FMO DATABASE

FMODB ID: 43RNN

Calculation Name: 3KF8-B-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF8

Chain ID: B

ChEMBL ID:

UniProt ID: C5M4J8

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	122
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-970565.182976
FMO2-HF: Nuclear repulsion	923443.984297
FMO2-HF: Total energy	-47121.19868
FMO2-MP2: Total energy	-47258.309888

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:1:ACE )

Summations of interaction energy for fragment #1(B:1: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.
0.604	3.203	4.271	-3.854	-3.015	-0.024

Interaction energy analysis for fragmet #1(B:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.039

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	3	LYS	1	0.968	1.000	3.837	0.046	0.949	-0.005	-0.424	-0.474	0.000
4	B	4	ILE	0	-0.028	-0.001	6.537	-0.146	-0.146	0.000	0.000	0.000	0.000
5	B	5	ILE	0	0.002	0.000	7.620	0.105	0.105	0.000	0.000	0.000	0.000
6	B	6	LEU	0	0.032	0.003	11.357	-0.002	-0.002	0.000	0.000	0.000	0.000
7	B	7	ILE	0	0.003	-0.001	14.015	0.007	0.007	0.000	0.000	0.000	0.000
8	B	8	PRO	0	0.024	-0.002	14.062	0.008	0.008	0.000	0.000	0.000	0.000
9	B	9	SER	0	0.021	0.006	14.189	-0.003	-0.003	0.000	0.000	0.000	0.000
10	B	10	ASN	0	-0.007	-0.005	13.057	0.013	0.013	0.000	0.000	0.000	0.000
11	B	11	ILE	0	-0.005	0.007	9.250	0.037	0.037	0.000	0.000	0.000	0.000
12	B	12	PRO	0	-0.004	-0.008	9.715	0.050	0.050	0.000	0.000	0.000	0.000
13	B	13	GLN	0	-0.028	-0.022	11.313	0.040	0.040	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.961	-0.972	7.595	0.316	0.316	0.000	0.000	0.000	0.000
15	B	15	PHE	0	-0.062	-0.042	2.986	-0.266	0.043	0.068	-0.168	-0.209	0.000
16	B	16	PRO	0	0.008	0.005	7.388	-0.097	-0.097	0.000	0.000	0.000	0.000
17	B	17	GLU	-1	-0.925	-0.973	8.581	0.435	0.435	0.000	0.000	0.000	0.000
18	B	18	ALA	0	-0.052	0.012	7.445	-0.020	-0.020	0.000	0.000	0.000	0.000
19	B	19	SER	0	0.017	-0.019	8.738	-0.044	-0.044	0.000	0.000	0.000	0.000
20	B	20	ILE	0	0.039	-0.001	10.951	-0.044	-0.044	0.000	0.000	0.000	0.000
21	B	21	SER	0	-0.077	-0.039	12.902	-0.030	-0.030	0.000	0.000	0.000	0.000
22	B	22	ASN	0	-0.076	-0.034	7.855	-0.022	-0.022	0.000	0.000	0.000	0.000
23	B	23	PRO	0	0.005	0.026	7.928	0.074	0.074	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.854	-0.933	2.548	-0.090	1.239	4.208	-3.249	-2.288	-0.024
25	B	25	ARG	1	0.792	0.896	4.666	1.153	1.211	0.000	-0.013	-0.044	0.000
26	B	26	LEU	0	-0.002	0.002	5.134	-0.519	-0.519	0.000	0.000	0.000	0.000
27	B	27	ARG	1	0.910	0.964	7.666	0.558	0.558	0.000	0.000	0.000	0.000
28	B	28	ILE	0	-0.021	0.002	10.702	0.045	0.045	0.000	0.000	0.000	0.000
29	B	29	LEU	0	0.002	0.019	13.238	0.014	0.014	0.000	0.000	0.000	0.000
30	B	30	ALA	0	0.000	-0.006	16.376	0.021	0.021	0.000	0.000	0.000	0.000
31	B	31	GLN	0	0.013	0.006	18.939	0.004	0.004	0.000	0.000	0.000	0.000
32	B	32	VAL	0	0.005	0.018	22.564	0.003	0.003	0.000	0.000	0.000	0.000
33	B	33	LYS	1	0.827	0.904	24.179	0.062	0.062	0.000	0.000	0.000	0.000
34	B	34	ASP	-1	-0.866	-0.935	26.002	-0.047	-0.047	0.000	0.000	0.000	0.000
35	B	35	PHE	0	-0.012	-0.014	26.188	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	36	ILE	0	0.026	0.014	27.304	0.006	0.006	0.000	0.000	0.000	0.000
