FMO DATABASE

FMODB ID: 3J9NL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-663460.662965
FMO2-HF: Nuclear repulsion	626372.673218
FMO2-HF: Total energy	-37087.989748
FMO2-MP2: Total energy	-37196.045586

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.
-10.081	-2.751	3.389	-3.908	-6.811	-0.033

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 : -0.071 / q_NPA : -0.042

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	0.000	-0.008	3.040	-1.764	0.621	0.246	-1.098	-1.534	-0.003
4	A	19	ILE	0	0.008	0.012	5.006	0.218	0.240	-0.001	-0.003	-0.017	0.000
5	A	20	ARG	1	0.779	0.859	8.726	0.584	0.584	0.000	0.000	0.000	0.000
6	A	21	ILE	0	0.038	0.018	11.360	0.066	0.066	0.000	0.000	0.000	0.000
7	A	22	LYS	1	0.839	0.919	14.179	0.205	0.205	0.000	0.000	0.000	0.000
8	A	23	ILE	0	0.009	0.015	17.259	0.021	0.021	0.000	0.000	0.000	0.000
9	A	24	PRO	0	0.029	-0.002	19.994	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	25	ASN	0	-0.018	-0.015	22.742	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	26	SER	0	0.019	-0.003	22.730	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	27	GLY	0	0.003	0.024	19.343	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	28	ALA	0	0.010	-0.005	14.906	0.009	0.009	0.000	0.000	0.000	0.000
14	A	29	VAL	0	-0.011	0.000	12.419	0.003	0.003	0.000	0.000	0.000	0.000
15	A	30	ASP	-1	-0.758	-0.850	8.387	-0.586	-0.586	0.000	0.000	0.000	0.000
16	A	31	TRP	0	0.025	0.010	8.435	-0.048	-0.048	0.000	0.000	0.000	0.000
17	A	32	THR	0	-0.009	-0.006	2.720	-0.613	-0.312	0.739	-0.193	-0.847	0.000
18	A	33	VAL	0	-0.027	-0.007	3.714	0.071	0.408	0.003	-0.075	-0.265	0.000
19	A	34	HIS	0	0.023	0.002	2.696	-6.212	-2.164	2.402	-2.524	-3.926	-0.030
20	A	35	SER	0	0.028	0.031	3.833	-0.276	-0.039	0.000	-0.015	-0.222	0.000
21	A	36	GLY	0	0.009	-0.013	5.707	-0.498	-0.498	0.000	0.000	0.000	0.000
22	A	37	PRO	0	-0.044	-0.024	8.647	-0.115	-0.115	0.000	0.000	0.000	0.000
23	A	38	GLN	0	0.011	-0.002	9.492	0.112	0.112	0.000	0.000	0.000	0.000
24	A	39	LEU	0	0.036	0.037	8.579	-0.084	-0.084	0.000	0.000	0.000	0.000
25	A	40	LEU	0	-0.072	-0.051	10.935	0.011	0.011	0.000	0.000	0.000	0.000
26	A	41	PHE	0	0.023	-0.006	14.339	-0.040	-0.040	0.000	0.000	0.000	0.000
27	A	42	ARG	1	0.768	0.853	16.483	-0.053	-0.053	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.759	-0.886	13.288	0.150	0.150	0.000	0.000	0.000	0.000
29	A	44	VAL	0	-0.007	-0.004	12.482	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	45	LEU	0	-0.026	-0.002	14.768	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	46	ASP	-1	-0.807	-0.871	17.037	0.000	0.000	0.000	0.000	0.000	0.000
32	A	47	VAL	0	0.001	0.003	11.911	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	48	ILE	0	-0.030	-0.021	15.183	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	49	GLY	0	0.009	0.009	17.307	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	50	GLN	0	-0.072	-0.047	15.496	0.002	0.002	0.000	0.000	0.000	0.000
36	A	51	VAL	0	-0.066	-0.025	14.829	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	52	LEU	0	-0.048	-0.020	18.193	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	53	PRO	0	0.012	0.021	21.576	0.011	0.011	0.000	0.000	0.000	0.000
39	A	54	GLU	-1	-0.927	-0.973	23.784	-0.081	-0.081	0.000	0.000	0.000	0.000
40	A	55	ALA	0	-0.021	-0.003	23.635	0.006	0.006	0.000	0.000	0.000	0.000
41	A	56	THR	0	-0.021	-0.015	24.705	0.003	0.003	0.000	0.000	0.000	0.000
42	A	57	THR	0	-0.030	-0.016	20.298	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	58	THR	0	-0.062	-0.040	23.723	0.009	0.009	0.000	0.000	0.000	0.000
44	A	59	ALA	0	-0.004	-0.007	21.774	0.013	0.013	0.000	0.000	0.000	0.000
