FMO DATABASE

FMODB ID: Q1Z2Y

Calculation Name: 3KF6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF6

Chain ID: A

ChEMBL ID:

UniProt ID: Q0E7J7

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1360112.009659
FMO2-HF: Nuclear repulsion	1302080.428315
FMO2-HF: Total energy	-58031.581344
FMO2-MP2: Total energy	-58198.731289

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:16:SER)

Summations of interaction energy for fragment #1(A:16:SER)

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.
-4.27	-1.453	-0.008	-1.362	-1.449	0.005

Interaction energy analysis for fragmet #1(A:16:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.000

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	A	18	TRP	0	0.075	0.004	3.779	1.040	2.746	-0.021	-1.050	-0.635	0.005
4	A	19	ASN	0	-0.036	0.011	3.491	-1.234	-0.983	0.003	-0.040	-0.214	0.000
5	A	20	PRO	0	-0.011	0.023	6.979	0.131	0.131	0.000	0.000	0.000	0.000
6	A	21	MET	0	-0.016	-0.014	9.820	-0.061	-0.061	0.000	0.000	0.000	0.000
7	A	22	PHE	0	0.028	0.014	12.556	0.015	0.015	0.000	0.000	0.000	0.000
8	A	23	ILE	0	0.043	0.001	15.494	0.016	0.016	0.000	0.000	0.000	0.000
9	A	24	SER	0	-0.015	-0.002	17.455	0.013	0.013	0.000	0.000	0.000	0.000
10	A	25	ASP	-1	-0.843	-0.934	14.142	-0.081	-0.081	0.000	0.000	0.000	0.000
11	A	26	VAL	0	-0.006	-0.003	12.707	0.011	0.011	0.000	0.000	0.000	0.000
12	A	27	HIS	0	-0.020	-0.023	14.373	0.037	0.037	0.000	0.000	0.000	0.000
13	A	28	LYS	1	0.889	0.956	16.143	0.004	0.004	0.000	0.000	0.000	0.000
14	A	29	ILE	0	-0.092	-0.020	10.357	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	30	SER	0	-0.030	-0.003	13.110	0.023	0.023	0.000	0.000	0.000	0.000
16	A	31	PHE	0	0.066	0.003	12.368	0.044	0.044	0.000	0.000	0.000	0.000
17	A	32	HIS	0	0.049	0.015	14.851	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	33	PRO	0	0.052	0.011	16.500	0.026	0.026	0.000	0.000	0.000	0.000
19	A	34	HIS	0	0.011	0.025	17.340	0.049	0.049	0.000	0.000	0.000	0.000
20	A	35	LEU	0	0.009	-0.014	14.636	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	36	GLN	0	0.038	0.031	11.343	0.129	0.129	0.000	0.000	0.000	0.000
22	A	37	ARG	1	0.926	0.983	13.064	-0.363	-0.363	0.000	0.000	0.000	0.000
23	A	38	TYR	0	-0.029	-0.009	9.567	0.042	0.042	0.000	0.000	0.000	0.000
24	A	39	ILE	0	-0.046	-0.033	6.275	0.461	0.461	0.000	0.000	0.000	0.000
25	A	40	GLY	0	0.076	0.048	8.585	-0.196	-0.196	0.000	0.000	0.000	0.000
26	A	41	PHE	0	-0.030	-0.017	8.183	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	42	TRP	0	0.052	0.015	8.800	0.052	0.052	0.000	0.000	0.000	0.000
28	A	43	MET	0	-0.030	-0.016	9.645	-0.161	-0.161	0.000	0.000	0.000	0.000
29	A	44	GLY	0	0.046	0.027	10.751	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	45	PHE	0	-0.027	-0.017	5.759	-0.066	-0.066	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.033	0.036	3.142	0.063	0.325	0.009	-0.062	-0.209	0.000
32	A	47	ILE	0	-0.033	-0.031	3.797	-1.345	-1.059	0.000	-0.098	-0.189	-0.001
33	A	48	ARG	1	0.944	0.958	5.131	-1.809	-1.809	0.000	0.000	0.000	0.000
34	A	49	TRP	0	-0.003	-0.007	4.134	-1.723	-1.411	0.001	-0.112	-0.202	0.001
35	A	50	ILE	0	0.007	-0.001	6.211	-0.089	-0.089	0.000	0.000	0.000	0.000
36	A	51	GLN	0	0.072	0.048	8.977	-0.087	-0.087	0.000	0.000	0.000	0.000
37	A	52	ILE	0	-0.044	-0.009	11.801	-0.075	-0.075	0.000	0.000	0.000	0.000
38	A	53	VAL	0	0.013	-0.025	15.121	0.002	0.002	0.000	0.000	0.000	0.000
39	A	54	GLY	0	0.037	0.029	18.467	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	55	TYR	0	-0.027	-0.020	21.877	0.008	0.008	0.000	0.000	0.000	0.000
41	A	56	ILE	0	-0.031	-0.013	24.930	0.010	0.010	0.000	0.000	0.000	0.000