37	B	37	PRO	0	0.007	-0.007	28.910	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	38	HIS	0	-0.024	-0.012	31.071	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.912	-0.961	27.715	-0.046	-0.046	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.048	-0.005	26.348	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	41	THR	0	0.002	-0.006	22.965	-0.011	-0.011	0.000	0.000	0.000	0.000
42	B	42	ILE	0	-0.024	0.010	20.064	0.008	0.008	0.000	0.000	0.000	0.000
43	B	43	VAL	0	-0.001	0.003	22.173	-0.005	-0.005	0.000	0.000	0.000	0.000
44	B	44	ILE	0	-0.011	-0.007	16.751	-0.001	-0.001	0.000	0.000	0.000	0.000
45	B	45	ASP	-1	-0.813	-0.933	20.090	-0.039	-0.039	0.000	0.000	0.000	0.000
46	B	46	LYS	1	0.932	0.991	18.814	0.009	0.009	0.000	0.000	0.000	0.000
47	B	47	VAL	0	-0.013	-0.005	19.666	0.007	0.007	0.000	0.000	0.000	0.000
48	B	48	PRO	0	-0.017	-0.032	21.894	0.008	0.008	0.000	0.000	0.000	0.000
49	B	49	THR	0	-0.043	-0.028	24.249	0.002	0.002	0.000	0.000	0.000	0.000
50	B	50	ILE	0	-0.006	0.034	19.139	0.004	0.004	0.000	0.000	0.000	0.000
51	B	51	THR	0	0.071	0.044	19.466	0.009	0.009	0.000	0.000	0.000	0.000
52	B	52	SER	0	-0.043	-0.027	22.533	-0.003	-0.003	0.000	0.000	0.000	0.000
53	B	53	GLU	-1	-0.905	-0.945	17.623	0.047	0.047	0.000	0.000	0.000	0.000
54	B	54	GLN	0	-0.036	-0.025	21.947	-0.009	-0.009	0.000	0.000	0.000	0.000
55	B	55	SER	0	0.007	-0.009	19.904	0.000	0.000	0.000	0.000	0.000	0.000
56	B	56	THR	0	-0.036	-0.018	20.025	0.005	0.005	0.000	0.000	0.000	0.000
57	B	57	TYR	0	-0.023	-0.010	20.126	-0.007	-0.007	0.000	0.000	0.000	0.000
58	B	58	ILE	0	0.026	0.027	15.773	0.007	0.007	0.000	0.000	0.000	0.000
59	B	59	ASN	0	-0.017	-0.024	19.933	-0.010	-0.010	0.000	0.000	0.000	0.000
60	B	60	ILE	0	0.037	0.026	16.104	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	61	CYS	0	0.007	0.021	19.593	0.003	0.003	0.000	0.000	0.000	0.000
62	B	62	ILE	0	0.015	-0.007	19.737	-0.014	-0.014	0.000	0.000	0.000	0.000
63	B	63	PHE	0	0.052	0.003	21.915	0.000	0.000	0.000	0.000	0.000	0.000
64	B	64	ASN	0	-0.065	-0.030	21.638	0.011	0.011	0.000	0.000	0.000	0.000
65	B	65	LEU	0	0.014	-0.004	18.692	-0.008	-0.008	0.000	0.000	0.000	0.000
66	B	66	LEU	0	-0.039	-0.022	23.132	0.002	0.002	0.000	0.000	0.000	0.000
67	B	67	GLU	-1	-0.959	-0.967	26.580	-0.095	-0.095	0.000	0.000	0.000	0.000
68	B	68	ALA	0	0.003	0.001	24.186	0.002	0.002	0.000	0.000	0.000	0.000
69	B	69	CYS	0	-0.061	-0.006	23.395	-0.009	-0.009	0.000	0.000	0.000	0.000
70	B	70	SER	0	0.034	0.029	25.405	0.014	0.014	0.000	0.000	0.000	0.000
71	B	71	SER	0	0.054	-0.013	27.082	-0.004	-0.004	0.000	0.000	0.000	0.000
72	B	72	ARG	1	0.923	0.977	28.076	0.084	0.084	0.000	0.000	0.000	0.000
73	B	73	VAL	0	0.015	0.014	22.554	0.003	0.003	0.000	0.000	0.000	0.000
74	B	74	LEU	0	-0.007	0.005	24.746	-0.003	-0.003	0.000	0.000	0.000	0.000
75	B	75	VAL	0	-0.089	-0.033	27.224	0.009	0.009	0.000	0.000	0.000	0.000
76	B	76	PRO	0	0.039	0.024	27.868	-0.005	-0.005	0.000	0.000	0.000	0.000
77	B	77	GLY	0	-0.029	-0.023	27.451	0.005	0.005	0.000	0.000	0.000	0.000
78	B	78	THR	0	-0.080	-0.038	24.788	0.002	0.002	0.000	0.000	0.000	0.000
