FMO DATABASE

FMODB ID: JLML9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-632538.337353
FMO2-HF: Nuclear repulsion	594857.442277
FMO2-HF: Total energy	-37680.895076
FMO2-MP2: Total energy	-37790.390587

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.
-6.919	-0.957	6.616	-5.806	-6.771	-0.039

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 : -0.010 / 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	-0.054	-0.021	3.860	0.507	2.533	-0.025	-1.104	-0.898	0.001
4	B	135	LYS	1	0.930	0.963	7.040	-1.837	-1.837	0.000	0.000	0.000	0.000
5	B	136	GLN	0	0.008	0.012	9.970	-0.276	-0.276	0.000	0.000	0.000	0.000
6	B	137	GLU	-1	-0.763	-0.911	8.096	1.761	1.761	0.000	0.000	0.000	0.000
7	B	138	SER	0	0.040	0.019	11.214	-0.113	-0.113	0.000	0.000	0.000	0.000
8	B	139	ALA	0	-0.072	-0.030	12.463	-0.071	-0.071	0.000	0.000	0.000	0.000
9	B	140	ILE	0	-0.008	-0.005	14.028	-0.042	-0.042	0.000	0.000	0.000	0.000
10	B	141	LYS	1	0.897	0.956	11.988	0.060	0.060	0.000	0.000	0.000	0.000
11	B	142	LYS	1	0.945	0.967	14.332	-0.143	-0.143	0.000	0.000	0.000	0.000
12	B	143	ILE	0	0.002	0.001	17.473	-0.022	-0.022	0.000	0.000	0.000	0.000
13	B	144	ASP	-1	-0.780	-0.904	16.413	0.172	0.172	0.000	0.000	0.000	0.000
14	B	145	ASN	0	-0.121	-0.073	16.412	-0.031	-0.031	0.000	0.000	0.000	0.000
15	B	146	THR	0	-0.033	-0.030	20.219	-0.008	-0.008	0.000	0.000	0.000	0.000
16	B	147	ILE	0	0.069	0.046	22.019	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	148	LYS	1	0.850	0.950	19.325	-0.071	-0.071	0.000	0.000	0.000	0.000
18	B	149	ASN	0	-0.100	-0.059	24.842	-0.008	-0.008	0.000	0.000	0.000	0.000
19	B	150	ALA	0	0.047	0.024	27.326	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	151	LEU	0	-0.030	-0.011	25.048	0.002	0.002	0.000	0.000	0.000	0.000
21	B	152	LYS	1	0.888	0.952	29.419	-0.030	-0.030	0.000	0.000	0.000	0.000
22	B	153	ASP	-1	-0.839	-0.927	32.738	0.016	0.016	0.000	0.000	0.000	0.000
23	B	154	HIS	0	-0.026	-0.031	35.289	0.002	0.002	0.000	0.000	0.000	0.000
24	B	155	ASP	-1	-0.814	-0.902	32.555	0.040	0.040	0.000	0.000	0.000	0.000
25	B	156	ILE	0	-0.018	-0.010	30.962	0.003	0.003	0.000	0.000	0.000	0.000
26	B	157	ILE	0	0.004	-0.002	34.913	0.001	0.001	0.000	0.000	0.000	0.000
27	B	158	GLY	0	0.024	0.015	38.201	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	159	THR	0	-0.008	-0.012	34.524	0.003	0.003	0.000	0.000	0.000	0.000
29	B	160	LEU	0	0.008	-0.003	37.282	0.001	0.001	0.000	0.000	0.000	0.000
30	B	161	LYS	1	0.840	0.910	39.476	-0.024	-0.024	0.000	0.000	0.000	0.000
31	B	162	ASP	-1	-0.741	-0.872	39.959	0.039	0.039	0.000	0.000	0.000	0.000
32	B	163	MET	0	-0.032	-0.012	37.473	0.001	0.001	0.000	0.000	0.000	0.000
33	B	164	ASP	-1	-0.862	-0.876	41.511	0.025	0.025	0.000	0.000	0.000	0.000
34	B	165	GLY	0	-0.008	-0.004	44.494	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	166	LYS	1	0.797	0.897	45.624	-0.024	-0.024	0.000	0.000	0.000	0.000
36	B	167	PRO	0	0.095	0.060	43.902	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	168	VAL	0	-0.020	-0.012	43.965	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	169	PRO	0	-0.027	-0.007	46.208	0.002	0.002	0.000	0.000	0.000	0.000
39	B	170	LYS	1	0.853	0.928	43.526	-0.042	-0.042	0.000	0.000	0.000	0.000
40	B	171	GLU	-1	-0.914	-0.965	49.409	0.022	0.022	0.000	0.000	0.000	0.000
41	B	172	ASN	0	-0.054	-0.030	49.579	0.000	0.000	0.000	0.000	0.000	0.000
42	B	173	GLY	0	0.040	0.042	52.162	0.000	0.000	0.000	0.000	0.000	0.000
43	B	174	GLY	0	-0.015	-0.014	48.737	0.002	0.002	0.000	0.000	0.000	0.000
44	B	175	TYR	0	0.020	-0.004	45.631	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	176	TRP	0	-0.022	-0.019	41.747	0.004	0.004	0.000	0.000	0.000	0.000
46	B	177	ASP	-1	-0.843	-0.918	38.956	0.051	0.051	0.000	0.000	0.000	0.000
