FMO DATABASE

FMODB ID: VR881

Calculation Name: 3KF6-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	141
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1371141.724443
FMO2-HF: Nuclear repulsion	1312939.197341
FMO2-HF: Total energy	-58202.527102
FMO2-MP2: Total energy	-58370.217385

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:15:ACE )

Summations of interaction energy for fragment #1(A:15:ACE )

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.
-1.621	-0.193	0.133	-0.649	-0.911	0

Interaction energy analysis for fragmet #1(A:15:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.006

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].
3	A	17	ARG	1	0.961	1.006	3.858	1.172	1.970	-0.005	-0.397	-0.396
4	A	18	TRP	0	0.074	0.002	5.822	0.320	0.320	0.000	0.000	0.000
5	A	19	ASN	0	-0.037	0.011	6.263	-0.046	-0.046	0.000	0.000	0.000
6	A	20	PRO	0	-0.015	0.022	9.870	0.068	0.068	0.000	0.000	0.000
7	A	21	MET	0	-0.009	-0.013	12.013	-0.030	-0.030	0.000	0.000	0.000
8	A	22	PHE	0	0.028	0.014	14.957	0.012	0.012	0.000	0.000	0.000
9	A	23	ILE	0	0.045	0.001	17.299	0.003	0.003	0.000	0.000	0.000
10	A	24	SER	0	-0.018	-0.002	18.624	0.005	0.005	0.000	0.000	0.000
11	A	25	ASP	-1	-0.842	-0.933	16.377	-0.042	-0.042	0.000	0.000	0.000
12	A	26	VAL	0	-0.009	-0.005	13.656	0.000	0.000	0.000	0.000	0.000
13	A	27	HIS	0	-0.022	-0.024	15.356	0.017	0.017	0.000	0.000	0.000
14	A	28	LYS	1	0.893	0.958	17.219	0.006	0.006	0.000	0.000	0.000
15	A	29	ILE	0	-0.093	-0.021	10.867	-0.020	-0.020	0.000	0.000	0.000
16	A	30	SER	0	-0.020	0.001	14.256	0.017	0.017	0.000	0.000	0.000
17	A	31	PHE	0	0.032	-0.016	10.692	0.011	0.011	0.000	0.000	0.000
18	A	32	HIS	0	0.063	0.017	14.204	-0.011	-0.011	0.000	0.000	0.000
19	A	33	PRO	0	-0.010	-0.021	15.451	0.016	0.016	0.000	0.000	0.000
20	A	34	HIS	0	0.017	0.033	15.567	0.042	0.042	0.000	0.000	0.000
21	A	35	LEU	0	0.078	0.048	10.714	-0.019	-0.019	0.000	0.000	0.000
22	A	36	GLN	0	-0.059	-0.036	10.161	0.076	0.076	0.000	0.000	0.000
23	A	37	ARG	1	0.911	0.962	11.963	-0.339	-0.339	0.000	0.000	0.000
24	A	38	TYR	0	-0.050	-0.021	7.369	0.092	0.092	0.000	0.000	0.000
25	A	39	ILE	0	-0.029	-0.014	4.988	0.396	0.396	0.000	0.000	0.000
26	A	40	GLY	0	0.082	0.045	7.514	-0.099	-0.099	0.000	0.000	0.000
27	A	41	PHE	0	-0.012	-0.012	8.956	-0.073	-0.073	0.000	0.000	0.000
28	A	42	TRP	0	0.058	0.018	11.268	0.033	0.033	0.000	0.000	0.000
29	A	43	MET	0	-0.037	-0.017	12.952	-0.051	-0.051	0.000	0.000	0.000
30	A	44	GLY	0	0.065	0.036	14.209	-0.019	-0.019	0.000	0.000	0.000