79	B	79	LEU	0	-0.013	0.008	22.685	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	80	VAL	0	0.010	-0.013	19.221	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	81	ASN	0	0.002	0.007	15.276	-0.018	-0.018	0.000	0.000	0.000	0.000
82	B	82	ILE	0	0.001	-0.020	14.458	0.014	0.014	0.000	0.000	0.000	0.000
83	B	83	ASP	-1	-0.821	-0.886	12.180	-0.598	-0.598	0.000	0.000	0.000	0.000
84	B	84	ALA	0	0.014	-0.006	10.967	0.084	0.084	0.000	0.000	0.000	0.000
85	B	85	PHE	0	-0.003	0.003	8.212	-0.213	-0.213	0.000	0.000	0.000	0.000
86	B	86	TYR	0	0.003	0.022	7.958	0.116	0.116	0.000	0.000	0.000	0.000
87	B	87	ASP	-1	-0.785	-0.902	8.862	-0.101	-0.101	0.000	0.000	0.000	0.000
88	B	88	GLY	0	0.043	0.028	11.015	0.051	0.051	0.000	0.000	0.000	0.000
89	B	89	GLU	-1	-1.046	-0.999	12.000	0.017	0.017	0.000	0.000	0.000	0.000
90	B	90	SER	0	-0.050	-0.034	14.858	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	91	ILE	0	-0.014	-0.027	12.661	-0.026	-0.026	0.000	0.000	0.000	0.000
92	B	92	ASN	0	-0.050	-0.022	13.141	0.044	0.044	0.000	0.000	0.000	0.000
93	B	93	PRO	0	-0.019	-0.011	13.744	-0.069	-0.069	0.000	0.000	0.000	0.000
94	B	94	VAL	0	-0.045	-0.038	13.622	0.016	0.016	0.000	0.000	0.000	0.000
95	B	95	ASP	-1	-0.887	-0.957	16.254	-0.245	-0.245	0.000	0.000	0.000	0.000
96	B	96	ILE	0	-0.025	-0.010	16.915	-0.018	-0.018	0.000	0.000	0.000	0.000
97	B	97	TYR	0	-0.028	-0.007	17.227	0.024	0.024	0.000	0.000	0.000	0.000
98	B	98	GLU	-1	-0.894	-0.961	21.083	-0.108	-0.108	0.000	0.000	0.000	0.000
99	B	99	VAL	0	-0.031	-0.002	19.637	-0.006	-0.006	0.000	0.000	0.000	0.000
100	B	100	ASN	0	0.002	-0.011	22.989	0.016	0.016	0.000	0.000	0.000	0.000
101	B	101	GLY	0	0.093	0.019	24.411	-0.006	-0.006	0.000	0.000	0.000	0.000
102	B	102	ALA	0	-0.029	-0.011	25.995	0.003	0.003	0.000	0.000	0.000	0.000
103	B	103	ASN	0	-0.030	-0.019	21.789	0.004	0.004	0.000	0.000	0.000	0.000
104	B	104	PHE	0	-0.004	0.003	18.955	-0.004	-0.004	0.000	0.000	0.000	0.000
105	B	105	THR	0	0.010	0.026	23.158	0.007	0.007	0.000	0.000	0.000	0.000
106	B	106	MET	0	0.034	0.007	23.022	-0.004	-0.004	0.000	0.000	0.000	0.000
107	B	107	GLU	-1	-0.865	-0.954	22.690	-0.040	-0.040	0.000	0.000	0.000	0.000
108	B	108	ASN	0	-0.023	-0.019	20.225	0.001	0.001	0.000	0.000	0.000	0.000
109	B	109	ILE	0	-0.021	-0.003	18.499	-0.014	-0.014	0.000	0.000	0.000	0.000
110	B	110	GLN	0	-0.009	-0.013	17.730	0.001	0.001	0.000	0.000	0.000	0.000
111	B	111	LEU	0	0.029	0.018	16.454	0.007	0.007	0.000	0.000	0.000	0.000
112	B	112	ILE	0	-0.044	-0.038	12.962	-0.012	-0.012	0.000	0.000	0.000	0.000
113	B	113	ASP	-1	-0.972	-0.971	12.984	0.050	0.050	0.000	0.000	0.000	0.000
114	B	114	GLU	-1	-0.855	-0.922	13.074	0.022	0.022	0.000	0.000	0.000	0.000
115	B	115	MET	0	-0.105	-0.043	11.770	0.023	0.023	0.000	0.000	0.000	0.000
116	B	116	ASN	0	-0.015	0.004	8.724	-0.146	-0.146	0.000	0.000	0.000	0.000
117	B	117	ASN	0	-0.015	-0.026	9.053	0.128	0.128	0.000	0.000	0.000	0.000
118	B	118	SER	0	-0.082	-0.031	10.657	0.031	0.031	0.000	0.000	0.000	0.000
119	B	119	ILE	0	0.016	0.001	9.891	-0.052	-0.052	0.000	0.000	0.000	0.000
120	B	120	GLY	0	0.023	0.008	10.704	0.057	0.057	0.000	0.000	0.000	0.000
121	B	121	LYS	1	0.873	0.948	12.882	-0.021	-0.021	0.000	0.000	0.000	0.000
122	B	122	NME	0	0.031	0.019	15.144	-0.016	-0.016	0.000	0.000	0.000	0.000

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