FMO DATABASE

FMODB ID: R5RL8

Calculation Name: 3WKR-C-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: 3WKR

Chain ID: C

ChEMBL ID:

UniProt ID: Q59072

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-382846.468421
FMO2-HF: Nuclear repulsion	355148.688303
FMO2-HF: Total energy	-27697.780117
FMO2-MP2: Total energy	-27779.146826

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(C:34:ILE)

Summations of interaction energy for fragment #1(C:34:ILE)

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.
-3.701	1.756	1.034	-2.368	-4.121	-0.001

Interaction energy analysis for fragmet #1(C:34:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.021

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

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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	C	36	TYR	0	0.055	0.000	3.805	-1.685	1.253	-0.032	-1.439	-1.467	0.008
4	C	37	LYS	1	0.909	0.949	5.447	1.130	1.130	0.000	0.000	0.000	0.000
5	C	38	ASP	-1	-0.828	-0.882	3.875	-1.127	-0.876	0.004	-0.102	-0.152	0.000
6	C	39	ALA	0	-0.030	-0.011	7.102	0.200	0.200	0.000	0.000	0.000	0.000
7	C	40	LYS	1	0.857	0.946	7.601	-0.284	-0.284	0.000	0.000	0.000	0.000
8	C	41	PRO	0	-0.010	-0.025	10.895	-0.003	-0.003	0.000	0.000	0.000	0.000
9	C	42	GLY	0	0.072	0.048	12.986	0.030	0.030	0.000	0.000	0.000	0.000
10	C	43	LYS	1	0.879	0.942	13.942	-0.004	-0.004	0.000	0.000	0.000	0.000
11	C	44	ILE	0	0.081	0.033	14.255	0.009	0.009	0.000	0.000	0.000	0.000
12	C	45	ASP	-1	-0.864	-0.921	14.714	0.010	0.010	0.000	0.000	0.000	0.000
13	C	46	VAL	0	0.038	0.003	16.511	-0.008	-0.008	0.000	0.000	0.000	0.000
14	C	47	ASN	0	-0.011	-0.011	19.177	-0.008	-0.008	0.000	0.000	0.000	0.000
15	C	48	GLU	-1	-0.804	-0.884	13.878	0.024	0.024	0.000	0.000	0.000	0.000
16	C	49	PHE	0	0.025	0.004	14.024	-0.004	-0.004	0.000	0.000	0.000	0.000
17	C	50	LYS	1	0.947	0.977	16.145	0.018	0.018	0.000	0.000	0.000	0.000
18	C	51	LYS	1	0.848	0.918	17.558	-0.011	-0.011	0.000	0.000	0.000	0.000
19	C	52	ALA	0	0.014	0.006	14.196	0.003	0.003	0.000	0.000	0.000	0.000
20	C	53	ILE	0	0.027	0.015	16.172	-0.006	-0.006	0.000	0.000	0.000	0.000
21	C	54	TYR	0	0.021	-0.009	18.614	0.002	0.002	0.000	0.000	0.000	0.000
22	C	55	LEU	0	0.013	0.025	17.018	0.003	0.003	0.000	0.000	0.000	0.000
23	C	56	LEU	0	0.001	-0.008	15.367	0.000	0.000	0.000	0.000	0.000	0.000
24	C	57	ILE	0	-0.023	-0.006	19.668	-0.001	-0.001	0.000	0.000	0.000	0.000
25	C	58	GLU	-1	-0.931	-0.966	23.053	-0.016	-0.016	0.000	0.000	0.000	0.000
26	C	59	ALA	0	-0.026	-0.026	20.962	0.003	0.003	0.000	0.000	0.000	0.000
27	C	60	ASP	-1	-0.887	-0.951	22.914	-0.071	-0.071	0.000	0.000	0.000	0.000
28	C	61	ASP	-1	-0.830	-0.909	24.660	-0.031	-0.031	0.000	0.000	0.000	0.000