31	A	45	PHE	0	-0.026	-0.016	9.886	-0.050	-0.050	0.000	0.000	0.000
32	A	46	PRO	0	0.031	0.033	6.177	0.139	0.139	0.000	0.000	0.000
33	A	47	ILE	0	-0.024	-0.023	5.980	-0.256	-0.256	0.000	0.000	0.000
34	A	48	ARG	1	0.935	0.952	3.234	-2.261	-1.944	0.049	-0.123	-0.242
35	A	49	TRP	0	-0.010	-0.010	3.017	-0.705	-0.392	0.089	-0.129	-0.273
36	A	50	ILE	0	0.011	0.001	6.197	-0.305	-0.305	0.000	0.000	0.000
37	A	51	GLN	0	0.073	0.047	9.653	0.018	0.018	0.000	0.000	0.000
38	A	52	ILE	0	-0.039	-0.006	12.923	-0.042	-0.042	0.000	0.000	0.000
39	A	53	VAL	0	0.009	-0.025	16.334	0.007	0.007	0.000	0.000	0.000
40	A	54	GLY	0	0.032	0.026	19.875	-0.009	-0.009	0.000	0.000	0.000
41	A	55	TYR	0	-0.018	-0.018	23.094	0.006	0.006	0.000	0.000	0.000
42	A	56	ILE	0	-0.034	-0.014	24.853	0.005	0.005	0.000	0.000	0.000
43	A	57	ALA	0	0.024	0.006	26.580	-0.006	-0.006	0.000	0.000	0.000
44	A	58	ALA	0	-0.008	-0.012	27.433	-0.003	-0.003	0.000	0.000	0.000
45	A	59	ILE	0	0.015	0.005	26.986	0.008	0.008	0.000	0.000	0.000
46	A	60	ASP	-1	-0.909	-0.940	27.145	0.078	0.078	0.000	0.000	0.000
47	A	61	ILE	0	-0.010	-0.012	27.133	0.010	0.010	0.000	0.000	0.000
48	A	62	TYR	0	-0.055	-0.032	26.100	-0.002	-0.002	0.000	0.000	0.000
49	A	63	GLU	-1	-0.916	-0.964	28.190	0.100	0.100	0.000	0.000	0.000
50	A	64	GLY	0	0.005	0.003	25.766	0.008	0.008	0.000	0.000	0.000
51	A	65	LYS	1	0.882	0.927	21.972	-0.145	-0.145	0.000	0.000	0.000
52	A	66	HIS	0	0.067	0.046	23.333	-0.014	-0.014	0.000	0.000	0.000
53	A	67	VAL	0	-0.043	-0.031	22.081	0.018	0.018	0.000	0.000	0.000
54	A	68	LEU	0	0.028	0.027	22.208	-0.012	-0.012	0.000	0.000	0.000
55	A	69	THR	0	0.012	0.010	22.190	0.012	0.012	0.000	0.000	0.000
56	A	70	VAL	0	-0.034	-0.015	20.996	-0.008	-0.008	0.000	0.000	0.000
57	A	71	ASP	-1	-0.761	-0.874	22.875	0.037	0.037	0.000	0.000	0.000
58	A	72	ASP	-1	-0.735	-0.839	20.546	0.027	0.027	0.000	0.000	0.000
59	A	73	CYS	0	-0.051	-0.023	23.685	-0.009	-0.009	0.000	0.000	0.000
60	A	74	SER	0	-0.112	-0.072	22.197	-0.006	-0.006	0.000	0.000	0.000
61	A	75	GLY	0	0.014	-0.001	24.355	-0.004	-0.004	0.000	0.000	0.000
62	A	76	MET	0	-0.055	-0.025	22.316	0.000	0.000	0.000	0.000	0.000
63	A	77	VAL	0	0.063	0.049	23.210	-0.001	-0.001	0.000	0.000	0.000
64	A	78	LEU	0	-0.017	-0.015	15.803	0.006	0.006	0.000	0.000	0.000
65	A	79	ARG	1	0.991	1.009	20.320	-0.109	-0.109	0.000	0.000	0.000
66	A	80	VAL	0	-0.015	-0.010	17.145	0.025	0.025	0.000	0.000	0.000
67	A	81	VAL	0	-0.006	-0.010	17.700	-0.016	-0.016	0.000	0.000	0.000
