FMO DATABASE

FMODB ID: YYL72

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

Total energy (hartree)

FMO2-HF: Electronic energy	-593730.271167
FMO2-HF: Nuclear repulsion	557564.649663
FMO2-HF: Total energy	-36165.621504
FMO2-MP2: Total energy	-36269.487396

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.
-73.327	-73.912	85.633	-48.303	-36.745	0.024

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 : -0.542 / q_NPA : -0.510

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	-0.040	-0.001	3.718	-12.231	-10.200	0.022	-1.271	-0.781	0.017
4	E	28	ILE	0	0.027	-0.006	5.939	0.700	0.700	0.000	0.000	0.000	0.000
5	E	29	ASP	-1	-0.762	-0.850	8.893	15.551	15.551	0.000	0.000	0.000	0.000
6	E	30	GLN	0	0.039	-0.012	12.081	0.459	0.459	0.000	0.000	0.000	0.000
7	E	31	ASP	-1	-0.841	-0.928	13.153	13.430	13.430	0.000	0.000	0.000	0.000
8	E	32	PHE	0	-0.059	-0.040	12.854	-0.678	-0.678	0.000	0.000	0.000	0.000
9	E	33	LEU	0	-0.028	0.001	8.441	-0.140	-0.140	0.000	0.000	0.000	0.000
10	E	34	ASP	-1	-0.755	-0.857	12.584	13.995	13.995	0.000	0.000	0.000	0.000
11	E	35	ALA	0	-0.092	-0.043	16.099	-0.582	-0.582	0.000	0.000	0.000	0.000
12	E	36	ALA	0	-0.014	-0.012	13.886	-0.510	-0.510	0.000	0.000	0.000	0.000
13	E	37	GLY	0	-0.040	-0.017	15.712	-0.034	-0.034	0.000	0.000	0.000	0.000
14	E	38	ILE	0	-0.034	0.006	9.097	0.141	0.141	0.000	0.000	0.000	0.000
15	E	39	LEU	0	-0.021	-0.021	11.049	-0.434	-0.434	0.000	0.000	0.000	0.000
16	E	40	GLU	-1	-0.842	-0.929	7.146	21.471	21.471	0.000	0.000	0.000	0.000
17	E	41	ASN	0	-0.105	-0.065	6.147	0.062	0.062	0.000	0.000	0.000	0.000
18	E	42	GLU	-1	-0.820	-0.865	7.121	19.071	19.071	0.000	0.000	0.000	0.000
19	E	43	ALA	0	-0.040	-0.029	6.585	1.862	1.862	0.000	0.000	0.000	0.000
20	E	44	ILE	0	-0.004	0.001	4.911	-1.749	-1.749	0.000	0.000	0.000	0.000
21	E	45	ASP	-1	-0.855	-0.915	7.482	29.121	29.121	0.000	0.000	0.000	0.000
22	E	46	ILE	0	-0.006	-0.015	5.996	-1.116	-1.116	0.000	0.000	0.000	0.000
23	E	47	TRP	0	-0.046	-0.034	9.932	-0.395	-0.395	0.000	0.000	0.000	0.000
24	E	48	ASN	0	-0.003	-0.015	11.271	-2.924	-2.924	0.000	0.000	0.000	0.000
25	E	49	VAL	0	-0.015	-0.020	13.654	-1.241	-1.241	0.000	0.000	0.000	0.000
26	E	50	THR	0	0.003	0.023	15.785	-1.191	-1.191	0.000	0.000	0.000	0.000
27	E	51	ASN	0	-0.042	-0.030	12.776	-0.815	-0.815	0.000	0.000	0.000	0.000
28	E	52	GLY	0	-0.006	0.007	16.577	-0.424	-0.424	0.000	0.000	0.000	0.000