47	B	178	HIS	0	0.007	-0.010	37.584	0.004	0.004	0.000	0.000	0.000	0.000
48	B	179	MET	0	-0.002	-0.005	35.791	0.002	0.002	0.000	0.000	0.000	0.000
49	B	180	GLN	0	-0.024	-0.004	34.543	0.003	0.003	0.000	0.000	0.000	0.000
50	B	181	GLU	-1	-0.885	-0.953	33.017	0.077	0.077	0.000	0.000	0.000	0.000
51	B	182	MET	0	-0.008	0.012	30.576	0.008	0.008	0.000	0.000	0.000	0.000
52	B	183	GLN	0	-0.030	-0.028	29.870	0.003	0.003	0.000	0.000	0.000	0.000
53	B	184	ASN	0	-0.034	-0.008	28.854	0.020	0.020	0.000	0.000	0.000	0.000
54	B	185	THR	0	-0.012	-0.008	26.449	0.013	0.013	0.000	0.000	0.000	0.000
55	B	186	LEU	0	-0.007	-0.008	25.108	0.011	0.011	0.000	0.000	0.000	0.000
56	B	187	ARG	1	0.948	0.988	24.235	-0.132	-0.132	0.000	0.000	0.000	0.000
57	B	188	GLY	0	-0.004	-0.002	22.688	0.022	0.022	0.000	0.000	0.000	0.000
58	B	189	LEU	0	0.012	-0.001	20.507	0.025	0.025	0.000	0.000	0.000	0.000
59	B	190	ARG	1	0.905	0.928	19.433	-0.089	-0.089	0.000	0.000	0.000	0.000
60	B	191	ASN	0	-0.020	0.007	19.180	0.049	0.049	0.000	0.000	0.000	0.000
61	B	192	HIS	1	0.850	0.924	16.450	-0.193	-0.193	0.000	0.000	0.000	0.000
62	B	193	ALA	0	0.076	0.034	14.781	0.050	0.050	0.000	0.000	0.000	0.000
63	B	194	ASP	-1	-0.842	-0.914	14.339	0.306	0.306	0.000	0.000	0.000	0.000
64	B	195	THR	0	-0.114	-0.052	12.028	0.078	0.078	0.000	0.000	0.000	0.000
65	B	196	LEU	0	-0.024	-0.026	9.902	0.217	0.217	0.000	0.000	0.000	0.000
66	B	197	LYS	1	0.892	0.968	9.897	-0.250	-0.250	0.000	0.000	0.000	0.000
67	B	198	ASN	0	-0.013	-0.010	9.503	-0.170	-0.170	0.000	0.000	0.000	0.000
68	B	199	VAL	0	-0.013	0.005	4.589	0.178	0.280	-0.001	-0.004	-0.096	0.000
69	B	200	ASN	0	0.027	0.016	2.767	-1.726	-0.776	1.054	-0.489	-1.514	-0.004
70	B	201	ASN	0	0.047	0.002	2.188	-5.993	-3.421	5.584	-4.135	-4.021	-0.036
71	B	202	PRO	0	0.060	0.035	4.096	0.270	0.582	0.004	-0.074	-0.242	0.000
72	B	203	GLU	-1	-0.794	-0.875	6.939	0.050	0.050	0.000	0.000	0.000	0.000
73	B	204	ALA	0	-0.004	-0.013	6.759	0.158	0.158	0.000	0.000	0.000	0.000
74	B	205	GLN	0	-0.010	-0.016	7.673	0.025	0.025	0.000	0.000	0.000	0.000
75	B	206	ALA	0	-0.011	0.001	10.005	0.035	0.035	0.000	0.000	0.000	0.000
76	B	207	ALA	0	-0.029	-0.016	12.113	0.028	0.028	0.000	0.000	0.000	0.000
77	B	208	TYR	0	0.031	0.017	12.184	0.037	0.037	0.000	0.000	0.000	0.000
78	B	209	GLY	0	0.050	0.033	13.970	0.002	0.002	0.000	0.000	0.000	0.000
79	B	210	ARG	0	0.101	0.044	14.083	0.025	0.025	0.000	0.000	0.000	0.000
80	B	211	ALA	0	-0.067	-0.032	17.057	0.001	0.001	0.000	0.000	0.000	0.000
81	B	212	THR	0	0.045	0.013	17.567	0.003	0.003	0.000	0.000	0.000	0.000
82	B	213	ASP	-1	-0.928	-0.948	19.975	-0.010	-0.010	0.000	0.000	0.000	0.000
83	B	214	ALA	0	-0.057	-0.032	21.745	-0.003	-0.003	0.000	0.000	0.000	0.000
84	B	215	ILE	0	-0.001	-0.007	20.566	0.001	0.001	0.000	0.000	0.000	0.000
85	B	216	ASN	0	0.020	0.007	22.901	0.001	0.001	0.000	0.000	0.000	0.000
86	B	217	LYS	1	0.923	0.992	25.735	-0.025	-0.025	0.000	0.000	0.000	0.000
87	B	218	ILE	0	-0.011	-0.009	26.361	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	219	GLU	-1	-0.822	-0.903	26.432	0.071	0.071	0.000	0.000	0.000	0.000
89	B	220	SER	0	-0.070	-0.056	29.093	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	221	ALA	0	-0.036	0.001	31.501	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	222	LEU	0	0.004	0.001	32.678	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	223	LYS	1	0.845	0.912	28.844	-0.047	-0.047	0.000	0.000	0.000	0.000
93	B	224	GLY	0	0.015	0.009	35.017	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	225	TYR	0	-0.062	-0.052	38.218	-0.003	-0.003	0.000	0.000	0.000	0.000
95	B	226	GLY	0	0.025	0.012	40.075	0.002	0.002	0.000	0.000	0.000	0.000
96	B	227	ILE	0	-0.070	-0.019	40.851	-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)