FMO DATABASE

FMODB ID: 53MQZ

Calculation Name: 4AOK-E-Xray372

Preferred Name:

Target Type:

Ligand Name: (2z,4s)-3-aza-5-carboxyl-2-methyl-4(methylcarboxy)pent-2-enoyl

ligand 3-letter code: 3A5

PDB ID: 4AOK

Chain ID: E

ChEMBL ID:

UniProt ID: P0A790

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	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	92
LigandCharge	3A5=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-593526.06275
FMO2-HF: Nuclear repulsion	557360.914735
FMO2-HF: Total energy	-36165.148014
FMO2-MP2: Total energy	-36269.082111

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(E:25:3A5)

Summations of interaction energy for fragment #1(E:25:3A5)

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.
-75.341	-53.043	58.028	-46.208	-34.12	-0.011

Interaction energy analysis for fragmet #1(E:25:3A5)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.553 / q_NPA : -0.528

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

Sort

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	E	27	ALA	0	-0.046	0.003	3.723	-12.227	-10.379	0.013	-1.102	-0.760	0.016
4	E	28	ILE	0	0.029	-0.008	5.695	0.623	0.623	0.000	0.000	0.000	0.000
5	E	29	ASP	-1	-0.767	-0.862	8.735	15.303	15.303	0.000	0.000	0.000	0.000
6	E	30	GLN	0	0.041	-0.007	12.219	0.327	0.327	0.000	0.000	0.000	0.000
7	E	31	ASP	-1	-0.851	-0.936	13.047	13.325	13.325	0.000	0.000	0.000	0.000
8	E	32	PHE	0	-0.065	-0.035	12.690	-0.642	-0.642	0.000	0.000	0.000	0.000
9	E	33	LEU	0	-0.029	-0.004	8.529	-0.134	-0.134	0.000	0.000	0.000	0.000
10	E	34	ASP	-1	-0.801	-0.890	12.585	13.701	13.701	0.000	0.000	0.000	0.000
11	E	35	ALA	0	-0.103	-0.050	16.106	-0.565	-0.565	0.000	0.000	0.000	0.000
12	E	36	ALA	0	-0.012	-0.011	13.942	-0.497	-0.497	0.000	0.000	0.000	0.000
13	E	37	GLY	0	-0.033	-0.014	15.829	-0.030	-0.030	0.000	0.000	0.000	0.000
14	E	38	ILE	0	-0.037	0.006	9.201	0.147	0.147	0.000	0.000	0.000	0.000
15	E	39	LEU	0	-0.016	-0.017	11.179	-0.436	-0.436	0.000	0.000	0.000	0.000
16	E	40	GLU	-1	-0.861	-0.938	7.184	20.789	20.789	0.000	0.000	0.000	0.000
17	E	41	ASN	0	-0.092	-0.065	6.361	0.056	0.056	0.000	0.000	0.000	0.000
18	E	42	GLU	-1	-0.845	-0.892	7.317	18.643	18.643	0.000	0.000	0.000	0.000
19	E	43	ALA	0	-0.041	-0.030	6.631	1.781	1.781	0.000	0.000	0.000	0.000
20	E	44	ILE	0	0.005	0.002	5.085	-1.660	-1.660	0.000	0.000	0.000	0.000
21	E	45	ASP	-1	-0.882	-0.936	7.634	28.786	28.786	0.000	0.000	0.000	0.000
22	E	46	ILE	0	-0.002	-0.013	6.092	-1.168	-1.168	0.000	0.000	0.000	0.000
23	E	47	TRP	0	-0.030	-0.025	9.917	-0.108	-0.108	0.000	0.000	0.000	0.000
