FMO DATABASE

FMODB ID: 2KZNR

Calculation Name: 3K8A-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K8A

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F924

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-720638.18051
FMO2-HF: Nuclear repulsion	680045.987794
FMO2-HF: Total energy	-40592.192716
FMO2-MP2: Total energy	-40709.061195

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:0:ACE )

Summations of interaction energy for fragment #1(A:0: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.
0.766	1.622	-0.005	-0.355	-0.497	0

Interaction energy analysis for fragmet #1(A:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.013

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].
3	A	2	GLY	0	-0.020	-0.002	3.840	1.199	2.055	-0.005	-0.355	-0.497
4	A	3	PHE	0	0.030	0.015	5.735	-0.096	-0.096	0.000	0.000	0.000
5	A	4	THR	0	-0.004	-0.014	9.539	0.072	0.072	0.000	0.000	0.000
6	A	5	ASN	0	-0.013	0.004	10.955	0.046	0.046	0.000	0.000	0.000
7	A	6	LEU	0	0.042	0.008	10.928	0.034	0.034	0.000	0.000	0.000
8	A	7	VAL	0	-0.018	0.001	14.359	-0.011	-0.011	0.000	0.000	0.000
9	A	8	SER	0	0.054	0.018	17.699	0.012	0.012	0.000	0.000	0.000
10	A	9	LEU	0	-0.048	-0.018	19.843	-0.009	-0.009	0.000	0.000	0.000
11	A	10	ALA	0	0.056	0.029	23.286	0.009	0.009	0.000	0.000	0.000
12	A	11	ALA	0	-0.030	-0.021	26.302	-0.004	-0.004	0.000	0.000	0.000
13	A	12	LEU	0	0.052	0.027	28.557	0.005	0.005	0.000	0.000	0.000
14	A	13	ILE	0	-0.062	-0.024	28.128	0.001	0.001	0.000	0.000	0.000
15	A	14	GLU	-1	-0.848	-0.914	30.651	0.020	0.020	0.000	0.000	0.000
16	A	15	LYS	1	0.927	0.954	32.155	-0.037	-0.037	0.000	0.000	0.000
17	A	16	ALA	0	0.029	0.004	30.825	0.003	0.003	0.000	0.000	0.000
18	A	17	PHE	0	-0.079	-0.039	30.499	-0.002	-0.002	0.000	0.000	0.000
19	A	18	PRO	0	0.016	0.011	31.636	0.003	0.003	0.000	0.000	0.000
20	A	19	ILE	0	0.048	0.032	28.513	0.002	0.002	0.000	0.000	0.000
21	A	20	ARG	1	0.821	0.910	26.323	-0.088	-0.088	0.000	0.000	0.000
22	A	21	TYR	0	0.042	0.007	27.234	0.004	0.004	0.000	0.000	0.000
23	A	22	THR	0	-0.082	-0.023	22.623	-0.001	-0.001	0.000	0.000	0.000
24	A	23	PRO	0	0.043	0.000	25.876	-0.001	-0.001	0.000	0.000	0.000
25	A	24	ALA	0	-0.011	-0.003	23.826	-0.003	-0.003	0.000	0.000	0.000
26	A	25	GLY	0	0.031	0.025	25.964	0.005	0.005	0.000	0.000	0.000
27	A	26	ILE	0	-0.059	-0.033	20.482	-0.004	-0.004	0.000	0.000	0.000
28	A	27	PRO	0	0.099	0.064	23.399	-0.005	-0.005	0.000	0.000	0.000
