FMO DATABASE

FMODB ID: NN93Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-660866.182815
FMO2-HF: Nuclear repulsion	623778.945599
FMO2-HF: Total energy	-37087.237216
FMO2-MP2: Total energy	-37195.294689

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.
-5.954	-1.209	2.351	-2.543	-4.552	-0.012

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 : -0.050 / q_NPA : -0.037

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	0.008	0.003	2.860	-0.996	0.937	0.128	-0.723	-1.338	0.001
4	A	19	ILE	0	0.002	0.003	4.775	0.238	0.275	-0.001	-0.006	-0.030	0.000
5	A	20	ARG	1	0.857	0.905	8.479	0.601	0.601	0.000	0.000	0.000	0.000
6	A	21	ILE	0	0.013	0.003	11.027	0.065	0.065	0.000	0.000	0.000	0.000
7	A	22	LYS	1	0.865	0.938	14.112	0.202	0.202	0.000	0.000	0.000	0.000
8	A	23	ILE	0	0.020	0.016	17.291	0.023	0.023	0.000	0.000	0.000	0.000
9	A	24	PRO	0	0.018	-0.004	19.773	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	25	ASN	0	-0.036	-0.030	22.767	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	26	SER	0	-0.013	-0.013	22.152	0.000	0.000	0.000	0.000	0.000	0.000
12	A	27	GLY	0	0.042	0.040	18.770	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	28	ALA	0	0.015	-0.011	14.538	0.011	0.011	0.000	0.000	0.000	0.000
14	A	29	VAL	0	0.002	0.019	12.604	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	30	ASP	-1	-0.794	-0.860	8.164	-0.616	-0.616	0.000	0.000	0.000	0.000
16	A	31	TRP	0	0.019	0.002	8.215	0.037	0.037	0.000	0.000	0.000	0.000
17	A	32	THR	0	-0.009	-0.009	2.275	-0.416	-0.717	1.732	-0.331	-1.100	0.000
18	A	33	VAL	0	-0.002	0.007	4.090	0.061	0.341	0.000	-0.049	-0.231	0.000
19	A	34	HIS	0	-0.008	-0.015	2.843	-2.885	-0.240	0.493	-1.420	-1.718	-0.013
20	A	35	SER	0	0.041	0.024	4.262	-0.338	-0.187	-0.001	-0.014	-0.135	0.000
21	A	36	GLY	0	0.015	-0.003	6.055	-0.481	-0.481	0.000	0.000	0.000	0.000
22	A	37	PRO	0	-0.077	-0.030	8.602	-0.203	-0.203	0.000	0.000	0.000	0.000
23	A	38	GLN	0	0.023	0.010	9.886	0.148	0.148	0.000	0.000	0.000	0.000
24	A	39	LEU	0	0.048	0.035	8.518	-0.065	-0.065	0.000	0.000	0.000	0.000
25	A	40	LEU	0	-0.050	-0.027	11.115	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	41	PHE	0	0.028	-0.008	14.433	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	42	ARG	1	0.861	0.930	16.631	-0.106	-0.106	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.760	-0.882	13.321	0.262	0.262	0.000	0.000	0.000	0.000
29	A	44	VAL	0	-0.029	-0.014	12.146	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	45	LEU	0	-0.052	-0.025	14.521	-0.038	-0.038	0.000	0.000	0.000	0.000
31	A	46	ASP	-1	-0.886	-0.938	16.788	0.059	0.059	0.000	0.000	0.000	0.000
32	A	47	VAL	0	0.005	0.004	11.959	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	48	ILE	0	-0.027	-0.018	15.153	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	49	GLY	0	0.005	0.008	17.270	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	50	GLN	0	-0.073	-0.041	15.608	0.017	0.017	0.000	0.000	0.000	0.000
36	A	51	VAL	0	-0.054	-0.023	14.774	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	52	LEU	0	-0.056	-0.034	18.084	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	53	PRO	0	0.022	0.030	21.433	0.010	0.010	0.000	0.000	0.000	0.000
39	A	54	GLU	-1	-0.961	-0.982	23.788	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	55	ALA	0	-0.025	-0.005	23.948	0.003	0.003	0.000	0.000	0.000	0.000
41	A	56	THR	0	-0.049	-0.020	25.364	0.007	0.007	0.000	0.000	0.000	0.000
42	A	57	THR	0	0.019	0.000	20.252	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	58	THR	0	-0.060	-0.042	23.232	0.008	0.008	0.000	0.000	0.000	0.000
44	A	59	ALA	0	-0.017	-0.006	21.592	0.014	0.014	0.000	0.000	0.000	0.000