42	A	57	ALA	0	0.020	0.004	26.413	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	58	ALA	0	-0.005	-0.012	27.630	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	59	ILE	0	0.013	0.004	27.571	0.012	0.012	0.000	0.000	0.000	0.000
45	A	60	ASP	-1	-0.909	-0.940	28.402	0.104	0.104	0.000	0.000	0.000	0.000
46	A	61	ILE	0	-0.009	-0.012	28.682	0.012	0.012	0.000	0.000	0.000	0.000
47	A	62	TYR	0	-0.054	-0.031	28.013	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.918	-0.965	30.093	0.119	0.119	0.000	0.000	0.000	0.000
49	A	64	GLY	0	0.007	0.004	27.701	0.010	0.010	0.000	0.000	0.000	0.000
50	A	65	LYS	1	0.882	0.927	23.955	-0.191	-0.191	0.000	0.000	0.000	0.000
51	A	66	HIS	0	0.068	0.046	24.964	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	67	VAL	0	-0.043	-0.031	23.433	0.025	0.025	0.000	0.000	0.000	0.000
53	A	68	LEU	0	0.025	0.027	22.963	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	69	THR	0	0.013	0.010	22.858	0.023	0.023	0.000	0.000	0.000	0.000
55	A	70	VAL	0	-0.033	-0.015	20.601	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	71	ASP	-1	-0.760	-0.873	22.385	0.058	0.058	0.000	0.000	0.000	0.000
57	A	72	ASP	-1	-0.734	-0.839	18.785	0.050	0.050	0.000	0.000	0.000	0.000
58	A	73	CYS	0	-0.053	-0.024	22.112	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.109	-0.072	20.460	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	75	GLY	0	0.008	-0.004	22.380	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	76	MET	0	-0.051	-0.023	21.249	0.000	0.000	0.000	0.000	0.000	0.000
62	A	77	VAL	0	0.066	0.050	22.310	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	78	LEU	0	-0.017	-0.015	15.928	0.014	0.014	0.000	0.000	0.000	0.000
64	A	79	ARG	1	0.988	1.008	20.534	-0.160	-0.160	0.000	0.000	0.000	0.000
65	A	80	VAL	0	-0.015	-0.010	18.117	0.042	0.042	0.000	0.000	0.000	0.000
66	A	81	VAL	0	-0.007	-0.010	19.255	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.024	-0.003	19.263	0.046	0.046	0.000	0.000	0.000	0.000
68	A	83	ILE	0	0.002	0.000	18.692	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	84	ILE	0	0.023	0.015	22.047	0.002	0.002	0.000	0.000	0.000	0.000
70	A	85	GLN	0	-0.038	-0.030	23.353	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	86	ASP	-1	-0.922	-0.950	18.682	0.319	0.319	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.862	-0.934	19.840	0.195	0.195	0.000	0.000	0.000	0.000
73	A	88	PHE	0	0.026	0.020	21.959	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	89	SER	0	-0.019	-0.006	23.927	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	90	MET	0	-0.020	0.007	17.881	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	91	SER	0	0.019	0.001	22.952	0.000	0.000	0.000	0.000	0.000	0.000
77	A	92	LYS	1	0.961	0.983	24.663	-0.089	-0.089	0.000	0.000	0.000	0.000
78	A	93	ARG	1	0.886	0.926	21.240	-0.129	-0.129	0.000	0.000	0.000	0.000
79	A	94	ALA	0	0.013	0.035	23.815	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	95	ILE	0	-0.023	-0.014	25.672	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	96	SER	0	-0.112	-0.060	28.678	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	97	MET	0	-0.027	0.000	25.939	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	98	SER	0	0.001	-0.002	29.420	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	99	PRO	0	0.002	-0.013	29.950	0.001	0.001	0.000	0.000	0.000	0.000
85	A	100	GLY	0	0.000	0.006	29.392	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	101	ASN	0	-0.005	0.002	27.586	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	102	VAL	0	0.074	0.044	22.928	0.009	0.009	0.000	0.000	0.000	0.000
88	A	103	VAL	0	0.000	0.010	20.708	0.000	0.000	0.000	0.000	0.000	0.000
89	A	104	CYS	0	-0.043	-0.015	16.575	0.007	0.007	0.000	0.000	0.000	0.000
90	A	105	VAL	0	0.020	0.000	15.617	0.011	0.011	0.000	0.000	0.000	0.000
