FMO DATABASE

FMODB ID: 39N9L

Calculation Name: 5J5V-B-Xray372

Preferred Name:

Target Type:

Ligand Name: (2s)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid

ligand 3-letter code: LLP

PDB ID: 5J5V

Chain ID: B

ChEMBL ID:

UniProt ID: Q0T963

Base Structure: X-ray

Registration Date: 2023-06-21

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-634894.020895
FMO2-HF: Nuclear repulsion	597212.763669
FMO2-HF: Total energy	-37681.257225
FMO2-MP2: Total energy	-37790.765423

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(B:132:LEU)

Summations of interaction energy for fragment #1(B:132:LEU)

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.
-6.719	-0.331	3.072	-4.092	-5.369	-0.029

Interaction energy analysis for fragmet #1(B:132:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.008

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	B	134	GLN	0	-0.064	-0.038	3.874	0.744	2.682	-0.023	-1.015	-0.899	0.001
4	B	135	LYS	1	0.931	0.969	7.282	-1.830	-1.830	0.000	0.000	0.000	0.000
5	B	136	GLN	0	-0.018	-0.029	9.939	-0.286	-0.286	0.000	0.000	0.000	0.000
6	B	137	GLU	-1	-0.736	-0.867	8.968	1.133	1.133	0.000	0.000	0.000	0.000
7	B	138	SER	0	0.056	0.030	11.336	-0.104	-0.104	0.000	0.000	0.000	0.000
8	B	139	ALA	0	-0.031	-0.007	12.858	-0.068	-0.068	0.000	0.000	0.000	0.000
9	B	140	ILE	0	0.005	0.002	14.505	-0.052	-0.052	0.000	0.000	0.000	0.000
10	B	141	LYS	1	0.911	0.951	12.900	0.156	0.156	0.000	0.000	0.000	0.000
11	B	142	LYS	1	0.954	0.986	15.183	-0.102	-0.102	0.000	0.000	0.000	0.000
12	B	143	ILE	0	-0.003	0.007	18.244	-0.017	-0.017	0.000	0.000	0.000	0.000
13	B	144	ASP	-1	-0.811	-0.933	17.489	0.085	0.085	0.000	0.000	0.000	0.000
14	B	145	ASN	0	-0.085	-0.044	16.795	-0.031	-0.031	0.000	0.000	0.000	0.000
15	B	146	THR	0	-0.035	-0.036	20.437	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	147	ILE	0	0.046	0.025	22.269	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	148	LYS	1	0.851	0.938	19.897	-0.026	-0.026	0.000	0.000	0.000	0.000
18	B	149	ASN	0	-0.097	-0.037	25.386	-0.003	-0.003	0.000	0.000	0.000	0.000
19	B	150	ALA	0	0.018	0.009	27.835	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	151	LEU	0	0.021	0.008	25.401	0.004	0.004	0.000	0.000	0.000	0.000
21	B	152	LYS	1	0.852	0.920	29.914	-0.012	-0.012	0.000	0.000	0.000	0.000
22	B	153	ASP	-1	-0.830	-0.915	33.342	-0.002	-0.002	0.000	0.000	0.000	0.000
23	B	154	HIS	0	0.018	-0.005	35.584	0.002	0.002	0.000	0.000	0.000	0.000
24	B	155	ASP	-1	-0.803	-0.887	32.988	0.022	0.022	0.000	0.000	0.000	0.000
25	B	156	ILE	0	-0.022	-0.007	31.400	0.004	0.004	0.000	0.000	0.000	0.000