45	A	60	PHE	0	0.014	-0.012	15.907	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	61	GLU	-1	-0.822	-0.899	19.915	-0.064	-0.064	0.000	0.000	0.000	0.000
47	A	62	TYR	0	0.042	0.001	16.385	-0.027	-0.027	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.930	-0.961	17.820	-0.160	-0.160	0.000	0.000	0.000	0.000
49	A	64	ASP	-1	-0.824	-0.927	18.413	-0.107	-0.107	0.000	0.000	0.000	0.000
50	A	65	GLU	-1	-0.955	-0.985	20.637	-0.091	-0.091	0.000	0.000	0.000	0.000
51	A	66	ASP	-1	-0.927	-0.946	21.777	-0.070	-0.070	0.000	0.000	0.000	0.000
52	A	67	GLY	0	-0.114	-0.054	22.781	0.000	0.000	0.000	0.000	0.000	0.000
53	A	68	ASP	-1	-0.919	-0.944	23.785	-0.066	-0.066	0.000	0.000	0.000	0.000
54	A	69	ARG	1	0.760	0.865	21.609	0.117	0.117	0.000	0.000	0.000	0.000
55	A	70	ILE	0	0.027	0.032	20.895	0.019	0.019	0.000	0.000	0.000	0.000
56	A	71	THR	0	-0.096	-0.073	21.145	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	72	VAL	0	-0.008	0.007	17.650	0.013	0.013	0.000	0.000	0.000	0.000
58	A	73	ARG	1	0.908	0.931	20.927	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	74	SER	0	0.045	0.025	20.984	0.011	0.011	0.000	0.000	0.000	0.000
60	A	75	ASP	-1	-0.801	-0.921	17.131	0.204	0.204	0.000	0.000	0.000	0.000
61	A	76	GLU	-1	-0.984	-0.977	17.821	0.124	0.124	0.000	0.000	0.000	0.000
62	A	77	GLU	-1	-0.829	-0.920	19.541	0.038	0.038	0.000	0.000	0.000	0.000
63	A	78	MET	0	-0.033	-0.005	13.342	-0.032	-0.032	0.000	0.000	0.000	0.000
64	A	79	LYS	1	0.881	0.934	14.121	-0.388	-0.388	0.000	0.000	0.000	0.000
65	A	80	ALA	0	0.024	0.015	15.440	0.012	0.012	0.000	0.000	0.000	0.000
66	A	81	MET	0	0.015	0.030	12.907	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	82	LEU	0	-0.035	-0.026	9.549	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	83	SER	0	-0.052	-0.021	11.766	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	84	TYR	0	0.057	0.040	13.852	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	85	TYR	0	-0.014	-0.037	7.343	-0.171	-0.171	0.000	0.000	0.000	0.000
71	A	86	TYR	0	-0.005	-0.025	6.268	0.037	0.037	0.000	0.000	0.000	0.000
72	A	87	SER	0	-0.015	-0.001	10.403	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	88	THR	0	0.012	0.012	13.588	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	89	VAL	0	-0.022	-0.008	7.532	-0.045	-0.045	0.000	0.000	0.000	0.000
75	A	90	MET	0	-0.075	-0.030	10.949	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	91	GLU	-1	-0.839	-0.938	11.998	-0.133	-0.133	0.000	0.000	0.000	0.000
77	A	92	GLN	0	0.012	-0.001	12.742	-0.073	-0.073	0.000	0.000	0.000	0.000
78	A	93	GLN	0	-0.037	-0.018	7.561	0.148	0.148	0.000	0.000	0.000	0.000
79	A	94	VAL	0	-0.042	-0.009	13.087	0.030	0.030	0.000	0.000	0.000	0.000
80	A	95	ASN	0	-0.096	-0.047	16.113	0.031	0.031	0.000	0.000	0.000	0.000
81	A	96	GLY	0	-0.031	0.001	16.280	0.015	0.015	0.000	0.000	0.000	0.000
82	A	97	GLN	0	-0.068	-0.040	16.130	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	98	LEU	0	-0.020	-0.014	12.500	-0.041	-0.041	0.000	0.000	0.000	0.000
84	A	99	ILE	0	-0.009	0.001	8.073	0.011	0.011	0.000	0.000	0.000	0.000
85	A	100	GLU	-1	-0.908	-0.943	10.138	-0.625	-0.625	0.000	0.000	0.000	0.000
86	A	101	PRO	0	-0.024	0.005	7.459	-0.142	-0.142	0.000	0.000	0.000	0.000
87	A	102	LEU	0	0.035	0.018	8.381	0.190	0.190	0.000	0.000	0.000	0.000
88	A	103	GLN	0	-0.046	-0.014	10.462	0.013	0.013	0.000	0.000	0.000	0.000
89	A	104	ILE	0	0.004	0.000	13.254	0.053	0.053	0.000	0.000	0.000	0.000
90	A	105	PHE	0	-0.038	-0.043	15.443	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.003	0.009	17.670	0.023	0.023	0.000	0.000	0.000	0.000
92	A	107	ARG	1	0.926	0.971	20.141	0.046	0.046	0.000	0.000	0.000	0.000
93	A	108	ALA	0	-0.003	0.008	23.582	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:VAL)