68	A	82	PHE	0	0.018	-0.006	17.695	0.035	0.035	0.000	0.000	0.000
69	A	83	ILE	0	0.008	0.001	16.818	-0.022	-0.022	0.000	0.000	0.000
70	A	84	ILE	0	0.021	0.015	20.363	0.006	0.006	0.000	0.000	0.000
71	A	85	GLN	0	-0.038	-0.029	21.712	-0.007	-0.007	0.000	0.000	0.000
72	A	86	ASP	-1	-0.921	-0.949	17.053	0.308	0.308	0.000	0.000	0.000
73	A	87	ASP	-1	-0.863	-0.935	18.753	0.193	0.193	0.000	0.000	0.000
74	A	88	PHE	0	0.028	0.021	20.823	-0.012	-0.012	0.000	0.000	0.000
75	A	89	SER	0	-0.019	-0.005	23.165	-0.012	-0.012	0.000	0.000	0.000
76	A	90	MET	0	-0.019	0.007	16.954	-0.015	-0.015	0.000	0.000	0.000
77	A	91	SER	0	0.017	0.000	22.275	-0.005	-0.005	0.000	0.000	0.000
78	A	92	LYS	1	0.963	0.984	23.654	-0.087	-0.087	0.000	0.000	0.000
79	A	93	ARG	1	0.886	0.927	20.974	-0.119	-0.119	0.000	0.000	0.000
80	A	94	ALA	0	0.011	0.034	22.890	-0.008	-0.008	0.000	0.000	0.000
81	A	95	ILE	0	-0.023	-0.014	24.822	-0.006	-0.006	0.000	0.000	0.000
82	A	96	SER	0	-0.107	-0.059	28.091	-0.008	-0.008	0.000	0.000	0.000
83	A	97	MET	0	-0.029	-0.001	25.500	-0.006	-0.006	0.000	0.000	0.000
84	A	98	SER	0	0.000	-0.003	28.939	-0.002	-0.002	0.000	0.000	0.000
85	A	99	PRO	0	0.001	-0.012	29.991	0.000	0.000	0.000	0.000	0.000
86	A	100	GLY	0	0.001	0.007	29.774	-0.004	-0.004	0.000	0.000	0.000
87	A	101	ASN	0	-0.005	0.002	27.932	0.001	0.001	0.000	0.000	0.000
88	A	102	VAL	0	0.075	0.044	24.149	0.005	0.005	0.000	0.000	0.000
89	A	103	VAL	0	0.001	0.010	21.073	0.003	0.003	0.000	0.000	0.000
90	A	104	CYS	0	-0.046	-0.016	17.742	-0.003	-0.003	0.000	0.000	0.000
91	A	105	VAL	0	0.025	0.003	15.100	0.014	0.014	0.000	0.000	0.000
92	A	106	PHE	0	-0.022	-0.007	7.677	-0.015	-0.015	0.000	0.000	0.000
93	A	107	GLY	0	0.073	0.020	11.052	0.010	0.010	0.000	0.000	0.000
94	A	108	LYS	1	0.902	0.966	7.962	-0.635	-0.635	0.000	0.000	0.000
95	A	109	ILE	0	-0.011	0.011	8.604	-0.111	-0.111	0.000	0.000	0.000
96	A	110	ASN	0	-0.075	-0.049	10.685	0.116	0.116	0.000	0.000	0.000
97	A	111	SER	0	0.059	0.029	13.473	-0.031	-0.031	0.000	0.000	0.000
98	A	112	PHE	0	-0.039	-0.012	15.510	-0.023	-0.023	0.000	0.000	0.000
99	A	113	ARG	1	0.968	0.983	18.128	-0.153	-0.153	0.000	0.000	0.000
100	A	114	SER	0	0.038	0.008	19.589	0.007	0.007	0.000	0.000	0.000
101	A	115	GLU	-1	-0.971	-0.963	20.794	0.094	0.094	0.000	0.000	0.000
102	A	116	VAL	0	-0.056	-0.021	14.247	0.018	0.018	0.000	0.000	0.000
103	A	117	GLU	-1	-0.836	-0.905	15.973	0.205	0.205	0.000	0.000	0.000
104	A	118	LEU	0	-0.032	-0.026	11.906	0.045	0.045	0.000	0.000	0.000
105	A	119	ILE	0	-0.013	0.001	12.840	-0.018	-0.018	0.000	0.000	0.000
