FMO DATABASE

FMODB ID: J3G99

Calculation Name: 2WKC-A-Xray372

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: 2023-06-20

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-551685.443654
FMO2-HF: Nuclear repulsion	518163.020002
FMO2-HF: Total energy	-33522.423651
FMO2-MP2: Total energy	-33622.783301

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.
-0.721	1.234	-0.013	-1.084	-0.859	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 : 0.062 / q_NPA : 0.034

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	-0.037	-0.016	3.865	0.167	2.122	-0.013	-1.084	-0.859	0.003
4	A	3	ILE	0	0.014	0.014	6.877	-0.123	-0.123	0.000	0.000	0.000	0.000
5	A	4	THR	0	0.052	0.014	10.519	0.145	0.145	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.006	0.013	13.621	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	6	THR	0	0.011	0.009	17.127	0.028	0.028	0.000	0.000	0.000	0.000
8	A	7	ALA	0	-0.019	-0.012	20.499	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	8	GLN	0	-0.017	-0.010	23.476	0.010	0.010	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.040	0.033	26.385	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.032	-0.047	27.404	0.018	0.018	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.850	-0.942	29.722	-0.097	-0.097	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.909	0.969	30.286	0.139	0.139	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.025	-0.002	25.010	0.008	0.008	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.013	-0.017	25.463	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.949	0.988	24.084	0.112	0.112	0.000	0.000	0.000	0.000
17	A	16	THR	0	0.023	0.003	28.351	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.034	-0.012	27.345	0.000	0.000	0.000	0.000	0.000	0.000
19	A	18	SER	0	0.048	0.006	30.381	0.003	0.003	0.000	0.000	0.000	0.000
20	A	19	THR	0	-0.060	-0.044	28.522	0.006	0.006	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.021	0.000	32.020	0.000	0.000	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.928	0.968	27.622	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.099	0.061	31.229	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.814	-0.881	31.317	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.789	0.896	25.683	0.006	0.006	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.862	0.928	26.924	0.059	0.059	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.031	-0.019	22.555	0.002	0.002	0.000	0.000	0.000	0.000
28	A	27	ILE	0	0.017	0.018	20.824	0.001	0.001	0.000	0.000	0.000	0.000
29	A	28	SER	0	-0.017	-0.030	20.767	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	29	VAL	0	-0.006	0.000	17.494	0.011	0.011	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.019	0.003	18.434	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.002	-0.018	13.248	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	32	PHE	0	-0.001	0.000	14.637	-0.103	-0.103	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.912	-0.948	17.187	-0.379	-0.379	0.000	0.000	0.000	0.000
35	A	34	LYS	1	0.817	0.892	20.725	0.230	0.230	0.000	0.000	0.000	0.000
36	A	35	GLU	-1	-0.790	-0.885	23.601	-0.276	-0.276	0.000	0.000	0.000	0.000
37	A	36	LYS	1	0.937	0.955	26.990	0.206	0.206	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.037	0.013	30.007	0.013	0.013	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.040	-0.002	25.970	0.014	0.014	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.048	0.018	28.392	0.000	0.000	0.000	0.000	0.000	0.000
41	A	40	VAL	0	0.037	0.023	22.775	0.009	0.009	0.000	0.000	0.000	0.000
42	A	41	LYS	1	0.864	0.923	23.217	0.204	0.204	0.000	0.000	0.000	0.000
43	A	42	VAL	0	0.004	0.016	19.423	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	43	ALA	0	0.029	0.031	16.459	0.035	0.035	0.000	0.000	0.000	0.000
45	A	44	TYR	0	-0.006	-0.015	18.054	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.025	0.022	15.867	0.021	0.021	0.000	0.000	0.000	0.000
47	A	46	SER	0	-0.015	-0.018	16.759	0.017	0.017	0.000	0.000	0.000	0.000
48	A	47	ALA	0	0.012	0.006	17.184	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	48	PHE	0	-0.008	-0.006	18.896	0.007	0.007	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.003	-0.002	20.859	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.019	0.002	22.206	0.013	0.013	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.863	-0.922	25.281	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	52	PHE	0	-0.009	-0.009	25.477	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.009	0.007	24.557	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	54	GLN	0	-0.010	-0.002	28.807	0.007	0.007	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.015	-0.008	30.262	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	56	GLY	0	0.022	0.016	30.976	0.007	0.007	0.000	0.000	0.000	0.000
58	A	57	ASP	-1	-0.772	-0.864	28.036	-0.104	-0.104	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.013	-0.007	25.060	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	59	VAL	0	-0.018	-0.009	22.282	0.013	0.013	0.000	0.000	0.000	0.000
61	A	60	THR	0	0.001	-0.007	16.893	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	61	VAL	0	-0.028	-0.002	15.252	0.042	0.042	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.004	-0.020	12.416	-0.069	-0.069	0.000	0.000	0.000	0.000
64	A	63	GLY	0	0.041	0.011	9.817	0.145	0.145	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.987	1.011	6.111	-0.978	-0.978	0.000	0.000	0.000	0.000
66	A	65	VAL	0	-0.002	-0.003	7.896	0.209	0.209	0.000	0.000	0.000	0.000
67	A	66	GLN	0	-0.032	-0.015	8.729	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.028	0.023	11.145	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	68	LYS	1	0.846	0.905	13.790	0.058	0.058	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.804	-0.889	16.708	-0.091	-0.091	0.000	0.000	0.000	0.000
71	A	70	SER	0	-0.067	-0.046	19.926	0.031	0.031	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.018	-0.001	23.283	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.898	-0.949	25.144	-0.076	-0.076	0.000	0.000	0.000	0.000
74	A	73	TYR	0	-0.025	-0.007	24.067	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	74	VAL	0	-0.009	-0.001	17.701	0.006	0.006	0.000	0.000	0.000	0.000
76	A	75	ASN	0	-0.041	-0.018	18.630	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	76	TYR	0	0.044	0.010	13.901	-0.031	-0.031	0.000	0.000	0.000	0.000
78	A	77	ASN	0	-0.012	0.001	14.534	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	78	PHE	0	0.044	0.012	12.280	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	79	VAL	0	-0.090	-0.046	10.609	0.077	0.077	0.000	0.000	0.000	0.000
81	A	80	PHE	0	-0.027	-0.022	11.575	0.027	0.027	0.000	0.000	0.000	0.000
82	A	81	PRO	0	-0.020	0.009	12.789	0.011	0.011	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.034	0.019	13.646	0.061	0.061	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.038	-0.031	15.615	-0.053	-0.053	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.880	-0.919	18.823	-0.201	-0.201	0.000	0.000	0.000	0.000
86	A	85	LYS	1	0.836	0.898	21.449	0.081	0.081	0.000	0.000	0.000	0.000
87	A	86	VAL	0	0.004	0.003	23.470	0.006	0.006	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.013	-0.006	25.838	0.010	0.010	0.000	0.000	0.000	0.000
89	A	88	ILE	0	0.001	-0.007	28.274	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	89	THR	0	-0.004	0.011	31.706	0.008	0.008	0.000	0.000	0.000	0.000

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