29	E	53	LYS	1	0.855	0.939	10.898	-28.459	-28.459	0.000	0.000	0.000	0.000
30	E	54	ARG	1	0.890	0.944	11.394	-20.492	-20.492	0.000	0.000	0.000	0.000
31	E	55	PHE	0	-0.025	-0.008	4.715	-0.613	-0.387	-0.001	-0.009	-0.216	0.000
32	E	56	SER	0	0.034	-0.002	6.838	-2.235	-2.235	0.000	0.000	0.000	0.000
33	E	57	THR	0	-0.072	-0.064	1.571	-17.730	-26.996	25.845	-10.594	-5.985	0.031
34	E	58	TYR	0	0.004	-0.007	1.871	-21.767	-20.687	15.291	-6.241	-10.130	-0.007
35	E	59	ALA	0	0.031	0.016	2.386	-1.010	-1.110	3.749	-1.786	-1.863	-0.024
36	E	60	ILE	0	-0.025	-0.020	2.499	-3.040	-1.801	1.316	-0.545	-2.010	-0.004
37	E	61	ALA	0	0.042	0.017	4.937	1.195	1.243	-0.001	-0.003	-0.044	0.000
38	E	62	ALA	0	-0.050	-0.026	8.669	0.460	0.460	0.000	0.000	0.000	0.000
39	E	63	GLU	-1	-0.953	-0.978	10.525	14.231	14.231	0.000	0.000	0.000	0.000
40	E	64	ARG	1	0.762	0.855	14.263	-13.592	-13.592	0.000	0.000	0.000	0.000
41	E	65	GLY	0	0.023	0.019	16.405	-0.565	-0.565	0.000	0.000	0.000	0.000
42	E	66	SER	0	-0.071	-0.048	14.297	0.206	0.206	0.000	0.000	0.000	0.000
43	E	67	ARG	1	0.736	0.837	15.665	-14.654	-14.654	0.000	0.000	0.000	0.000
44	E	68	ILE	0	-0.044	-0.009	9.642	0.845	0.845	0.000	0.000	0.000	0.000
45	E	69	ILE	0	0.026	0.002	8.513	0.064	0.064	0.000	0.000	0.000	0.000
46	E	70	SER	0	-0.087	-0.035	6.134	-2.267	-2.267	0.000	0.000	0.000	0.000
47	E	71	VAL	0	-0.001	-0.004	3.396	5.931	6.329	0.143	-0.360	-0.181	0.003
48	E	72	ASN	0	0.153	0.020	1.870	-41.425	-38.738	14.094	-13.609	-3.173	-0.056
49	E	73	GLY	0	0.029	0.013	2.109	7.840	10.212	7.536	-7.018	-2.890	-0.027
50	E	74	ALA	0	-0.034	-0.027	2.114	-13.500	-14.770	7.530	-2.267	-3.993	0.046
51	E	75	ALA	0	0.075	0.022	1.894	-29.256	-30.002	10.066	-4.197	-5.123	0.042
52	E	76	ALA	0	0.016	0.017	3.812	-13.374	-12.658	0.043	-0.403	-0.356	0.003
53	E	77	HIS	0	-0.038	-0.006	6.151	-9.633	-9.633	0.000	0.000	0.000	0.000
54	E	78	CYS	0	-0.116	-0.074	6.781	-7.276	-7.276	0.000	0.000	0.000	0.000
55	E	79	ALA	0	0.012	0.004	8.035	-3.433	-3.433	0.000	0.000	0.000	0.000
56	E	80	SER	0	-0.015	0.007	9.531	1.247	1.247	0.000	0.000	0.000	0.000
57	E	81	VAL	0	0.025	-0.002	11.613	-0.131	-0.131	0.000	0.000	0.000	0.000
58	E	82	GLY	0	-0.010	-0.001	12.846	-1.339	-1.339	0.000	0.000	0.000	0.000
59	E	83	ASP	-1	-0.832	-0.904	12.337	23.595	23.595	0.000	0.000	0.000	0.000
60	E	84	ILE	0	-0.002	-0.003	13.626	0.536	0.536	0.000	0.000	0.000	0.000
