FMO DATABASE

FMODB ID: 4351N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1362163.613736
FMO2-HF: Nuclear repulsion	1304130.9836
FMO2-HF: Total energy	-58032.630136
FMO2-MP2: Total energy	-58199.737737

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.
-3.813	-1.055	0.055	-1.256	-1.557	0.006

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 : 0.029 / q_NPA : 0.003

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	0.028	3.880	1.891	3.347	-0.015	-0.811	-0.629	0.002
4	A	19	ASN	0	-0.008	-0.008	3.759	-1.927	-1.742	-0.001	-0.021	-0.163	0.000
5	A	20	PRO	0	-0.010	0.020	7.335	0.067	0.067	0.000	0.000	0.000	0.000
6	A	21	MET	0	-0.018	-0.007	10.138	-0.063	-0.063	0.000	0.000	0.000	0.000
7	A	22	PHE	0	0.033	0.016	12.819	0.007	0.007	0.000	0.000	0.000	0.000
8	A	23	ILE	0	0.038	0.017	15.986	0.035	0.035	0.000	0.000	0.000	0.000
9	A	24	SER	0	-0.023	-0.020	17.914	0.019	0.019	0.000	0.000	0.000	0.000
10	A	25	ASP	-1	-0.817	-0.905	14.621	0.007	0.007	0.000	0.000	0.000	0.000
11	A	26	VAL	0	0.015	0.002	13.118	0.023	0.023	0.000	0.000	0.000	0.000
12	A	27	HIS	0	-0.019	-0.018	14.829	0.029	0.029	0.000	0.000	0.000	0.000
13	A	28	LYS	1	0.798	0.898	16.407	-0.100	-0.100	0.000	0.000	0.000	0.000
14	A	29	ILE	0	-0.094	-0.027	10.932	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	30	SER	0	-0.023	-0.006	13.683	0.007	0.007	0.000	0.000	0.000	0.000
16	A	31	PHE	0	0.069	0.008	12.479	0.061	0.061	0.000	0.000	0.000	0.000
17	A	32	HIS	0	0.067	0.024	14.620	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	33	PRO	0	0.038	0.015	16.269	0.024	0.024	0.000	0.000	0.000	0.000
19	A	34	HIS	0	0.009	0.015	17.817	0.037	0.037	0.000	0.000	0.000	0.000
20	A	35	LEU	0	0.020	-0.004	14.866	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	36	GLN	0	0.019	0.032	11.623	0.065	0.065	0.000	0.000	0.000	0.000
22	A	37	ARG	1	0.914	0.962	13.193	-0.317	-0.317	0.000	0.000	0.000	0.000
23	A	38	TYR	0	-0.012	-0.013	9.911	0.038	0.038	0.000	0.000	0.000	0.000
24	A	39	ILE	0	-0.036	-0.011	6.612	0.430	0.430	0.000	0.000	0.000	0.000
25	A	40	GLY	0	0.071	0.042	8.936	-0.172	-0.172	0.000	0.000	0.000	0.000
26	A	41	PHE	0	-0.028	-0.015	8.503	0.019	0.019	0.000	0.000	0.000	0.000
27	A	42	TRP	0	0.050	0.025	9.516	0.035	0.035	0.000	0.000	0.000	0.000
28	A	43	MET	0	-0.043	-0.026	10.478	-0.147	-0.147	0.000	0.000	0.000	0.000
29	A	44	GLY	0	0.066	0.053	11.404	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	45	PHE	0	-0.014	-0.007	6.308	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.019	0.023	3.533	0.203	0.359	0.000	-0.028	-0.128	0.000
32	A	47	ILE	0	-0.035	-0.027	4.521	-0.575	-0.476	-0.001	-0.008	-0.090	0.000
33	A	48	ARG	1	0.947	0.940	5.064	-1.727	-1.727	0.000	0.000	0.000	0.000
34	A	49	TRP	0	0.004	0.014	3.065	-2.426	-1.564	0.072	-0.388	-0.547	0.004
35	A	50	ILE	0	0.028	0.003	6.551	0.244	0.244	0.000	0.000	0.000	0.000
36	A	51	GLN	0	0.046	0.042	9.359	-0.197	-0.197	0.000	0.000	0.000	0.000
37	A	52	ILE	0	-0.019	0.000	12.111	-0.064	-0.064	0.000	0.000	0.000	0.000
38	A	53	VAL	0	-0.011	-0.038	15.477	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	54	GLY	0	0.039	0.037	18.726	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	55	TYR	0	-0.044	-0.033	22.243	0.004	0.004	0.000	0.000	0.000	0.000
41	A	56	ILE	0	-0.006	-0.007	24.775	0.015	0.015	0.000	0.000	0.000	0.000
42	A	57	ALA	0	0.028	0.013	26.454	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	58	ALA	0	0.005	-0.006	27.713	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	59	ILE	0	-0.011	-0.009	27.416	0.016	0.016	0.000	0.000	0.000	0.000
45	A	60	ASP	-1	-0.759	-0.832	27.620	0.145	0.145	0.000	0.000	0.000	0.000
