FMO DATABASE

FMODB ID: N1QGQ

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	OptHSide
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	-550162.855494
FMO2-HF: Nuclear repulsion	516640.629481
FMO2-HF: Total energy	-33522.226014
FMO2-MP2: Total energy	-33622.514955

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.
-0.827	1.141	-0.016	-1.032	-0.919	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 : 0.033 / q_NPA : 0.021

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	-0.034	-0.018	3.795	0.233	2.201	-0.016	-1.032	-0.919	0.003
4	A	3	ILE	0	0.005	0.004	6.847	-0.010	-0.010	0.000	0.000	0.000	0.000
5	A	4	THR	0	0.047	0.017	10.327	0.152	0.152	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.013	0.017	13.503	0.009	0.009	0.000	0.000	0.000	0.000
7	A	6	THR	0	0.002	0.003	16.779	0.029	0.029	0.000	0.000	0.000	0.000
8	A	7	ALA	0	-0.021	-0.013	20.243	0.006	0.006	0.000	0.000	0.000	0.000
9	A	8	GLN	0	-0.020	-0.009	23.098	0.009	0.009	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.010	0.023	26.514	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.021	-0.037	27.503	0.018	0.018	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.850	-0.946	29.795	-0.093	-0.093	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.902	0.965	29.912	0.147	0.147	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.023	-0.002	24.859	0.013	0.013	0.000	0.000	0.000	0.000
15	A	14	THR	0	0.009	-0.001	25.315	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.953	0.988	24.345	0.094	0.094	0.000	0.000	0.000	0.000
17	A	16	THR	0	0.032	0.008	28.152	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.043	-0.010	27.031	0.004	0.004	0.000	0.000	0.000	0.000
19	A	18	SER	0	0.063	0.032	30.242	0.002	0.002	0.000	0.000	0.000	0.000
20	A	19	THR	0	-0.061	-0.039	28.064	0.008	0.008	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.040	0.007	31.529	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.909	0.941	27.558	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.064	0.059	31.540	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.863	-0.928	31.276	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.866	0.942	25.050	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.895	0.936	26.565	0.074	0.074	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.038	-0.010	22.082	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	27	ILE	0	0.027	0.020	20.664	0.001	0.001	0.000	0.000	0.000	0.000
29	A	28	SER	0	-0.010	-0.014	20.781	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	29	VAL	0	-0.005	-0.005	17.396	0.010	0.010	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.012	0.002	18.411	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.001	-0.013	13.081	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	32	PHE	0	0.003	0.004	14.381	-0.101	-0.101	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.923	-0.952	16.792	-0.398	-0.398	0.000	0.000	0.000	0.000
35	A	34	LYS	1	0.817	0.896	20.292	0.212	0.212	0.000	0.000	0.000	0.000
36	A	35	GLU	-1	-0.813	-0.890	23.035	-0.254	-0.254	0.000	0.000	0.000	0.000
37	A	36	LYS	1	0.923	0.942	26.328	0.208	0.208	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.015	0.014	29.524	0.007	0.007	0.000	0.000	0.000	0.000
39	A	38	SER	0	0.015	0.014	25.546	0.011	0.011	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.045	0.002	27.857	0.004	0.004	0.000	0.000	0.000	0.000
41	A	40	VAL	0	0.027	0.018	22.131	0.013	0.013	0.000	0.000	0.000	0.000
42	A	41	LYS	1	0.891	0.949	22.893	0.154	0.154	0.000	0.000	0.000	0.000
43	A	42	VAL	0	0.002	0.011	19.035	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	43	ALA	0	0.029	0.028	16.105	0.033	0.033	0.000	0.000	0.000	0.000
45	A	44	TYR	0	-0.011	-0.017	17.905	-0.042	-0.042	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.024	0.016	15.878	0.026	0.026	0.000	0.000	0.000	0.000
47	A	46	SER	0	-0.044	-0.028	16.843	0.006	0.006	0.000	0.000	0.000	0.000
48	A	47	ALA	0	0.016	0.001	16.898	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	48	PHE	0	-0.028	-0.016	18.622	0.007	0.007	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.013	0.000	20.678	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.006	-0.004	22.206	0.016	0.016	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.859	-0.925	25.085	-0.048	-0.048	0.000	0.000	0.000	0.000
53	A	52	PHE	0	-0.019	-0.015	25.461	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.027	0.003	24.600	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	54	GLN	0	0.010	0.011	28.750	0.009	0.009	0.000	0.000	0.000	0.000
56	A	55	LEU	0	0.008	-0.003	30.064	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	56	GLY	0	0.001	0.008	30.796	0.007	0.007	0.000	0.000	0.000	0.000
58	A	57	ASP	-1	-0.773	-0.875	27.835	-0.130	-0.130	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.012	-0.013	24.708	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	59	VAL	0	-0.023	-0.009	21.820	0.007	0.007	0.000	0.000	0.000	0.000
61	A	60	THR	0	0.057	0.028	16.949	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	61	VAL	0	-0.025	-0.006	15.175	0.035	0.035	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.005	-0.018	12.355	-0.087	-0.087	0.000	0.000	0.000	0.000
64	A	63	GLY	0	0.054	0.031	9.415	0.143	0.143	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.980	0.996	5.807	-1.129	-1.129	0.000	0.000	0.000	0.000
66	A	65	VAL	0	0.012	0.002	7.921	0.185	0.185	0.000	0.000	0.000	0.000
67	A	66	GLN	0	-0.046	-0.015	8.914	0.002	0.002	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.020	0.008	11.101	-0.050	-0.050	0.000	0.000	0.000	0.000
69	A	68	LYS	1	0.855	0.920	13.520	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.819	-0.915	16.626	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	70	SER	0	-0.057	-0.030	19.868	0.027	0.027	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.008	0.002	23.201	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.904	-0.949	25.177	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	73	TYR	0	-0.056	-0.021	23.849	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	74	VAL	0	0.045	0.029	17.361	0.012	0.012	0.000	0.000	0.000	0.000
76	A	75	ASN	0	-0.092	-0.046	18.646	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	76	TYR	0	0.060	0.025	13.395	0.002	0.002	0.000	0.000	0.000	0.000
78	A	77	ASN	0	-0.008	-0.004	14.415	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	78	PHE	0	0.058	0.019	12.026	0.009	0.009	0.000	0.000	0.000	0.000
80	A	79	VAL	0	-0.092	-0.046	10.560	0.078	0.078	0.000	0.000	0.000	0.000
81	A	80	PHE	0	-0.047	-0.031	11.755	0.005	0.005	0.000	0.000	0.000	0.000
82	A	81	PRO	0	-0.013	0.017	12.838	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.033	0.012	13.795	0.061	0.061	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.035	-0.029	15.717	-0.047	-0.047	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.924	-0.947	18.933	-0.279	-0.279	0.000	0.000	0.000	0.000
86	A	85	LYS	1	0.826	0.895	21.430	0.110	0.110	0.000	0.000	0.000	0.000
87	A	86	VAL	0	0.012	0.006	23.407	0.000	0.000	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.027	-0.018	25.802	0.014	0.014	0.000	0.000	0.000	0.000
89	A	88	ILE	0	-0.005	-0.002	28.142	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	89	THR	0	0.011	0.015	31.629	0.009	0.009	0.000	0.000	0.000	0.000

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