24	E	48	ASN	0	-0.003	-0.016	11.503	-2.928	-2.928	0.000	0.000	0.000	0.000
25	E	49	VAL	0	-0.017	-0.021	13.763	-1.230	-1.230	0.000	0.000	0.000	0.000
26	E	50	THR	0	0.012	0.028	15.877	-1.145	-1.145	0.000	0.000	0.000	0.000
27	E	51	ASN	0	-0.023	-0.017	12.673	-0.963	-0.963	0.000	0.000	0.000	0.000
28	E	52	GLY	0	-0.005	0.007	16.488	-0.411	-0.411	0.000	0.000	0.000	0.000
29	E	53	LYS	1	0.880	0.953	10.923	-28.192	-28.192	0.000	0.000	0.000	0.000
30	E	54	ARG	1	0.897	0.945	11.327	-20.772	-20.772	0.000	0.000	0.000	0.000
31	E	55	PHE	0	-0.025	-0.009	4.581	-0.558	-0.313	-0.001	-0.011	-0.233	0.000
32	E	56	SER	0	0.043	0.017	6.723	-2.542	-2.542	0.000	0.000	0.000	0.000
33	E	57	THR	0	-0.067	-0.043	1.833	-17.361	-15.749	10.674	-6.391	-5.896	0.028
34	E	58	TYR	0	0.013	0.005	2.241	-17.344	-11.186	4.990	-3.745	-7.402	-0.024
35	E	59	ALA	0	0.026	0.016	2.605	-1.455	-0.671	2.407	-1.640	-1.550	-0.020
36	E	60	ILE	0	-0.014	-0.010	2.381	-2.874	-2.050	2.484	-0.823	-2.485	-0.005
37	E	61	ALA	0	0.046	0.022	4.838	1.292	1.357	-0.001	-0.005	-0.059	0.000
38	E	62	ALA	0	-0.047	-0.024	8.536	0.492	0.492	0.000	0.000	0.000	0.000
39	E	63	GLU	-1	-0.950	-0.976	10.301	14.154	14.154	0.000	0.000	0.000	0.000
40	E	64	ARG	1	0.812	0.892	14.040	-13.383	-13.383	0.000	0.000	0.000	0.000
41	E	65	GLY	0	0.028	0.021	16.225	-0.542	-0.542	0.000	0.000	0.000	0.000
42	E	66	SER	0	-0.079	-0.052	14.034	0.232	0.232	0.000	0.000	0.000	0.000
43	E	67	ARG	1	0.824	0.874	15.491	-14.524	-14.524	0.000	0.000	0.000	0.000
44	E	68	ILE	0	-0.055	-0.016	9.633	0.870	0.870	0.000	0.000	0.000	0.000
45	E	69	ILE	0	0.027	-0.002	8.512	-0.001	-0.001	0.000	0.000	0.000	0.000
46	E	70	SER	0	-0.108	-0.038	6.030	-2.498	-2.498	0.000	0.000	0.000	0.000
47	E	71	VAL	0	0.005	-0.003	3.478	6.082	6.501	0.105	-0.372	-0.152	0.003
48	E	72	ASN	0	0.179	0.024	1.940	-45.551	-38.586	14.757	-18.594	-3.129	-0.072
49	E	73	GLY	0	0.021	0.003	2.135	5.666	7.798	7.690	-6.867	-2.956	-0.033
50	E	74	ALA	0	-0.027	-0.022	2.343	-13.363	-12.590	5.393	-2.207	-3.959	0.042
51	E	75	ALA	0	0.063	0.022	1.935	-27.658	-27.957	9.466	-3.992	-5.175	0.050
52	E	76	ALA	0	0.013	0.009	3.767	-13.588	-12.816	0.051	-0.459	-0.364	0.004
53	E	77	HIS	0	-0.043	-0.006	6.132	-9.432	-9.432	0.000	0.000	0.000	0.000
54	E	78	CYS	0	-0.135	-0.086	6.427	-6.705	-6.705	0.000	0.000	0.000	0.000
55	E	79	ALA	0	0.019	0.002	8.233	-3.624	-3.624	0.000	0.000	0.000	0.000
56	E	80	SER	0	-0.024	0.007	9.643	1.385	1.385	0.000	0.000	0.000	0.000
57	E	81	VAL	0	0.024	-0.001	11.839	-0.116	-0.116	0.000	0.000	0.000	0.000
58	E	82	GLY	0	-0.013	-0.002	12.941	-1.315	-1.315	0.000	0.000	0.000	0.000