91	A	106	PHE	0	-0.020	-0.005	7.524	0.050	0.050	0.000	0.000	0.000	0.000
92	A	107	GLY	0	0.080	0.022	11.549	-0.058	-0.058	0.000	0.000	0.000	0.000
93	A	108	LYS	1	0.904	0.968	9.840	-0.527	-0.527	0.000	0.000	0.000	0.000
94	A	109	ILE	0	-0.021	0.006	9.274	-0.208	-0.208	0.000	0.000	0.000	0.000
95	A	110	ASN	0	-0.082	-0.056	12.568	0.104	0.104	0.000	0.000	0.000	0.000
96	A	111	SER	0	0.012	-0.002	15.528	-0.043	-0.043	0.000	0.000	0.000	0.000
97	A	112	PHE	0	-0.019	0.000	17.406	-0.036	-0.036	0.000	0.000	0.000	0.000
98	A	113	ARG	1	0.951	0.975	20.213	-0.214	-0.214	0.000	0.000	0.000	0.000
99	A	114	SER	0	0.037	0.007	21.267	0.013	0.013	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.976	-0.966	21.588	0.152	0.152	0.000	0.000	0.000	0.000
101	A	116	VAL	0	-0.048	-0.017	14.966	0.022	0.022	0.000	0.000	0.000	0.000
102	A	117	GLU	-1	-0.843	-0.909	17.419	0.277	0.277	0.000	0.000	0.000	0.000
103	A	118	LEU	0	-0.030	-0.025	12.600	0.081	0.081	0.000	0.000	0.000	0.000
104	A	119	ILE	0	-0.015	0.000	14.744	-0.048	-0.048	0.000	0.000	0.000	0.000
105	A	120	ALA	0	-0.006	-0.008	14.386	0.109	0.109	0.000	0.000	0.000	0.000
106	A	121	GLN	0	-0.062	-0.034	10.116	-0.030	-0.030	0.000	0.000	0.000	0.000
107	A	122	SER	0	0.011	-0.029	14.451	-0.048	-0.048	0.000	0.000	0.000	0.000
108	A	123	PHE	0	-0.001	-0.006	16.313	0.032	0.032	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.930	-0.945	18.746	0.022	0.022	0.000	0.000	0.000	0.000
110	A	125	GLU	-1	-0.815	-0.916	21.388	0.056	0.056	0.000	0.000	0.000	0.000
111	A	126	LEU	0	-0.066	-0.036	20.121	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	127	ARG	1	0.899	0.933	24.381	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	128	ASP	-1	-0.818	-0.883	26.412	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	129	PRO	0	0.017	-0.007	26.636	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	130	ASN	0	-0.053	-0.022	26.749	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	131	ASP	-1	-0.885	-0.952	22.313	-0.034	-0.034	0.000	0.000	0.000	0.000
117	A	132	GLU	-1	-0.867	-0.948	21.647	0.009	0.009	0.000	0.000	0.000	0.000
118	A	133	TRP	0	0.009	0.002	21.836	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	134	LYS	1	0.941	0.980	20.719	0.060	0.060	0.000	0.000	0.000	0.000
120	A	135	ALA	0	-0.016	-0.001	17.761	-0.029	-0.029	0.000	0.000	0.000	0.000
121	A	136	TRP	0	0.082	0.034	17.345	-0.028	-0.028	0.000	0.000	0.000	0.000
122	A	137	GLN	0	-0.007	-0.002	18.784	-0.019	-0.019	0.000	0.000	0.000	0.000
123	A	138	LYS	1	0.874	0.936	12.946	0.145	0.145	0.000	0.000	0.000	0.000
124	A	139	ARG	1	0.816	0.901	13.861	-0.079	-0.079	0.000	0.000	0.000	0.000
125	A	140	MET	0	0.018	0.017	14.921	-0.033	-0.033	0.000	0.000	0.000	0.000
126	A	141	ARG	1	0.916	0.962	15.379	0.285	0.285	0.000	0.000	0.000	0.000
127	A	142	TYR	0	-0.038	-0.056	5.790	-0.160	-0.160	0.000	0.000	0.000	0.000
128	A	143	LYS	1	0.933	0.963	12.202	0.047	0.047	0.000	0.000	0.000	0.000
129	A	144	LYS	1	0.938	0.980	13.820	0.158	0.158	0.000	0.000	0.000	0.000
130	A	145	ASN	0	-0.025	-0.019	12.415	0.036	0.036	0.000	0.000	0.000	0.000
131	A	146	LEU	0	0.018	0.020	7.626	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	147	THR	0	0.019	-0.013	11.575	0.026	0.026	0.000	0.000	0.000	0.000
133	A	148	LYS	1	0.902	0.948	14.805	0.301	0.301	0.000	0.000	0.000	0.000
134	A	149	ILE	0	0.018	0.016	10.031	0.027	0.027	0.000	0.000	0.000	0.000
135	A	150	SER	0	-0.020	-0.003	12.229	0.052	0.052	0.000	0.000	0.000	0.000
136	A	151	LYS	1	0.946	0.953	13.387	0.250	0.250	0.000	0.000	0.000	0.000
137	A	152	ASN	0	-0.044	-0.016	16.032	0.056	0.056	0.000	0.000	0.000	0.000
138	A	153	HIS	0	-0.024	0.001	11.993	0.010	0.010	0.000	0.000	0.000	0.000
139	A	154	HIS	0	-0.030	0.011	12.367	0.079	0.079	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)