FMO DATABASE

FMODB ID: 39N6L

Calculation Name: 1WK2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WK2

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM30

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-648998.928378
FMO2-HF: Nuclear repulsion	613166.660119
FMO2-HF: Total energy	-35832.268258
FMO2-MP2: Total energy	-35938.692023

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:1:MET)

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

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.
-4.309	-1.562	7.493	-3.633	-6.605	-0.016

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.003

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	3	ARG	1	0.890	0.927	3.764	1.167	2.715	-0.009	-0.722	-0.816	0.003
4	A	4	PRO	0	0.003	0.028	5.350	-0.454	-0.454	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.951	0.954	6.334	0.942	0.942	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.006	0.000	8.854	0.135	0.135	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.006	0.010	10.153	-0.112	-0.112	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.003	0.005	12.821	0.088	0.088	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.012	-0.014	15.213	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.006	-0.001	16.546	0.032	0.032	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.965	0.979	19.799	0.166	0.166	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.788	-0.862	21.323	-0.325	-0.325	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.012	-0.011	23.350	0.021	0.021	0.000	0.000	0.000	0.000
14	A	14	TYR	0	0.025	-0.004	19.805	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.027	0.011	17.457	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.018	-0.017	16.689	-0.059	-0.059	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.020	-0.014	17.335	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.045	-0.018	12.775	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.032	-0.013	12.513	-0.076	-0.076	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.824	-0.900	13.435	-0.485	-0.485	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.004	0.000	13.089	0.017	0.017	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.923	0.965	13.926	0.327	0.327	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.826	0.930	16.006	0.312	0.312	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.111	0.045	13.009	-0.050	-0.050	0.000	0.000	0.000	0.000
25	A	25	TRP	0	0.011	0.012	13.360	0.024	0.024	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.831	-0.895	15.107	-0.218	-0.218	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.002	0.002	16.754	0.036	0.036	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.812	0.886	17.881	0.153	0.153	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.993	0.988	20.812	0.040	0.040	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.942	0.975	20.981	-0.060	-0.060	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.977	1.000	18.226	-0.212	-0.212	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.017	-0.018	13.825	0.005	0.005	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.939	0.941	14.017	-0.430	-0.430	0.000	0.000	0.000	0.000
34	A	34	HIS	0	-0.017	-0.003	7.217	0.330	0.330	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.850	0.929	7.207	-0.834	-0.834	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.043	0.033	3.674	0.748	1.014	0.006	-0.082	-0.190	0.000
37	A	37	PRO	0	0.023	0.031	2.299	-0.658	-1.283	4.894	-1.342	-2.926	0.000
38	A	38	LEU	0	-0.058	-0.025	4.899	0.317	0.422	-0.001	-0.020	-0.084	0.000
39	A	39	GLY	0	-0.007	-0.003	8.584	-0.126	-0.126	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.002	0.013	11.002	0.145	0.145	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.007	-0.029	14.185	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.027	0.009	17.303	0.052	0.052	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.006	0.005	20.747	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.021	-0.017	22.262	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.959	0.979	20.256	0.272	0.272	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.023	-0.007	12.583	0.007	0.007	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.023	-0.009	14.755	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.102	0.028	12.500	0.009	0.009	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.052	0.007	5.129	0.430	0.430	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.071	0.032	7.478	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.805	-0.885	2.586	-8.389	-7.467	2.510	-1.351	-2.081	-0.019
52	A	52	LEU	0	-0.043	-0.018	5.348	0.205	0.252	-0.001	-0.001	-0.045	0.000
53	A	53	VAL	0	0.071	0.031	5.224	0.453	0.453	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.021	-0.011	7.678	0.290	0.290	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.037	-0.008	11.456	-0.097	-0.097	0.000	0.000	0.000	0.000
56	A	86	PRO	0	0.050	0.020	27.955	0.001	0.001	0.000	0.000	0.000	0.000
57	A	87	LEU	0	-0.103	-0.060	23.749	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	88	TYR	0	0.017	0.008	19.487	0.020	0.020	0.000	0.000	0.000	0.000
59	A	89	ALA	0	0.036	0.012	17.725	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	90	TRP	0	-0.043	-0.019	13.331	0.026	0.026	0.000	0.000	0.000	0.000
61	A	91	VAL	0	0.034	0.014	10.533	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	92	LEU	0	-0.069	-0.045	8.977	0.004	0.004	0.000	0.000	0.000	0.000
63	A	93	GLU	-1	-0.889	-0.942	6.003	-0.816	-0.816	0.000	0.000	0.000	0.000
64	A	94	ASN	0	-0.006	-0.025	3.043	0.727	1.211	0.094	-0.115	-0.463	0.000
65	A	95	ALA	0	-0.041	-0.008	6.548	-0.146	-0.146	0.000	0.000	0.000	0.000
66	A	96	PHE	0	0.001	0.005	6.269	0.171	0.171	0.000	0.000	0.000	0.000
67	A	97	ARG	1	0.855	0.919	10.745	0.416	0.416	0.000	0.000	0.000	0.000
68	A	98	TYR	0	-0.126	-0.089	9.164	0.072	0.072	0.000	0.000	0.000	0.000
69	A	99	GLU	-1	-0.891	-0.946	14.434	-0.404	-0.404	0.000	0.000	0.000	0.000
70	A	100	LYS	1	0.962	0.976	17.534	0.372	0.372	0.000	0.000	0.000	0.000
71	A	101	PRO	0	-0.037	-0.007	17.731	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	102	LEU	0	0.042	0.024	14.368	0.040	0.040	0.000	0.000	0.000	0.000
73	A	103	HIS	0	0.043	0.030	18.341	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	104	VAL	0	-0.023	0.005	17.795	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	105	PRO	0	0.011	-0.007	20.287	0.021	0.021	0.000	0.000	0.000	0.000
76	A	106	ARG	1	0.909	0.940	17.298	0.381	0.381	0.000	0.000	0.000	0.000
77	A	107	ARG	1	1.023	0.995	18.635	0.112	0.112	0.000	0.000	0.000	0.000
78	A	108	PRO	0	0.043	0.027	16.606	0.000	0.000	0.000	0.000	0.000	0.000
79	A	109	GLY	0	-0.012	0.016	14.005	-0.054	-0.054	0.000	0.000	0.000	0.000
80	A	110	ARG	1	0.859	0.924	11.318	0.539	0.539	0.000	0.000	0.000	0.000
81	A	111	VAL	0	-0.014	-0.003	15.399	0.013	0.013	0.000	0.000	0.000	0.000
82	A	112	MET	0	-0.007	-0.005	16.897	-0.020	-0.020	0.000	0.000	0.000	0.000
83	A	113	PHE	0	0.023	0.003	14.796	0.013	0.013	0.000	0.000	0.000	0.000
84	A	114	VAL	0	0.028	0.017	18.194	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	115	ASP	-1	-0.782	-0.831	15.648	0.252	0.252	0.000	0.000	0.000	0.000
86	A	116	LEU	0	0.028	-0.006	17.044	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	117	SER	0	-0.040	-0.037	14.521	0.021	0.021	0.000	0.000	0.000	0.000
88	A	118	GLU	-1	-0.929	-0.974	16.631	0.301	0.301	0.000	0.000	0.000	0.000
89	A	119	VAL	0	-0.060	-0.010	19.793	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	120	ARG	1	0.968	0.993	22.075	-0.132	-0.132	0.000	0.000	0.000	0.000

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