FMO DATABASE

FMODB ID: N939Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-632314.393407
FMO2-HF: Nuclear repulsion	594634.221652
FMO2-HF: Total energy	-37680.171755
FMO2-MP2: Total energy	-37789.709934

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.
-4.933	-0.555	7.788	-5.761	-6.403	-0.03

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 : -0.008 / q_NPA : -0.010

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	0.032	0.036	3.860	0.360	2.400	-0.026	-1.121	-0.893	0.001
4	B	135	LYS	1	0.951	0.982	7.040	-1.548	-1.548	0.000	0.000	0.000	0.000
5	B	136	GLN	0	0.018	0.000	9.970	-0.233	-0.233	0.000	0.000	0.000	0.000
6	B	137	GLU	-1	-0.827	-0.941	7.345	2.273	2.273	0.000	0.000	0.000	0.000
7	B	138	SER	0	0.054	0.029	11.244	-0.105	-0.105	0.000	0.000	0.000	0.000
8	B	139	ALA	0	-0.076	-0.029	12.480	-0.061	-0.061	0.000	0.000	0.000	0.000
9	B	140	ILE	0	-0.004	-0.003	13.939	-0.040	-0.040	0.000	0.000	0.000	0.000
10	B	141	LYS	1	0.921	0.982	11.815	0.076	0.076	0.000	0.000	0.000	0.000
11	B	142	LYS	1	0.930	0.961	14.347	-0.105	-0.105	0.000	0.000	0.000	0.000
12	B	143	ILE	0	-0.026	-0.010	17.484	-0.019	-0.019	0.000	0.000	0.000	0.000
13	B	144	ASP	-1	-0.797	-0.908	16.086	0.196	0.196	0.000	0.000	0.000	0.000
14	B	145	ASN	0	-0.071	-0.065	16.586	-0.017	-0.017	0.000	0.000	0.000	0.000
15	B	146	THR	0	-0.051	-0.038	20.226	-0.008	-0.008	0.000	0.000	0.000	0.000
16	B	147	ILE	0	0.061	0.045	21.836	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	148	LYS	1	0.845	0.939	19.499	-0.074	-0.074	0.000	0.000	0.000	0.000
18	B	149	ASN	0	-0.097	-0.054	24.851	-0.008	-0.008	0.000	0.000	0.000	0.000
19	B	150	ALA	0	0.053	0.029	27.333	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	151	LEU	0	-0.030	-0.016	25.294	0.003	0.003	0.000	0.000	0.000	0.000
21	B	152	LYS	1	0.911	0.961	29.430	-0.028	-0.028	0.000	0.000	0.000	0.000
22	B	153	ASP	-1	-0.822	-0.913	32.747	0.021	0.021	0.000	0.000	0.000	0.000
23	B	154	HIS	0	-0.035	-0.040	35.296	0.003	0.003	0.000	0.000	0.000	0.000
24	B	155	ASP	-1	-0.851	-0.915	32.918	0.044	0.044	0.000	0.000	0.000	0.000
25	B	156	ILE	0	-0.036	-0.018	31.227	0.004	0.004	0.000	0.000	0.000	0.000
26	B	157	ILE	0	0.005	-0.004	34.928	0.001	0.001	0.000	0.000	0.000	0.000
27	B	158	GLY	0	0.023	0.013	38.215	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	159	THR	0	-0.001	-0.008	34.614	0.003	0.003	0.000	0.000	0.000	0.000
29	B	160	LEU	0	0.009	-0.001	37.349	0.001	0.001	0.000	0.000	0.000	0.000
30	B	161	LYS	1	0.838	0.926	39.494	-0.029	-0.029	0.000	0.000	0.000	0.000
31	B	162	ASP	-1	-0.750	-0.882	39.963	0.044	0.044	0.000	0.000	0.000	0.000
32	B	163	MET	0	-0.043	-0.016	37.690	0.001	0.001	0.000	0.000	0.000	0.000
33	B	164	ASP	-1	-0.861	-0.903	41.547	0.031	0.031	0.000	0.000	0.000	0.000
34	B	165	GLY	0	-0.014	-0.006	44.518	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	166	LYS	1	0.792	0.894	45.641	-0.028	-0.028	0.000	0.000	0.000	0.000
36	B	167	PRO	0	0.106	0.068	44.044	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	168	VAL	0	-0.015	-0.015	43.901	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	169	PRO	0	-0.024	-0.009	46.230	0.002	0.002	0.000	0.000	0.000	0.000
39	B	170	LYS	1	0.902	0.956	44.163	-0.042	-0.042	0.000	0.000	0.000	0.000
40	B	171	GLU	-1	-0.895	-0.961	49.434	0.022	0.022	0.000	0.000	0.000	0.000
41	B	172	ASN	0	-0.087	-0.045	49.695	0.000	0.000	0.000	0.000	0.000	0.000
42	B	173	GLY	0	0.037	0.042	52.159	0.000	0.000	0.000	0.000	0.000	0.000
43	B	174	GLY	0	-0.011	-0.012	48.767	0.002	0.002	0.000	0.000	0.000	0.000
44	B	175	TYR	0	0.002	-0.012	45.714	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	176	TRP	0	-0.039	-0.025	41.726	0.003	0.003	0.000	0.000	0.000	0.000
46	B	177	ASP	-1	-0.834	-0.914	39.071	0.055	0.055	0.000	0.000	0.000	0.000