45	A	60	PHE	0	0.022	-0.002	15.942	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	61	GLU	-1	-0.814	-0.871	19.831	-0.074	-0.074	0.000	0.000	0.000	0.000
47	A	62	TYR	0	0.035	-0.003	16.466	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.823	-0.903	17.920	-0.174	-0.174	0.000	0.000	0.000	0.000
49	A	64	ASP	-1	-0.831	-0.903	18.625	-0.111	-0.111	0.000	0.000	0.000	0.000
50	A	65	GLU	-1	-0.911	-0.971	20.793	-0.086	-0.086	0.000	0.000	0.000	0.000
51	A	66	ASP	-1	-0.958	-0.966	22.140	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	67	GLY	0	-0.090	-0.036	22.917	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	68	ASP	-1	-0.915	-0.948	23.964	-0.068	-0.068	0.000	0.000	0.000	0.000
54	A	69	ARG	1	0.730	0.826	21.314	0.122	0.122	0.000	0.000	0.000	0.000
55	A	70	ILE	0	0.012	0.014	21.182	0.013	0.013	0.000	0.000	0.000	0.000
56	A	71	THR	0	-0.065	-0.047	21.122	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	72	VAL	0	-0.020	0.000	17.720	0.011	0.011	0.000	0.000	0.000	0.000
58	A	73	ARG	1	0.840	0.890	21.076	0.016	0.016	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.004	-0.034	21.180	0.014	0.014	0.000	0.000	0.000	0.000
60	A	75	ASP	-1	-0.727	-0.883	16.153	0.160	0.160	0.000	0.000	0.000	0.000
61	A	76	GLU	-1	-0.963	-0.965	17.484	0.103	0.103	0.000	0.000	0.000	0.000
62	A	77	GLU	-1	-0.762	-0.840	19.187	0.011	0.011	0.000	0.000	0.000	0.000
63	A	78	MET	0	-0.028	0.006	12.797	-0.035	-0.035	0.000	0.000	0.000	0.000
64	A	79	LYS	1	0.809	0.897	13.465	-0.292	-0.292	0.000	0.000	0.000	0.000
65	A	80	ALA	0	0.015	0.028	15.487	0.012	0.012	0.000	0.000	0.000	0.000
66	A	81	MET	0	0.017	0.030	13.293	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	82	LEU	0	-0.028	-0.024	9.385	-0.044	-0.044	0.000	0.000	0.000	0.000
68	A	83	SER	0	-0.039	-0.027	11.942	0.006	0.006	0.000	0.000	0.000	0.000
69	A	84	TYR	0	-0.006	-0.003	14.186	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	85	TYR	0	-0.009	-0.017	7.568	-0.155	-0.155	0.000	0.000	0.000	0.000
71	A	86	TYR	0	0.003	-0.022	5.775	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	87	SER	0	-0.031	-0.020	10.458	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	88	THR	0	-0.007	-0.002	13.723	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	89	VAL	0	-0.008	-0.005	7.610	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	90	MET	0	-0.066	-0.018	11.074	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	91	GLU	-1	-0.835	-0.934	12.218	-0.102	-0.102	0.000	0.000	0.000	0.000
77	A	92	GLN	0	-0.006	0.001	13.025	-0.043	-0.043	0.000	0.000	0.000	0.000
78	A	93	GLN	0	-0.037	-0.020	7.429	0.136	0.136	0.000	0.000	0.000	0.000
79	A	94	VAL	0	-0.031	-0.010	13.197	0.031	0.031	0.000	0.000	0.000	0.000
80	A	95	ASN	0	-0.120	-0.065	16.236	0.032	0.032	0.000	0.000	0.000	0.000
81	A	96	GLY	0	-0.034	-0.010	16.677	0.007	0.007	0.000	0.000	0.000	0.000
82	A	97	GLN	0	-0.052	-0.024	16.366	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	98	LEU	0	-0.023	-0.013	13.303	-0.032	-0.032	0.000	0.000	0.000	0.000
84	A	99	ILE	0	-0.014	-0.004	8.795	0.012	0.012	0.000	0.000	0.000	0.000
85	A	100	GLU	-1	-0.831	-0.908	10.804	-0.531	-0.531	0.000	0.000	0.000	0.000
86	A	101	PRO	0	-0.043	-0.002	7.547	-0.120	-0.120	0.000	0.000	0.000	0.000
87	A	102	LEU	0	0.035	0.008	8.503	0.183	0.183	0.000	0.000	0.000	0.000
88	A	103	GLN	0	-0.093	-0.040	10.549	0.017	0.017	0.000	0.000	0.000	0.000
89	A	104	ILE	0	0.008	0.007	13.347	0.046	0.046	0.000	0.000	0.000	0.000
90	A	105	PHE	0	-0.026	-0.014	15.586	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.017	0.013	17.890	0.022	0.022	0.000	0.000	0.000	0.000
92	A	107	ARG	1	0.877	0.930	20.404	0.069	0.069	0.000	0.000	0.000	0.000
93	A	108	ALA	0	0.033	0.035	23.870	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)