106	A	120	ALA	0	-0.003	-0.006	12.875	0.070	0.070	0.000	0.000	0.000
107	A	121	GLN	0	-0.063	-0.035	9.129	-0.034	-0.034	0.000	0.000	0.000
108	A	122	SER	0	0.005	-0.028	13.757	-0.045	-0.045	0.000	0.000	0.000
109	A	123	PHE	0	0.004	-0.006	15.925	0.008	0.008	0.000	0.000	0.000
110	A	124	GLU	-1	-0.931	-0.944	18.529	0.048	0.048	0.000	0.000	0.000
111	A	125	GLU	-1	-0.814	-0.916	21.528	0.051	0.051	0.000	0.000	0.000
112	A	126	LEU	0	-0.071	-0.038	21.648	-0.005	-0.005	0.000	0.000	0.000
113	A	127	ARG	1	0.905	0.935	25.485	-0.042	-0.042	0.000	0.000	0.000
114	A	128	ASP	-1	-0.818	-0.884	28.174	-0.001	-0.001	0.000	0.000	0.000
115	A	129	PRO	0	0.017	-0.006	28.517	-0.001	-0.001	0.000	0.000	0.000
116	A	130	ASN	0	-0.051	-0.022	29.313	-0.005	-0.005	0.000	0.000	0.000
117	A	131	ASP	-1	-0.886	-0.952	24.256	0.003	0.003	0.000	0.000	0.000
118	A	132	GLU	-1	-0.870	-0.950	24.005	0.018	0.018	0.000	0.000	0.000
119	A	133	TRP	0	0.011	0.002	24.387	-0.009	-0.009	0.000	0.000	0.000
120	A	134	LYS	1	0.944	0.981	23.654	0.013	0.013	0.000	0.000	0.000
121	A	135	ALA	0	-0.018	-0.002	20.299	-0.014	-0.014	0.000	0.000	0.000
122	A	136	TRP	0	0.083	0.035	20.270	-0.016	-0.016	0.000	0.000	0.000
123	A	137	GLN	0	-0.005	-0.001	22.104	-0.009	-0.009	0.000	0.000	0.000
124	A	138	LYS	1	0.876	0.936	16.079	0.048	0.048	0.000	0.000	0.000
125	A	139	ARG	1	0.813	0.900	15.760	-0.029	-0.029	0.000	0.000	0.000
126	A	140	MET	0	0.018	0.016	18.474	-0.015	-0.015	0.000	0.000	0.000
127	A	141	ARG	1	0.917	0.963	19.986	0.118	0.118	0.000	0.000	0.000
128	A	142	TYR	0	-0.037	-0.055	9.793	-0.038	-0.038	0.000	0.000	0.000
129	A	143	LYS	1	0.932	0.962	16.409	0.031	0.031	0.000	0.000	0.000
130	A	144	LYS	1	0.940	0.981	17.674	0.071	0.071	0.000	0.000	0.000
131	A	145	ASN	0	-0.022	-0.018	17.401	0.007	0.007	0.000	0.000	0.000
132	A	146	LEU	0	0.015	0.019	11.819	-0.008	-0.008	0.000	0.000	0.000
133	A	147	THR	0	0.022	-0.012	16.009	0.005	0.005	0.000	0.000	0.000
134	A	148	LYS	1	0.903	0.949	19.060	0.136	0.136	0.000	0.000	0.000
135	A	149	ILE	0	0.021	0.018	15.296	0.007	0.007	0.000	0.000	0.000
136	A	150	SER	0	-0.015	0.000	16.638	0.009	0.009	0.000	0.000	0.000
137	A	151	LYS	1	0.944	0.950	18.023	0.117	0.117	0.000	0.000	0.000
138	A	152	ASN	0	-0.028	-0.013	21.013	0.023	0.023	0.000	0.000	0.000
139	A	153	HIS	0	-0.022	0.000	16.405	0.008	0.008	0.000	0.000	0.000
140	A	154	HIS	0	-0.064	-0.006	16.434	0.010	0.010	0.000	0.000	0.000
141	A	155	NME	0	0.002	0.009	21.541	0.013	0.013	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ACE )