29	A	28	VAL	0	-0.087	-0.052	23.185	0.012	0.012	0.000	0.000	0.000
30	A	29	LEU	0	0.036	0.024	24.392	-0.009	-0.009	0.000	0.000	0.000
31	A	30	ASP	-1	-0.870	-0.915	25.165	0.083	0.083	0.000	0.000	0.000
32	A	31	ILE	0	0.012	-0.005	26.137	-0.004	-0.004	0.000	0.000	0.000
33	A	32	ILE	0	-0.012	-0.003	27.669	0.001	0.001	0.000	0.000	0.000
34	A	33	LEU	0	-0.017	0.000	24.276	0.000	0.000	0.000	0.000	0.000
35	A	34	LYS	1	0.981	1.011	28.679	-0.012	-0.012	0.000	0.000	0.000
36	A	35	HIS	0	-0.056	-0.045	28.147	-0.003	-0.003	0.000	0.000	0.000
37	A	36	GLU	-1	-0.928	-0.976	30.524	-0.004	-0.004	0.000	0.000	0.000
38	A	37	SER	0	-0.046	-0.018	30.234	-0.001	-0.001	0.000	0.000	0.000
39	A	38	TRP	0	0.049	0.014	32.761	-0.001	-0.001	0.000	0.000	0.000
40	A	39	GLN	0	-0.044	-0.023	28.311	-0.006	-0.006	0.000	0.000	0.000
41	A	40	GLU	-1	-0.868	-0.942	30.865	-0.035	-0.035	0.000	0.000	0.000
42	A	41	GLU	-1	-0.984	-1.013	30.786	-0.047	-0.047	0.000	0.000	0.000
43	A	42	ASN	0	-0.045	-0.018	32.392	-0.001	-0.001	0.000	0.000	0.000
44	A	43	GLY	0	-0.007	-0.001	34.336	0.002	0.002	0.000	0.000	0.000
45	A	44	GLN	0	-0.019	0.003	36.370	0.001	0.001	0.000	0.000	0.000
46	A	45	GLN	0	0.013	0.007	35.577	-0.001	-0.001	0.000	0.000	0.000
47	A	46	CYS	0	-0.025	-0.006	33.816	0.002	0.002	0.000	0.000	0.000
48	A	47	LEU	0	-0.011	0.001	34.658	0.000	0.000	0.000	0.000	0.000
49	A	48	VAL	0	-0.041	-0.016	29.771	-0.001	-0.001	0.000	0.000	0.000
50	A	49	GLN	0	0.021	0.014	33.191	0.005	0.005	0.000	0.000	0.000
51	A	50	LEU	0	-0.042	-0.033	26.013	-0.001	-0.001	0.000	0.000	0.000
52	A	51	GLU	-1	-0.898	-0.944	30.544	0.019	0.019	0.000	0.000	0.000
53	A	52	ILE	0	-0.052	-0.021	23.412	-0.001	-0.001	0.000	0.000	0.000
54	A	53	PRO	0	0.013	0.016	26.225	0.005	0.005	0.000	0.000	0.000
55	A	54	ALA	0	0.014	-0.013	22.863	0.000	0.000	0.000	0.000	0.000
56	A	55	ARG	1	0.893	0.951	20.259	-0.116	-0.116	0.000	0.000	0.000
57	A	56	ILE	0	0.045	0.037	20.710	0.011	0.011	0.000	0.000	0.000
58	A	57	LEU	0	-0.028	-0.034	17.797	-0.001	-0.001	0.000	0.000	0.000
59	A	58	GLY	0	0.009	-0.003	20.855	0.003	0.003	0.000	0.000	0.000
60	A	59	ARG	1	0.982	0.994	21.525	-0.132	-0.132	0.000	0.000	0.000
61	A	60	GLN	0	0.035	0.006	18.614	-0.017	-0.017	0.000	0.000	0.000
62	A	61	ALA	0	-0.008	-0.006	23.189	-0.012	-0.012	0.000	0.000	0.000
63	A	62	GLU	-1	-0.907	-0.966	24.771	0.099	0.099	0.000	0.000	0.000
64	A	63	GLU	-1	-0.934	-0.974	24.983	0.097	0.097	0.000	0.000	0.000
65	A	64	TRP	0	0.047	0.002	25.080	-0.010	-0.010	0.000	0.000	0.000
