781	0.000	0.000	0.000	0.000
44	B	49	SER	0	-0.022	-0.013	16.991	-0.110	-0.110	0.000	0.000	0.000	0.000
45	B	50	GLU	-1	-0.896	-0.943	12.695	-19.125	-19.125	0.000	0.000	0.000	0.000
46	B	51	GLN	0	-0.079	-0.032	11.582	-2.038	-2.038	0.000	0.000	0.000	0.000
47	B	52	PRO	0	0.007	0.011	10.606	-2.098	-2.098	0.000	0.000	0.000	0.000
48	B	53	ASP	-1	-0.818	-0.891	7.247	-30.998	-30.998	0.000	0.000	0.000	0.000
49	B	54	LEU	0	-0.034	-0.014	10.626	0.753	0.753	0.000	0.000	0.000	0.000
50	B	55	VAL	0	0.018	0.015	13.604	-0.594	-0.594	0.000	0.000	0.000	0.000
51	B	56	VAL	0	-0.053	-0.028	16.431	0.247	0.247	0.000	0.000	0.000	0.000
52	B	57	LEU	0	0.011	0.001	18.819	0.014	0.014	0.000	0.000	0.000	0.000
53	B	58	ASP	-1	-0.691	-0.808	22.129	-10.665	-10.665	0.000	0.000	0.000	0.000
54	B	59	VAL	0	0.026	0.006	25.692	-0.024	-0.024	0.000	0.000	0.000	0.000
55	B	60	MET	0	-0.045	-0.016	28.656	0.384	0.384	0.000	0.000	0.000	0.000
56	B	61	LEU	0	0.006	0.001	24.763	-0.350	-0.350	0.000	0.000	0.000	0.000
57	B	62	PRO	0	0.027	0.025	28.172	0.382	0.382	0.000	0.000	0.000	0.000
58	B	63	GLY	0	-0.009	0.005	29.092	-0.326	-0.326	0.000	0.000	0.000	0.000
59	B	64	ALA	0	-0.049	-0.041	28.280	0.248	0.248	0.000	0.000	0.000	0.000
60	B	65	ASP	-1	-0.735	-0.825	28.553	-10.082	-10.082	0.000	0.000	0.000	0.000
61	B	66	GLY	0	0.045	0.005	26.233	-0.210	-0.210	0.000	0.000	0.000	0.000
62	B	67	LEU	0	0.005	0.001	26.354	-0.345	-0.345	0.000	0.000	0.000	0.000
63	B	68	THR	0	-0.042	-0.061	28.300	-0.024	-0.024	0.000	0.000	0.000	0.000
64	B	69	VAL	0	-0.066	-0.026	22.729	-0.185	-0.185	0.000	0.000	0.000	0.000
65	B	70	CYS	0	-0.038	-0.020	23.514	-0.487	-0.487	0.000	0.000	0.000	0.000
66	B	71	ARG	1	0.830	0.907	24.542	9.537	9.537	0.000	0.000	0.000	0.000
67	B	72	GLU	-1	-0.828	-0.915	26.257	-10.015	-10.015	0.000	0.000	0.000	0.000
68	B	73	VAL	0	-0.066	-0.033	20.621	-0.183	-0.183	0.000	0.000	0.000	0.000
69	B	74	ARG	1	0.806	0.886	19.113	13.781	13.781	0.000	0.000	0.000	0.000
70	B	75	PRO	0	-0.035	-0.013	22.573	-0.244	-0.244	0.000	0.000	0.000	0.000
71	B	76	HIS	0	-0.036	-0.014	21.246	-0.142	-0.142	0.000	0.000	0.000	0.000
72	B	77	TYR	0	-0.055	-0.047	13.762	-0.505	-0.505	0.000	0.000	0.000	0.000
73	B	78	HIS	0	0.006	0.000	17.703	0.252	0.252	0.000	0.000	0.000	0.000
74	B	79	GLN	0	-0.020	0.015	12.672	-0.401	-0.401	0.000	0.000	0.000	0.000
75	B	80	PRO	0	-0.014	-0.014	14.206	0.799	0.799	0.000	0.000	0.000	0.000
76	B	81	ILE	0	0.009	0.013	16.577	-0.608	-0.608	0.000	0.000	0.000	0.000
77	B	82	LEU	0	-0.042	-0.009	18.935	0.497	0.497	0.000	0.000	0.000	0.000
78	B	83	MET	0	0.010	0.013	20.599	0.021	0.021	0.000	0.000	0.000	0.000
79	B	84	LEU	0	-0.047	-0.042	21.778	-0.047	-0.047	0.000	0.000	0.000	0.000
80	B	85	THR	0	-0.022	-0.031	24.540	0.156	0.156	0.000	0.000	0.000	0.000
81	B	86	ALA	0	0.009	0.001	28.053	0.052	0.052	0.000	0.000	0.000	0.000
82	B	87	ARG	1	0.814	0.892	31.224	9.225	9.225	0.000	0.000	0.000	0.000