46	A	61	ILE	0	-0.027	-0.029	27.792	0.012	0.012	0.000	0.000	0.000	0.000
47	A	62	TYR	0	-0.083	-0.053	26.869	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.915	-0.957	29.039	0.139	0.139	0.000	0.000	0.000	0.000
49	A	64	GLY	0	0.007	0.010	26.742	0.012	0.012	0.000	0.000	0.000	0.000
50	A	65	LYS	1	0.796	0.887	21.400	-0.271	-0.271	0.000	0.000	0.000	0.000
51	A	66	HIS	0	0.093	0.051	24.270	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	67	VAL	0	-0.046	-0.043	22.527	0.032	0.032	0.000	0.000	0.000	0.000
53	A	68	LEU	0	0.009	0.032	22.121	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	69	THR	0	0.008	0.002	22.755	0.028	0.028	0.000	0.000	0.000	0.000
55	A	70	VAL	0	-0.032	-0.019	20.977	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	71	ASP	-1	-0.762	-0.875	23.030	0.111	0.111	0.000	0.000	0.000	0.000
57	A	72	ASP	-1	-0.707	-0.818	19.198	0.135	0.135	0.000	0.000	0.000	0.000
58	A	73	CYS	0	-0.029	-0.008	22.633	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.103	-0.071	20.606	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	75	GLY	0	0.024	0.013	22.543	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	76	MET	0	-0.056	-0.025	21.691	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	77	VAL	0	0.066	0.045	23.112	0.000	0.000	0.000	0.000	0.000	0.000
63	A	78	LEU	0	-0.021	-0.013	16.336	0.019	0.019	0.000	0.000	0.000	0.000
64	A	79	ARG	1	0.904	0.955	21.036	-0.199	-0.199	0.000	0.000	0.000	0.000
65	A	80	VAL	0	-0.015	-0.015	17.357	0.055	0.055	0.000	0.000	0.000	0.000
66	A	81	VAL	0	-0.029	-0.013	18.398	-0.038	-0.038	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.023	-0.016	18.415	0.051	0.051	0.000	0.000	0.000	0.000
68	A	83	ILE	0	0.002	0.008	18.459	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	84	ILE	0	0.005	-0.006	21.533	0.002	0.002	0.000	0.000	0.000	0.000
70	A	85	GLN	0	-0.057	-0.040	21.733	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	86	ASP	-1	-0.892	-0.935	18.286	0.339	0.339	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.825	-0.924	19.133	0.218	0.218	0.000	0.000	0.000	0.000
73	A	88	PHE	0	0.039	0.037	21.125	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	89	SER	0	-0.029	-0.003	23.165	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	90	MET	0	-0.028	-0.002	16.731	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	91	SER	0	0.010	-0.010	22.029	0.003	0.003	0.000	0.000	0.000	0.000
77	A	92	LYS	1	0.949	0.973	23.835	-0.109	-0.109	0.000	0.000	0.000	0.000
78	A	93	ARG	1	0.847	0.912	20.562	-0.169	-0.169	0.000	0.000	0.000	0.000
79	A	94	ALA	0	-0.002	0.019	22.941	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	95	ILE	0	-0.015	-0.014	24.850	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	96	SER	0	-0.087	-0.043	27.824	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	97	MET	0	-0.042	-0.003	25.410	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	98	SER	0	0.005	-0.008	28.881	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	99	PRO	0	-0.013	-0.017	29.765	0.004	0.004	0.000	0.000	0.000	0.000
85	A	100	GLY	0	0.004	0.016	29.746	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	101	ASN	0	-0.031	-0.022	27.649	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	102	VAL	0	0.040	0.023	23.760	0.013	0.013	0.000	0.000	0.000	0.000
88	A	103	VAL	0	-0.001	0.000	21.239	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	104	CYS	0	-0.101	-0.058	16.772	0.019	0.019	0.000	0.000	0.000	0.000
90	A	105	VAL	0	0.042	0.013	15.554	0.000	0.000	0.000	0.000	0.000	0.000
91	A	106	PHE	0	-0.033	-0.011	6.768	0.072	0.072	0.000	0.000	0.000	0.000
92	A	107	GLY	0	0.071	0.023	10.987	-0.115	-0.115	0.000	0.000	0.000	0.000