59	E	83	ASP	-1	-0.853	-0.918	12.451	23.371	23.371	0.000	0.000	0.000	0.000
60	E	84	ILE	0	0.000	-0.006	13.729	0.492	0.492	0.000	0.000	0.000	0.000
61	E	85	VAL	0	-0.004	-0.007	10.166	0.451	0.451	0.000	0.000	0.000	0.000
62	E	86	ILE	0	-0.024	-0.007	13.416	-1.449	-1.449	0.000	0.000	0.000	0.000
63	E	87	ILE	0	0.016	0.011	8.742	1.839	1.839	0.000	0.000	0.000	0.000
64	E	88	ALA	0	-0.023	-0.003	11.554	-1.892	-1.892	0.000	0.000	0.000	0.000
65	E	89	SER	0	0.007	-0.007	11.086	1.652	1.652	0.000	0.000	0.000	0.000
66	E	90	PHE	0	-0.021	-0.004	12.575	-1.455	-1.455	0.000	0.000	0.000	0.000
67	E	91	VAL	0	0.034	0.022	14.700	0.226	0.226	0.000	0.000	0.000	0.000
68	E	92	THR	0	-0.055	-0.031	17.413	-0.284	-0.284	0.000	0.000	0.000	0.000
69	E	93	MET	0	0.008	0.006	20.442	-0.288	-0.288	0.000	0.000	0.000	0.000
70	E	94	PRO	0	-0.008	0.005	23.863	0.076	0.076	0.000	0.000	0.000	0.000
71	E	95	ASP	-1	-0.830	-0.920	27.466	9.621	9.621	0.000	0.000	0.000	0.000
72	E	96	GLU	-1	-0.978	-0.981	29.228	8.785	8.785	0.000	0.000	0.000	0.000
73	E	97	GLU	-1	-0.819	-0.923	27.313	9.596	9.596	0.000	0.000	0.000	0.000
74	E	98	ALA	0	-0.026	-0.026	25.925	0.159	0.159	0.000	0.000	0.000	0.000
75	E	99	ARG	1	0.777	0.880	26.915	-9.138	-9.138	0.000	0.000	0.000	0.000
76	E	100	THR	0	-0.059	-0.024	29.422	-0.141	-0.141	0.000	0.000	0.000	0.000
77	E	101	TRP	0	0.023	0.019	20.196	-0.224	-0.224	0.000	0.000	0.000	0.000
78	E	102	ARG	1	0.903	0.944	25.022	-10.048	-10.048	0.000	0.000	0.000	0.000
79	E	103	PRO	0	0.004	0.008	20.056	0.154	0.154	0.000	0.000	0.000	0.000
80	E	104	ASN	0	0.002	0.019	18.230	-0.969	-0.969	0.000	0.000	0.000	0.000
81	E	105	VAL	0	-0.008	-0.002	18.193	0.753	0.753	0.000	0.000	0.000	0.000
82	E	106	ALA	0	0.002	0.007	17.285	-0.669	-0.669	0.000	0.000	0.000	0.000
83	E	107	TYR	0	-0.036	-0.018	18.656	0.634	0.634	0.000	0.000	0.000	0.000
84	E	108	PHE	0	0.067	0.006	16.141	-0.269	-0.269	0.000	0.000	0.000	0.000
85	E	109	GLU	-1	-0.949	-0.987	20.402	12.235	12.235	0.000	0.000	0.000	0.000
86	E	110	GLY	0	0.016	0.018	21.379	0.004	0.004	0.000	0.000	0.000	0.000
87	E	111	ASP	-1	-0.872	-0.911	18.252	16.628	16.628	0.000	0.000	0.000	0.000
88	E	112	ASN	0	-0.011	-0.003	13.898	-0.353	-0.353	0.000	0.000	0.000	0.000
89	E	113	GLU	-1	-0.917	-0.948	17.952	12.871	12.871	0.000	0.000	0.000	0.000
90	E	114	MET	0	-0.001	0.006	17.827	-0.310	-0.310	0.000	0.000	0.000	0.000
91	E	115	LYS	1	0.854	0.926	21.090	-12.377	-12.377	0.000	0.000	0.000	0.000
92	E	116	ARG	1	0.932	0.984	23.170	-11.134	-11.134	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:25:3A5)