83	B	88	THR	0	0.019	-0.002	32.169	-0.267	-0.267	0.000	0.000	0.000	0.000
84	B	89	GLU	-1	-0.894	-0.927	33.758	-8.364	-8.364	0.000	0.000	0.000	0.000
85	B	90	ASP	-1	-0.897	-0.949	34.998	-8.663	-8.663	0.000	0.000	0.000	0.000
86	B	91	MET	0	-0.030	-0.014	35.549	-0.151	-0.151	0.000	0.000	0.000	0.000
87	B	92	ASP	-1	-0.810	-0.895	33.040	-8.953	-8.953	0.000	0.000	0.000	0.000
88	B	93	GLN	0	-0.029	-0.019	30.495	-0.441	-0.441	0.000	0.000	0.000	0.000
89	B	94	VAL	0	0.006	0.001	30.744	-0.284	-0.284	0.000	0.000	0.000	0.000
90	B	95	LEU	0	-0.007	-0.001	31.962	-0.140	-0.140	0.000	0.000	0.000	0.000
91	B	96	GLY	0	0.019	-0.016	28.997	-0.133	-0.133	0.000	0.000	0.000	0.000
92	B	97	LEU	0	-0.049	-0.022	26.324	-0.359	-0.359	0.000	0.000	0.000	0.000
93	B	98	GLU	-1	-0.929	-0.961	27.981	-9.749	-9.749	0.000	0.000	0.000	0.000
94	B	99	MET	0	-0.096	-0.028	28.368	0.128	0.128	0.000	0.000	0.000	0.000
95	B	100	GLY	0	0.022	0.011	25.643	-0.203	-0.203	0.000	0.000	0.000	0.000
96	B	101	ALA	0	0.006	0.007	23.166	-0.645	-0.645	0.000	0.000	0.000	0.000
97	B	102	ASP	-1	-0.824	-0.906	20.097	-14.438	-14.438	0.000	0.000	0.000	0.000
98	B	103	ASP	-1	-0.847	-0.928	21.892	-13.351	-13.351	0.000	0.000	0.000	0.000
99	B	104	TYR	0	-0.002	-0.014	23.654	-0.124	-0.124	0.000	0.000	0.000	0.000
100	B	105	VAL	0	-0.086	-0.037	23.283	0.150	0.150	0.000	0.000	0.000	0.000
101	B	106	ALA	0	0.059	0.036	26.400	0.036	0.036	0.000	0.000	0.000	0.000
102	B	107	LYS	1	0.748	0.865	25.599	11.268	11.268	0.000	0.000	0.000	0.000
103	B	108	PRO	0	0.003	-0.006	28.097	0.328	0.328	0.000	0.000	0.000	0.000
104	B	109	VAL	0	0.040	0.013	23.290	0.086	0.086	0.000	0.000	0.000	0.000
105	B	110	GLN	0	0.019	0.010	24.529	-0.341	-0.341	0.000	0.000	0.000	0.000
106	B	111	PRO	0	0.064	0.025	19.749	-0.427	-0.427	0.000	0.000	0.000	0.000
107	B	112	ARG	1	0.943	0.971	18.019	16.057	16.057	0.000	0.000	0.000	0.000
108	B	113	VAL	0	-0.014	-0.009	19.459	-0.508	-0.508	0.000	0.000	0.000	0.000
109	B	114	LEU	0	0.050	0.036	18.674	-0.258	-0.258	0.000	0.000	0.000	0.000
110	B	115	LEU	0	0.013	0.009	12.794	-0.467	-0.467	0.000	0.000	0.000	0.000
111	B	116	ALA	0	-0.069	-0.034	15.820	-0.992	-0.992	0.000	0.000	0.000	0.000
112	B	117	ARG	1	0.895	0.936	17.659	12.607	12.607	0.000	0.000	0.000	0.000
113	B	118	ILE	0	0.070	0.038	13.542	-0.216	-0.216	0.000	0.000	0.000	0.000
114	B	119	ARG	1	0.939	0.963	10.290	24.035	24.035	0.000	0.000	0.000	0.000
115	B	120	ALA	0	-0.060	-0.029	14.121	-0.352	-0.352	0.000	0.000	0.000	0.000
116	B	121	LEU	0	0.036	0.017	16.684	0.165	0.165	0.000	0.000	0.000	0.000
117	B	122	LEU	0	0.059	0.034	10.182	-0.207	-0.207	0.000	0.000	0.000	0.000
118	B	123	ARG	1	0.857	0.950	12.813	16.681	16.681	0.000	0.000	0.000	0.000
119	B	124	ARG	1	0.894	0.937	13.985	15.171	15.171	0.000	0.000	0.000	0.000
120	B	125	THR	0	-0.010	0.011	11.934	0.515	0.515	0.000	0.000	0.000	0.000

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