FMO DATABASE

FMODB ID: JQLM9

Calculation Name: 2O2V-A-Xray372

Preferred Name: Mitogen-activated protein kinase kinase kinase 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2O2V

Chain ID: A

ChEMBL ID: CHEMBL5970

UniProt ID: Q99759

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-661789.539176
FMO2-HF: Nuclear repulsion	624701.790717
FMO2-HF: Total energy	-37087.748459
FMO2-MP2: Total energy	-37195.792192

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:16:VAL)

Summations of interaction energy for fragment #1(A:16:VAL)

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.
-6.685	-1.278	2.326	-2.756	-4.976	-0.015

Interaction energy analysis for fragmet #1(A:16:VAL)

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 : -0.043

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	18	VAL	0	0.006	-0.001	2.839	-1.053	0.896	0.138	-0.744	-1.342	0.001
4	A	19	ILE	0	0.006	0.007	4.855	0.229	0.266	-0.001	-0.005	-0.030	0.000
5	A	20	ARG	1	0.850	0.907	8.539	0.559	0.559	0.000	0.000	0.000	0.000
6	A	21	ILE	0	0.006	0.000	11.097	0.062	0.062	0.000	0.000	0.000	0.000
7	A	22	LYS	1	0.864	0.929	14.153	0.183	0.183	0.000	0.000	0.000	0.000
8	A	23	ILE	0	0.019	0.015	17.297	0.020	0.020	0.000	0.000	0.000	0.000
9	A	24	PRO	0	0.017	-0.004	19.805	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	25	ASN	0	-0.037	-0.027	22.799	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	26	SER	0	-0.009	-0.010	22.205	0.000	0.000	0.000	0.000	0.000	0.000
12	A	27	GLY	0	0.042	0.042	18.818	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	28	ALA	0	0.010	-0.008	14.605	0.011	0.011	0.000	0.000	0.000	0.000
14	A	29	VAL	0	0.002	0.017	12.592	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	30	ASP	-1	-0.781	-0.855	8.196	-0.573	-0.573	0.000	0.000	0.000	0.000
16	A	31	TRP	0	0.012	-0.001	8.358	0.032	0.032	0.000	0.000	0.000	0.000
17	A	32	THR	0	-0.015	-0.012	2.498	-0.430	-0.580	1.566	-0.298	-1.118	0.000
18	A	33	VAL	0	-0.007	0.004	4.123	0.017	0.297	0.000	-0.050	-0.231	0.000
19	A	34	HIS	0	-0.005	-0.013	2.846	-3.811	-0.694	0.624	-1.640	-2.101	-0.016
20	A	35	SER	0	0.039	0.043	4.258	-0.315	-0.141	-0.001	-0.019	-0.154	0.000
21	A	36	GLY	0	-0.029	-0.033	6.020	-0.485	-0.485	0.000	0.000	0.000	0.000
22	A	37	PRO	0	-0.033	-0.050	8.854	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	38	GLN	0	0.024	0.036	9.849	0.116	0.116	0.000	0.000	0.000	0.000
24	A	39	LEU	0	0.047	0.038	8.567	-0.066	-0.066	0.000	0.000	0.000	0.000
25	A	40	LEU	0	-0.063	-0.048	11.085	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	41	PHE	0	0.027	-0.002	14.414	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	42	ARG	1	0.777	0.864	16.610	-0.083	-0.083	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.738	-0.873	13.273	0.213	0.213	0.000	0.000	0.000	0.000
29	A	44	VAL	0	-0.028	-0.010	12.223	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	45	LEU	0	-0.048	-0.020	14.517	-0.033	-0.033	0.000	0.000	0.000	0.000
31	A	46	ASP	-1	-0.810	-0.884	16.942	0.031	0.031	0.000	0.000	0.000	0.000
32	A	47	VAL	0	-0.009	0.005	11.941	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	48	ILE	0	-0.016	-0.016	15.149	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	49	GLY	0	0.008	0.010	17.302	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	50	GLN	0	-0.065	-0.035	15.841	0.006	0.006	0.000	0.000	0.000	0.000
36	A	51	VAL	0	-0.058	-0.025	14.842	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	52	LEU	0	-0.060	-0.035	18.110	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	53	PRO	0	0.019	0.027	21.471	0.010	0.010	0.000	0.000	0.000	0.000
39	A	54	GLU	-1	-0.954	-0.980	23.802	-0.064	-0.064	0.000	0.000	0.000	0.000
40	A	55	ALA	0	-0.032	-0.006	23.914	0.003	0.003	0.000	0.000	0.000	0.000
41	A	56	THR	0	-0.044	-0.021	25.394	0.006	0.006	0.000	0.000	0.000	0.000