26	B	157	ILE	0	0.014	0.003	35.503	0.001	0.001	0.000	0.000	0.000	0.000
27	B	158	GLY	0	0.016	0.008	38.974	0.000	0.000	0.000	0.000	0.000	0.000
28	B	159	THR	0	-0.017	-0.020	35.024	0.003	0.003	0.000	0.000	0.000	0.000
29	B	160	LEU	0	0.010	-0.001	37.881	0.001	0.001	0.000	0.000	0.000	0.000
30	B	161	LYS	1	0.831	0.914	40.121	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	162	ASP	-1	-0.745	-0.884	40.363	0.031	0.031	0.000	0.000	0.000	0.000
32	B	163	MET	0	-0.016	-0.010	37.818	0.001	0.001	0.000	0.000	0.000	0.000
33	B	164	ASP	-1	-0.873	-0.887	42.025	0.017	0.017	0.000	0.000	0.000	0.000
34	B	165	GLY	0	0.004	0.006	45.054	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	166	LYS	1	0.799	0.899	46.181	-0.017	-0.017	0.000	0.000	0.000	0.000
36	B	167	PRO	0	0.082	0.055	44.125	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	168	VAL	0	-0.022	-0.010	44.357	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	169	PRO	0	0.006	-0.001	46.635	0.002	0.002	0.000	0.000	0.000	0.000
39	B	170	LYS	1	0.845	0.926	44.068	-0.035	-0.035	0.000	0.000	0.000	0.000
40	B	171	GLU	-1	-0.918	-0.957	50.217	0.018	0.018	0.000	0.000	0.000	0.000
41	B	172	ASN	0	-0.049	-0.023	50.165	0.000	0.000	0.000	0.000	0.000	0.000
42	B	173	GLY	0	0.027	0.024	53.085	0.001	0.001	0.000	0.000	0.000	0.000
43	B	174	GLY	0	-0.020	-0.014	49.477	0.002	0.002	0.000	0.000	0.000	0.000
44	B	175	TYR	0	0.015	-0.004	46.095	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	176	TRP	0	-0.026	-0.020	42.277	0.004	0.004	0.000	0.000	0.000	0.000
46	B	177	ASP	-1	-0.811	-0.903	39.234	0.045	0.045	0.000	0.000	0.000	0.000
47	B	178	HIS	0	-0.015	-0.010	37.638	0.003	0.003	0.000	0.000	0.000	0.000
48	B	179	MET	0	0.022	0.007	35.886	0.001	0.001	0.000	0.000	0.000	0.000
49	B	180	GLN	0	-0.067	-0.030	34.775	0.008	0.008	0.000	0.000	0.000	0.000
50	B	181	GLU	-1	-0.820	-0.913	33.037	0.068	0.068	0.000	0.000	0.000	0.000
51	B	182	MET	0	-0.012	0.019	31.149	0.005	0.005	0.000	0.000	0.000	0.000
52	B	183	GLN	0	-0.025	-0.022	30.188	0.002	0.002	0.000	0.000	0.000	0.000
53	B	184	ASN	0	-0.086	-0.039	29.195	0.020	0.020	0.000	0.000	0.000	0.000
54	B	185	THR	0	-0.003	-0.012	26.979	0.012	0.012	0.000	0.000	0.000	0.000
55	B	186	LEU	0	-0.008	-0.009	25.602	0.008	0.008	0.000	0.000	0.000	0.000
56	B	187	ARG	1	0.936	0.973	24.748	-0.126	-0.126	0.000	0.000	0.000	0.000
57	B	188	GLY	0	-0.004	-0.005	23.374	0.021	0.021	0.000	0.000	0.000	0.000
58	B	189	LEU	0	-0.012	-0.013	21.224	0.020	0.020	0.000	0.000	0.000	0.000
59	B	190	ARG	1	0.919	0.941	19.888	-0.073	-0.073	0.000	0.000	0.000	0.000
60	B	191	ASN	0	0.007	0.016	19.324	0.043	0.043	0.000	0.000	0.000	0.000
61	B	192	HIS	1	0.848	0.943	16.842	-0.141	-0.141	0.000	0.000	0.000	0.000