93	A	108	LYS	1	0.811	0.920	9.429	-0.364	-0.364	0.000	0.000	0.000	0.000
94	A	109	ILE	0	-0.006	0.006	9.975	-0.224	-0.224	0.000	0.000	0.000	0.000
95	A	110	ASN	0	-0.057	-0.039	12.515	0.050	0.050	0.000	0.000	0.000	0.000
96	A	111	SER	0	0.041	0.022	15.207	-0.036	-0.036	0.000	0.000	0.000	0.000
97	A	112	PHE	0	-0.025	-0.003	17.450	-0.044	-0.044	0.000	0.000	0.000	0.000
98	A	113	ARG	1	0.883	0.937	20.207	-0.256	-0.256	0.000	0.000	0.000	0.000
99	A	114	SER	0	0.057	0.021	21.062	0.020	0.020	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.941	-0.951	22.160	0.199	0.199	0.000	0.000	0.000	0.000
101	A	116	VAL	0	-0.043	-0.021	15.447	0.023	0.023	0.000	0.000	0.000	0.000
102	A	117	GLU	-1	-0.756	-0.868	17.882	0.315	0.315	0.000	0.000	0.000	0.000
103	A	118	LEU	0	-0.027	-0.027	12.202	0.092	0.092	0.000	0.000	0.000	0.000
104	A	119	ILE	0	0.003	0.004	14.343	-0.055	-0.055	0.000	0.000	0.000	0.000
105	A	120	ALA	0	0.032	0.030	13.567	0.142	0.142	0.000	0.000	0.000	0.000
106	A	121	GLN	0	-0.067	-0.049	9.778	0.132	0.132	0.000	0.000	0.000	0.000
107	A	122	SER	0	0.016	-0.007	13.681	-0.044	-0.044	0.000	0.000	0.000	0.000
108	A	123	PHE	0	0.035	0.006	15.443	0.043	0.043	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.882	-0.905	17.714	0.090	0.090	0.000	0.000	0.000	0.000
110	A	125	GLU	-1	-0.772	-0.876	20.618	0.093	0.093	0.000	0.000	0.000	0.000
111	A	126	LEU	0	-0.068	-0.029	20.593	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	127	ARG	1	0.911	0.926	24.428	-0.061	-0.061	0.000	0.000	0.000	0.000
113	A	128	ASP	-1	-0.752	-0.831	26.931	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	129	PRO	0	0.024	0.001	27.173	0.003	0.003	0.000	0.000	0.000	0.000
115	A	130	ASN	0	-0.043	-0.032	27.015	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	131	ASP	-1	-0.832	-0.920	22.930	0.009	0.009	0.000	0.000	0.000	0.000
117	A	132	GLU	-1	-0.820	-0.919	21.931	0.070	0.070	0.000	0.000	0.000	0.000
118	A	133	TRP	0	0.008	0.011	21.922	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	134	LYS	1	0.793	0.878	20.738	0.003	0.003	0.000	0.000	0.000	0.000
120	A	135	ALA	0	-0.023	-0.007	17.848	-0.021	-0.021	0.000	0.000	0.000	0.000
121	A	136	TRP	0	0.045	0.014	17.420	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	137	GLN	0	-0.009	-0.002	18.748	-0.019	-0.019	0.000	0.000	0.000	0.000
123	A	138	LYS	1	0.807	0.906	13.095	-0.023	-0.023	0.000	0.000	0.000	0.000
124	A	139	ARG	1	0.811	0.897	14.033	-0.220	-0.220	0.000	0.000	0.000	0.000
125	A	140	MET	0	0.006	0.000	14.859	-0.040	-0.040	0.000	0.000	0.000	0.000
126	A	141	ARG	1	0.930	0.966	15.887	0.241	0.241	0.000	0.000	0.000	0.000
127	A	142	TYR	0	-0.013	-0.021	5.686	-0.275	-0.275	0.000	0.000	0.000	0.000
128	A	143	LYS	1	0.919	0.946	12.362	-0.034	-0.034	0.000	0.000	0.000	0.000
129	A	144	LYS	1	0.959	0.986	13.745	0.100	0.100	0.000	0.000	0.000	0.000
130	A	145	ASN	0	0.002	0.001	13.360	0.048	0.048	0.000	0.000	0.000	0.000
131	A	146	LEU	0	0.038	0.026	7.818	-0.015	-0.015	0.000	0.000	0.000	0.000
132	A	147	THR	0	-0.006	-0.028	11.904	0.019	0.019	0.000	0.000	0.000	0.000
133	A	148	LYS	1	0.857	0.934	15.363	0.319	0.319	0.000	0.000	0.000	0.000
134	A	149	ILE	0	0.022	0.009	10.419	0.016	0.016	0.000	0.000	0.000	0.000
135	A	150	SER	0	-0.022	-0.014	13.054	0.025	0.025	0.000	0.000	0.000	0.000
136	A	151	LYS	1	0.943	0.960	14.018	0.221	0.221	0.000	0.000	0.000	0.000
137	A	152	ASN	0	-0.030	-0.011	16.346	0.054	0.054	0.000	0.000	0.000	0.000
138	A	153	HIS	0	-0.035	0.009	13.084	-0.041	-0.041	0.000	0.000	0.000	0.000
139	A	154	HIS	0	-0.019	-0.004	12.317	0.086	0.086	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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