42	A	57	THR	0	0.017	0.003	20.307	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	58	THR	0	-0.061	-0.043	23.263	0.008	0.008	0.000	0.000	0.000	0.000
44	A	59	ALA	0	-0.019	-0.012	21.597	0.013	0.013	0.000	0.000	0.000	0.000
45	A	60	PHE	0	0.021	-0.008	15.783	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	61	GLU	-1	-0.797	-0.871	19.982	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	62	TYR	0	0.023	-0.004	16.430	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.873	-0.919	17.961	-0.141	-0.141	0.000	0.000	0.000	0.000
49	A	64	ASP	-1	-0.822	-0.919	18.559	-0.081	-0.081	0.000	0.000	0.000	0.000
50	A	65	GLU	-1	-0.927	-0.974	20.784	-0.062	-0.062	0.000	0.000	0.000	0.000
51	A	66	ASP	-1	-0.947	-0.960	21.942	-0.051	-0.051	0.000	0.000	0.000	0.000
52	A	67	GLY	0	-0.125	-0.058	22.935	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	68	ASP	-1	-0.906	-0.955	23.940	-0.050	-0.050	0.000	0.000	0.000	0.000
54	A	69	ARG	1	0.714	0.844	21.374	0.103	0.103	0.000	0.000	0.000	0.000
55	A	70	ILE	0	0.044	0.035	21.103	0.015	0.015	0.000	0.000	0.000	0.000
56	A	71	THR	0	-0.092	-0.068	21.241	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	72	VAL	0	-0.018	0.000	17.593	0.012	0.012	0.000	0.000	0.000	0.000
58	A	73	ARG	1	0.877	0.917	20.909	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.001	-0.034	20.949	0.012	0.012	0.000	0.000	0.000	0.000
60	A	75	ASP	-1	-0.740	-0.894	16.404	0.212	0.212	0.000	0.000	0.000	0.000
61	A	76	GLU	-1	-0.966	-0.969	17.786	0.124	0.124	0.000	0.000	0.000	0.000
62	A	77	GLU	-1	-0.761	-0.842	19.504	0.045	0.045	0.000	0.000	0.000	0.000
63	A	78	MET	0	-0.040	-0.004	13.055	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	79	LYS	1	0.816	0.901	13.792	-0.334	-0.334	0.000	0.000	0.000	0.000
65	A	80	ALA	0	0.026	0.024	15.469	0.018	0.018	0.000	0.000	0.000	0.000
66	A	81	MET	0	0.015	0.032	13.024	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	82	LEU	0	-0.030	-0.022	9.442	-0.038	-0.038	0.000	0.000	0.000	0.000
68	A	83	SER	0	-0.049	-0.029	11.860	0.013	0.013	0.000	0.000	0.000	0.000
69	A	84	TYR	0	0.025	0.028	13.941	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	85	TYR	0	-0.009	-0.023	7.470	-0.151	-0.151	0.000	0.000	0.000	0.000
71	A	86	TYR	0	0.001	-0.020	6.009	-0.085	-0.085	0.000	0.000	0.000	0.000
72	A	87	SER	0	-0.034	-0.021	10.486	-0.039	-0.039	0.000	0.000	0.000	0.000
73	A	88	THR	0	0.011	0.008	13.612	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	89	VAL	0	-0.019	-0.010	7.554	-0.040	-0.040	0.000	0.000	0.000	0.000
75	A	90	MET	0	-0.069	-0.027	11.005	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	91	GLU	-1	-0.839	-0.936	12.049	-0.091	-0.091	0.000	0.000	0.000	0.000
77	A	92	GLN	0	0.009	0.009	12.875	-0.060	-0.060	0.000	0.000	0.000	0.000
78	A	93	GLN	0	-0.032	-0.017	7.420	0.129	0.129	0.000	0.000	0.000	0.000
79	A	94	VAL	0	-0.039	-0.009	13.104	0.022	0.022	0.000	0.000	0.000	0.000
80	A	95	ASN	0	-0.111	-0.064	16.133	0.023	0.023	0.000	0.000	0.000	0.000
81	A	96	GLY	0	-0.027	0.004	16.372	0.010	0.010	0.000	0.000	0.000	0.000
82	A	97	GLN	0	-0.067	-0.037	16.261	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	98	LEU	0	-0.017	-0.014	12.733	-0.033	-0.033	0.000	0.000	0.000	0.000
84	A	99	ILE	0	-0.014	-0.002	8.235	0.011	0.011	0.000	0.000	0.000	0.000
85	A	100	GLU	-1	-0.895	-0.945	10.310	-0.551	-0.551	0.000	0.000	0.000	0.000
86	A	101	PRO	0	-0.038	-0.003	7.505	-0.123	-0.123	0.000	0.000	0.000	0.000
87	A	102	LEU	0	0.039	0.020	8.512	0.172	0.172	0.000	0.000	0.000	0.000
88	A	103	GLN	0	-0.048	-0.017	10.594	0.001	0.001	0.000	0.000	0.000	0.000
89	A	104	ILE	0	0.004	0.000	13.353	0.050	0.050	0.000	0.000	0.000	0.000
90	A	105	PHE	0	-0.030	-0.036	15.526	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.004	0.008	17.660	0.021	0.021	0.000	0.000	0.000	0.000
92	A	107	ARG	1	0.916	0.951	20.180	0.044	0.044	0.000	0.000	0.000	0.000
93	A	108	ALA	0	0.005	0.014	23.622	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:16:VAL)