62	B	193	ALA	0	0.094	0.038	15.272	0.041	0.041	0.000	0.000	0.000	0.000
63	B	194	ASP	-1	-0.837	-0.918	14.760	0.269	0.269	0.000	0.000	0.000	0.000
64	B	195	THR	0	-0.088	-0.038	12.547	0.074	0.074	0.000	0.000	0.000	0.000
65	B	196	LEU	0	-0.036	-0.031	10.655	0.179	0.179	0.000	0.000	0.000	0.000
66	B	197	LYS	1	0.832	0.924	10.070	-0.191	-0.191	0.000	0.000	0.000	0.000
67	B	198	ASN	0	0.007	0.010	9.828	-0.167	-0.167	0.000	0.000	0.000	0.000
68	B	199	VAL	0	-0.033	-0.008	5.486	0.345	0.345	0.000	0.000	0.000	0.000
69	B	200	ASN	0	0.019	0.016	3.082	-1.874	-0.815	0.428	-0.369	-1.118	-0.003
70	B	201	ASN	0	0.005	-0.024	2.420	-5.748	-2.559	2.668	-2.686	-3.172	-0.027
71	B	202	PRO	0	0.058	0.030	4.493	0.416	0.618	-0.001	-0.022	-0.180	0.000
72	B	203	GLU	-1	-0.819	-0.879	7.226	-0.027	-0.027	0.000	0.000	0.000	0.000
73	B	204	ALA	0	0.013	-0.003	7.375	0.169	0.169	0.000	0.000	0.000	0.000
74	B	205	GLN	0	-0.016	-0.024	7.989	0.060	0.060	0.000	0.000	0.000	0.000
75	B	206	ALA	0	0.027	0.019	10.445	0.064	0.064	0.000	0.000	0.000	0.000
76	B	207	ALA	0	-0.066	-0.023	12.451	0.044	0.044	0.000	0.000	0.000	0.000
77	B	208	TYR	0	0.038	0.012	12.678	0.057	0.057	0.000	0.000	0.000	0.000
78	B	209	GLY	0	0.043	0.031	14.407	0.012	0.012	0.000	0.000	0.000	0.000
79	B	210	ARG	0	0.125	0.050	13.942	0.036	0.036	0.000	0.000	0.000	0.000
80	B	211	ALA	0	-0.055	-0.018	17.353	0.011	0.011	0.000	0.000	0.000	0.000
81	B	212	THR	0	-0.045	-0.037	17.940	0.004	0.004	0.000	0.000	0.000	0.000
82	B	213	ASP	-1	-0.887	-0.937	20.382	-0.053	-0.053	0.000	0.000	0.000	0.000
83	B	214	ALA	0	-0.050	-0.026	22.225	0.002	0.002	0.000	0.000	0.000	0.000
84	B	215	ILE	0	-0.007	-0.010	21.049	0.004	0.004	0.000	0.000	0.000	0.000
85	B	216	ASN	0	0.003	-0.005	23.209	0.003	0.003	0.000	0.000	0.000	0.000
86	B	217	LYS	1	0.863	0.953	26.326	0.001	0.001	0.000	0.000	0.000	0.000
87	B	218	ILE	0	-0.003	0.002	26.955	0.000	0.000	0.000	0.000	0.000	0.000
88	B	219	GLU	-1	-0.802	-0.891	26.945	0.052	0.052	0.000	0.000	0.000	0.000
89	B	220	SER	0	-0.063	-0.049	29.603	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	221	ALA	0	-0.020	0.007	32.037	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	222	LEU	0	-0.008	-0.010	32.605	0.001	0.001	0.000	0.000	0.000	0.000
92	B	223	LYS	1	0.825	0.896	28.852	-0.028	-0.028	0.000	0.000	0.000	0.000
93	B	224	GLY	0	0.037	0.014	35.094	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	225	TYR	0	-0.064	-0.049	38.535	-0.002	-0.002	0.000	0.000	0.000	0.000
95	B	226	GLY	0	0.008	0.007	40.464	0.002	0.002	0.000	0.000	0.000	0.000
96	B	227	ILE	0	-0.067	-0.016	40.836	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:132:LEU)