47	B	178	HIS	0	0.009	-0.007	37.598	0.004	0.004	0.000	0.000	0.000	0.000
48	B	179	MET	0	-0.005	0.004	35.814	0.002	0.002	0.000	0.000	0.000	0.000
49	B	180	GLN	0	-0.015	-0.003	34.542	0.003	0.003	0.000	0.000	0.000	0.000
50	B	181	GLU	-1	-0.910	-0.958	33.073	0.076	0.076	0.000	0.000	0.000	0.000
51	B	182	MET	0	-0.002	0.012	30.706	0.009	0.009	0.000	0.000	0.000	0.000
52	B	183	GLN	0	-0.039	-0.032	29.905	0.005	0.005	0.000	0.000	0.000	0.000
53	B	184	ASN	0	-0.025	-0.004	28.834	0.019	0.019	0.000	0.000	0.000	0.000
54	B	185	THR	0	-0.012	-0.007	26.308	0.013	0.013	0.000	0.000	0.000	0.000
55	B	186	LEU	0	0.001	-0.006	25.133	0.013	0.013	0.000	0.000	0.000	0.000
56	B	187	ARG	1	0.948	0.991	24.263	-0.136	-0.136	0.000	0.000	0.000	0.000
57	B	188	GLY	0	-0.008	-0.003	22.720	0.022	0.022	0.000	0.000	0.000	0.000
58	B	189	LEU	0	0.010	-0.008	20.522	0.026	0.026	0.000	0.000	0.000	0.000
59	B	190	ARG	1	0.921	0.937	19.460	-0.107	-0.107	0.000	0.000	0.000	0.000
60	B	191	ASN	0	-0.019	0.010	19.047	0.055	0.055	0.000	0.000	0.000	0.000
61	B	192	HIS	1	0.866	0.922	16.479	-0.208	-0.208	0.000	0.000	0.000	0.000
62	B	193	ALA	0	0.071	0.030	14.811	0.052	0.052	0.000	0.000	0.000	0.000
63	B	194	ASP	-1	-0.893	-0.946	14.369	0.356	0.356	0.000	0.000	0.000	0.000
64	B	195	THR	0	-0.126	-0.061	11.937	0.087	0.087	0.000	0.000	0.000	0.000
65	B	196	LEU	0	-0.041	-0.030	9.767	0.210	0.210	0.000	0.000	0.000	0.000
66	B	197	LYS	1	0.971	1.014	9.924	-0.262	-0.262	0.000	0.000	0.000	0.000
67	B	198	ASN	0	-0.020	-0.020	9.503	-0.152	-0.152	0.000	0.000	0.000	0.000
68	B	199	VAL	0	0.000	0.014	4.732	0.135	0.233	-0.001	-0.004	-0.093	0.000
69	B	200	ASN	0	0.021	0.016	2.140	-1.327	-1.490	2.641	-0.697	-1.780	0.000
70	B	201	ASN	0	0.007	-0.035	2.178	-5.044	-2.908	5.171	-3.870	-3.437	-0.031
71	B	202	PRO	0	0.058	0.043	4.080	0.311	0.578	0.003	-0.069	-0.200	0.000
72	B	203	GLU	-1	-0.862	-0.933	7.123	-0.059	-0.059	0.000	0.000	0.000	0.000
73	B	204	ALA	0	0.006	-0.013	6.804	0.149	0.149	0.000	0.000	0.000	0.000
74	B	205	GLN	0	0.001	-0.003	7.624	-0.021	-0.021	0.000	0.000	0.000	0.000
75	B	206	ALA	0	-0.001	0.004	10.004	0.019	0.019	0.000	0.000	0.000	0.000
76	B	207	ALA	0	-0.044	-0.029	12.082	0.015	0.015	0.000	0.000	0.000	0.000
77	B	208	TYR	0	0.048	0.034	12.179	0.024	0.024	0.000	0.000	0.000	0.000
78	B	209	GLY	0	0.049	0.029	13.982	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	210	ARG	0	0.120	0.072	14.192	0.008	0.008	0.000	0.000	0.000	0.000
80	B	211	ALA	0	-0.074	-0.028	17.107	-0.004	-0.004	0.000	0.000	0.000	0.000
81	B	212	THR	0	-0.027	-0.013	17.440	-0.004	-0.004	0.000	0.000	0.000	0.000
82	B	213	ASP	-1	-0.878	-0.929	19.989	0.020	0.020	0.000	0.000	0.000	0.000
83	B	214	ALA	0	-0.066	-0.041	21.755	-0.006	-0.006	0.000	0.000	0.000	0.000
84	B	215	ILE	0	-0.002	-0.003	20.829	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	216	ASN	0	0.031	0.013	22.826	0.002	0.002	0.000	0.000	0.000	0.000
86	B	217	LYS	1	0.916	0.970	25.743	-0.037	-0.037	0.000	0.000	0.000	0.000
87	B	218	ILE	0	-0.011	-0.013	26.611	-0.004	-0.004	0.000	0.000	0.000	0.000
88	B	219	GLU	-1	-0.882	-0.943	26.426	0.097	0.097	0.000	0.000	0.000	0.000
89	B	220	SER	0	-0.067	-0.045	29.233	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	221	ALA	0	-0.036	0.004	31.514	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	222	LEU	0	0.016	0.005	32.395	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	223	LYS	1	0.910	0.956	29.929	-0.060	-0.060	0.000	0.000	0.000	0.000
93	B	224	GLY	0	0.009	0.007	35.035	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	225	TYR	0	-0.063	-0.043	38.232	-0.004	-0.004	0.000	0.000	0.000	0.000
95	B	226	GLY	0	0.030	0.014	40.093	0.002	0.002	0.000	0.000	0.000	0.000
96	B	227	ILE	0	-0.071	-0.020	41.123	-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)