61	E	85	VAL	0	-0.008	-0.013	10.114	0.413	0.413	0.000	0.000	0.000	0.000
62	E	86	ILE	0	-0.026	-0.006	13.319	-1.449	-1.449	0.000	0.000	0.000	0.000
63	E	87	ILE	0	0.022	0.012	8.659	1.735	1.735	0.000	0.000	0.000	0.000
64	E	88	ALA	0	-0.023	-0.007	11.498	-1.909	-1.909	0.000	0.000	0.000	0.000
65	E	89	SER	0	-0.004	-0.013	11.013	1.717	1.717	0.000	0.000	0.000	0.000
66	E	90	PHE	0	-0.022	-0.008	12.507	-1.444	-1.444	0.000	0.000	0.000	0.000
67	E	91	VAL	0	0.028	0.018	14.588	0.256	0.256	0.000	0.000	0.000	0.000
68	E	92	THR	0	-0.042	-0.025	17.307	-0.255	-0.255	0.000	0.000	0.000	0.000
69	E	93	MET	0	0.000	0.000	20.311	-0.288	-0.288	0.000	0.000	0.000	0.000
70	E	94	PRO	0	-0.017	0.004	23.747	0.069	0.069	0.000	0.000	0.000	0.000
71	E	95	ASP	-1	-0.813	-0.881	27.338	9.584	9.584	0.000	0.000	0.000	0.000
72	E	96	GLU	-1	-0.975	-0.986	29.095	8.787	8.787	0.000	0.000	0.000	0.000
73	E	97	GLU	-1	-0.796	-0.915	27.235	9.821	9.821	0.000	0.000	0.000	0.000
74	E	98	ALA	0	-0.035	-0.027	25.833	0.158	0.158	0.000	0.000	0.000	0.000
75	E	99	ARG	1	0.752	0.839	26.815	-9.180	-9.180	0.000	0.000	0.000	0.000
76	E	100	THR	0	-0.059	-0.021	29.362	-0.138	-0.138	0.000	0.000	0.000	0.000
77	E	101	TRP	0	0.028	0.019	19.785	-0.175	-0.175	0.000	0.000	0.000	0.000
78	E	102	ARG	1	0.904	0.948	24.927	-10.076	-10.076	0.000	0.000	0.000	0.000
79	E	103	PRO	0	0.000	0.006	19.914	0.137	0.137	0.000	0.000	0.000	0.000
80	E	104	ASN	0	0.008	0.019	18.146	-0.981	-0.981	0.000	0.000	0.000	0.000
81	E	105	VAL	0	-0.018	-0.007	18.089	0.761	0.761	0.000	0.000	0.000	0.000
82	E	106	ALA	0	0.008	0.010	17.253	-0.675	-0.675	0.000	0.000	0.000	0.000
83	E	107	TYR	0	-0.028	-0.019	18.646	0.634	0.634	0.000	0.000	0.000	0.000
84	E	108	PHE	0	0.071	0.011	16.097	-0.281	-0.281	0.000	0.000	0.000	0.000
85	E	109	GLU	-1	-0.978	-0.990	20.341	12.135	12.135	0.000	0.000	0.000	0.000
86	E	110	GLY	0	0.031	0.021	21.313	0.017	0.017	0.000	0.000	0.000	0.000
87	E	111	ASP	-1	-0.874	-0.923	18.373	16.404	16.404	0.000	0.000	0.000	0.000
88	E	112	ASN	0	-0.020	-0.020	13.723	-0.146	-0.146	0.000	0.000	0.000	0.000
89	E	113	GLU	-1	-0.833	-0.900	17.897	13.159	13.159	0.000	0.000	0.000	0.000
90	E	114	MET	0	-0.010	0.009	17.531	-0.311	-0.311	0.000	0.000	0.000	0.000
91	E	115	LYS	1	0.847	0.918	21.181	-12.300	-12.300	0.000	0.000	0.000	0.000
92	E	116	ARG	1	0.943	0.985	23.312	-11.264	-11.264	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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