66	A	65	GLN	0	-0.052	-0.030	28.187	-0.007	-0.007	0.000	0.000	0.000
67	A	66	TYR	0	-0.026	-0.021	30.260	-0.004	-0.004	0.000	0.000	0.000
68	A	67	ARG	1	0.782	0.895	29.914	-0.053	-0.053	0.000	0.000	0.000
69	A	68	GLN	0	-0.031	-0.021	32.251	0.000	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.003	0.003	33.964	-0.002	-0.002	0.000	0.000	0.000
71	A	70	ASP	-1	-0.821	-0.894	31.648	0.034	0.034	0.000	0.000	0.000
72	A	71	CYS	0	-0.032	-0.011	30.800	0.000	0.000	0.000	0.000	0.000
73	A	72	ALA	0	0.012	0.009	25.804	0.002	0.002	0.000	0.000	0.000
74	A	73	THR	0	0.020	0.005	21.979	-0.006	-0.006	0.000	0.000	0.000
75	A	74	VAL	0	-0.027	-0.009	20.209	0.012	0.012	0.000	0.000	0.000
76	A	75	GLU	-1	-0.897	-0.944	15.183	0.019	0.019	0.000	0.000	0.000
77	A	76	GLY	0	-0.010	-0.022	14.841	0.032	0.032	0.000	0.000	0.000
78	A	77	PHE	0	-0.025	0.018	12.261	-0.015	-0.015	0.000	0.000	0.000
79	A	78	LEU	0	0.044	0.015	15.083	0.014	0.014	0.000	0.000	0.000
80	A	79	ALA	0	-0.034	-0.030	16.733	0.003	0.003	0.000	0.000	0.000
81	A	80	GLN	0	0.034	0.016	18.754	-0.007	-0.007	0.000	0.000	0.000
82	A	81	LYS	1	0.987	1.002	21.976	-0.052	-0.052	0.000	0.000	0.000
83	A	82	SER	0	0.001	0.003	23.031	-0.004	-0.004	0.000	0.000	0.000
84	A	83	ARG	1	1.013	0.997	22.304	-0.037	-0.037	0.000	0.000	0.000
85	A	84	ARG	1	0.879	0.929	24.151	-0.019	-0.019	0.000	0.000	0.000
86	A	85	SER	0	0.017	0.003	25.612	-0.004	-0.004	0.000	0.000	0.000
87	A	86	LEU	0	-0.054	-0.021	26.622	-0.001	-0.001	0.000	0.000	0.000
88	A	87	MET	0	0.105	0.079	26.602	-0.006	-0.006	0.000	0.000	0.000
89	A	88	PRO	0	-0.008	-0.016	22.544	0.009	0.009	0.000	0.000	0.000
90	A	89	MET	0	-0.021	-0.017	20.374	0.006	0.006	0.000	0.000	0.000
91	A	90	LEU	0	0.031	0.020	18.374	0.002	0.002	0.000	0.000	0.000
92	A	91	ARG	1	0.844	0.924	15.824	-0.151	-0.151	0.000	0.000	0.000
93	A	92	ILE	0	0.020	0.024	16.518	0.009	0.009	0.000	0.000	0.000
94	A	93	GLN	0	0.017	0.003	12.499	-0.015	-0.015	0.000	0.000	0.000
95	A	94	ASN	0	-0.058	-0.038	15.766	-0.006	-0.006	0.000	0.000	0.000
96	A	95	ILE	0	0.033	0.020	18.111	-0.011	-0.011	0.000	0.000	0.000
97	A	96	LYS	1	0.915	0.980	19.749	-0.065	-0.065	0.000	0.000	0.000
98	A	97	GLU	-1	-0.819	-0.904	24.249	0.041	0.041	0.000	0.000	0.000
99	A	98	TYR	0	-0.063	-0.033	27.088	-0.002	-0.002	0.000	0.000	0.000
100	A	99	LYS	1	0.912	0.941	27.948	-0.023	-0.023	0.000	0.000	0.000
101	A	100	GLY	-1	-0.916	-0.930	27.587	-0.006	-0.006	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE )