FMO DATABASE

FMODB ID: 9Y562

Calculation Name: 2WKC-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WKC

Chain ID: A

ChEMBL ID:

UniProt ID: Q6JM09

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-550781.502719
FMO2-HF: Nuclear repulsion	517240.457537
FMO2-HF: Total energy	-33541.045182
FMO2-MP2: Total energy	-33641.420873

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:GLY )

Summations of interaction energy for fragment #1(A:0:GLY )

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.
-1.102	0.954	-0.009	-1.104	-0.944	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.024

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	2	ILE	0	-0.022	-0.010	3.795	0.112	2.168	-0.009	-1.104	-0.944	0.003
4	A	3	ILE	0	0.010	0.005	6.847	-0.005	-0.005	0.000	0.000	0.000	0.000
5	A	4	THR	0	0.035	0.007	10.328	0.202	0.202	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.016	0.013	13.503	0.010	0.010	0.000	0.000	0.000	0.000
7	A	6	THR	0	0.018	0.023	16.780	0.052	0.052	0.000	0.000	0.000	0.000
8	A	7	ALA	0	-0.019	-0.010	20.243	0.005	0.005	0.000	0.000	0.000	0.000
9	A	8	GLN	0	-0.024	-0.007	23.098	0.008	0.008	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.004	0.025	26.520	0.000	0.000	0.000	0.000	0.000	0.000
11	A	10	ASN	0	0.012	-0.016	27.504	0.016	0.016	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.851	-0.950	29.797	-0.085	-0.085	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.890	0.957	29.952	0.144	0.144	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.031	0.001	24.909	0.013	0.013	0.000	0.000	0.000	0.000
15	A	14	THR	0	0.014	-0.005	25.317	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.957	0.986	24.575	0.079	0.079	0.000	0.000	0.000	0.000
17	A	16	THR	0	0.038	0.012	28.155	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.045	-0.010	26.984	0.004	0.004	0.000	0.000	0.000	0.000
19	A	18	SER	0	0.076	0.034	30.244	0.002	0.002	0.000	0.000	0.000	0.000
20	A	19	THR	0	-0.078	-0.055	28.103	0.008	0.008	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.027	-0.002	31.532	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.911	0.946	27.234	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.067	0.059	31.542	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.902	-0.939	31.278	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.915	0.964	24.759	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.935	0.974	26.503	0.067	0.067	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.043	-0.010	22.086	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	27	ILE	0	0.033	0.022	20.585	0.000	0.000	0.000	0.000	0.000	0.000
29	A	28	SER	0	-0.013	-0.013	20.773	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	29	VAL	0	-0.002	-0.005	17.410	0.007	0.007	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.014	-0.002	18.414	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.005	-0.011	12.656	-0.036	-0.036	0.000	0.000	0.000	0.000
33	A	32	PHE	0	0.015	0.009	14.317	-0.100	-0.100	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.933	-0.958	16.796	-0.399	-0.399	0.000	0.000	0.000	0.000
35	A	34	LYS	1	0.888	0.945	20.297	0.209	0.209	0.000	0.000	0.000	0.000
36	A	35	GLU	-1	-0.891	-0.939	23.040	-0.231	-0.231	0.000	0.000	0.000	0.000
37	A	36	LYS	1	0.926	0.942	26.334	0.209	0.209	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.020	0.017	29.529	0.007	0.007	0.000	0.000	0.000	0.000
39	A	38	SER	0	0.040	0.037	25.473	0.007	0.007	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.017	-0.019	27.749	0.005	0.005	0.000	0.000	0.000	0.000
41	A	40	VAL	0	-0.002	0.013	22.094	0.011	0.011	0.000	0.000	0.000	0.000
42	A	41	LYS	1	0.924	0.953	22.968	0.136	0.136	0.000	0.000	0.000	0.000
43	A	42	VAL	0	-0.011	0.003	19.034	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	43	ALA	0	0.040	0.032	16.141	0.032	0.032	0.000	0.000	0.000	0.000
45	A	44	TYR	0	-0.013	-0.016	17.909	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.015	0.010	15.879	0.027	0.027	0.000	0.000	0.000	0.000
47	A	46	SER	0	-0.048	-0.033	16.846	0.004	0.004	0.000	0.000	0.000	0.000
48	A	47	ALA	0	0.022	0.003	16.851	0.001	0.001	0.000	0.000	0.000	0.000
49	A	48	PHE	0	-0.026	-0.015	18.624	0.006	0.006	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.005	-0.002	20.680	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.009	-0.002	22.242	0.017	0.017	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.850	-0.927	25.086	-0.041	-0.041	0.000	0.000	0.000	0.000
53	A	52	PHE	0	-0.046	-0.028	25.675	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.029	0.003	24.635	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	54	GLN	0	-0.009	-0.018	28.751	0.009	0.009	0.000	0.000	0.000	0.000
56	A	55	LEU	0	0.002	-0.007	30.244	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	56	GLY	0	-0.006	0.004	30.784	0.006	0.006	0.000	0.000	0.000	0.000
58	A	57	ASP	-1	-0.796	-0.885	27.842	-0.125	-0.125	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.021	-0.019	24.654	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	59	VAL	0	-0.020	-0.007	21.657	0.006	0.006	0.000	0.000	0.000	0.000
61	A	60	THR	0	0.037	0.005	16.985	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	61	VAL	0	-0.020	-0.010	15.029	0.033	0.033	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.006	-0.011	12.331	-0.091	-0.091	0.000	0.000	0.000	0.000
64	A	63	GLY	0	0.052	0.032	9.417	0.137	0.137	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.985	0.995	5.446	-1.291	-1.291	0.000	0.000	0.000	0.000
66	A	65	VAL	0	0.009	0.007	7.923	0.177	0.177	0.000	0.000	0.000	0.000
67	A	66	GLN	0	-0.055	-0.024	8.915	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.023	0.009	11.101	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	68	LYS	1	0.887	0.946	13.521	-0.064	-0.064	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.834	-0.921	16.627	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	70	SER	0	-0.054	-0.037	19.869	0.025	0.025	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.014	-0.001	23.202	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.910	-0.954	25.178	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	73	TYR	0	-0.065	-0.026	23.850	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	74	VAL	0	0.059	0.039	17.334	0.013	0.013	0.000	0.000	0.000	0.000
76	A	75	ASN	0	-0.084	-0.044	18.648	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	76	TYR	0	0.055	0.024	13.465	0.005	0.005	0.000	0.000	0.000	0.000
78	A	77	ASN	0	-0.019	-0.012	14.408	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	78	PHE	0	0.052	0.019	12.236	0.009	0.009	0.000	0.000	0.000	0.000
80	A	79	VAL	0	-0.084	-0.043	10.582	0.079	0.079	0.000	0.000	0.000	0.000
81	A	80	PHE	0	-0.048	-0.033	11.757	0.006	0.006	0.000	0.000	0.000	0.000
82	A	81	PRO	0	-0.021	0.017	12.835	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.041	0.010	13.741	0.058	0.058	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.038	-0.024	15.717	-0.046	-0.046	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.929	-0.950	18.933	-0.264	-0.264	0.000	0.000	0.000	0.000
86	A	85	LYS	1	0.878	0.928	21.430	0.109	0.109	0.000	0.000	0.000	0.000
87	A	86	VAL	0	0.017	0.010	23.397	0.000	0.000	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.032	-0.021	25.801	0.015	0.015	0.000	0.000	0.000	0.000
89	A	88	ILE	0	-0.001	-0.001	28.059	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	89	THR	0	0.013	0.001	31.628	0.007	0.007	0.000	0.000	0.000	0.000
91	A	90	NME	0	-0.015	0.005	34.318	0.006	0.006	0.000	0.000	0.000	0.000

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