29	C	62	PHE	0	-0.050	-0.031	24.766	0.002	0.002	0.000	0.000	0.000	0.000
30	C	63	LEU	0	-0.019	-0.009	23.115	0.001	0.001	0.000	0.000	0.000	0.000
31	C	64	TYR	0	-0.036	0.000	27.283	0.001	0.001	0.000	0.000	0.000	0.000
32	C	65	LYS	1	0.823	0.894	30.394	0.026	0.026	0.000	0.000	0.000	0.000
33	C	66	LYS	1	0.824	0.905	28.616	0.024	0.024	0.000	0.000	0.000	0.000
34	C	67	ALA	0	0.009	0.050	30.957	-0.002	-0.002	0.000	0.000	0.000	0.000
35	C	68	PRO	0	-0.030	-0.041	32.107	0.004	0.004	0.000	0.000	0.000	0.000
36	C	69	LYS	1	0.949	0.961	30.862	0.035	0.035	0.000	0.000	0.000	0.000
37	C	70	HIS	0	-0.035	-0.006	26.315	-0.004	-0.004	0.000	0.000	0.000	0.000
38	C	71	GLU	-1	-0.941	-0.966	26.616	-0.035	-0.035	0.000	0.000	0.000	0.000
39	C	72	LEU	0	-0.023	-0.006	23.685	0.003	0.003	0.000	0.000	0.000	0.000
40	C	73	ASN	0	0.039	0.017	27.683	0.003	0.003	0.000	0.000	0.000	0.000
41	C	74	GLU	-1	-0.807	-0.902	26.648	0.022	0.022	0.000	0.000	0.000	0.000
42	C	75	GLU	-1	-0.914	-0.963	26.133	0.011	0.011	0.000	0.000	0.000	0.000
43	C	76	GLU	-1	-0.765	-0.880	26.634	-0.015	-0.015	0.000	0.000	0.000	0.000
44	C	77	ALA	0	0.041	0.028	22.725	-0.003	-0.003	0.000	0.000	0.000	0.000
45	C	78	LYS	1	0.806	0.898	21.903	-0.024	-0.024	0.000	0.000	0.000	0.000
46	C	79	GLU	-1	-0.975	-0.984	22.054	-0.003	-0.003	0.000	0.000	0.000	0.000
47	C	80	PHE	0	0.011	0.009	19.636	-0.002	-0.002	0.000	0.000	0.000	0.000
48	C	81	CYS	0	-0.037	-0.047	17.736	-0.007	-0.007	0.000	0.000	0.000	0.000
49	C	82	LYS	1	0.949	0.987	17.167	-0.016	-0.016	0.000	0.000	0.000	0.000
50	C	83	LEU	0	0.011	0.008	18.032	0.006	0.006	0.000	0.000	0.000	0.000
51	C	84	ILE	0	0.023	0.010	13.856	-0.005	-0.005	0.000	0.000	0.000	0.000
52	C	85	ILE	0	0.016	0.009	13.021	-0.005	-0.005	0.000	0.000	0.000	0.000
53	C	86	LYS	1	0.896	0.936	12.926	-0.043	-0.043	0.000	0.000	0.000	0.000
54	C	87	CYS	0	-0.062	-0.014	14.243	-0.005	-0.005	0.000	0.000	0.000	0.000
55	C	88	GLN	0	0.053	0.010	8.931	0.023	0.023	0.000	0.000	0.000	0.000
56	C	89	GLU	-1	-0.860	-0.900	9.072	0.082	0.082	0.000	0.000	0.000	0.000
57	C	90	HIS	1	0.802	0.875	10.708	0.007	0.007	0.000	0.000	0.000	0.000
58	C	91	LEU	0	0.031	0.010	8.740	0.002	0.002	0.000	0.000	0.000	0.000
59	C	92	ASN	0	0.025	0.005	5.371	-0.096	-0.096	0.000	0.000	0.000	0.000
60	C	93	LYS	1	0.850	0.929	7.109	-0.060	-0.060	0.000	0.000	0.000	0.000
61	C	94	ILE	0	-0.049	-0.009	9.981	0.005	0.005	0.000	0.000	0.000	0.000
62	C	95	LEU	0	0.020	0.003	3.460	-0.270	-0.014	0.009	-0.040	-0.225	0.000
63	C	96	ALA	0	0.014	0.018	7.193	0.041	0.041	0.000	0.000	0.000	0.000
64	C	97	ASN	0	-0.071	-0.026	8.702	0.047	0.047	0.000	0.000	0.000	0.000
65	C	98	PHE	0	-0.065	-0.030	7.909	-0.018	-0.018	0.000	0.000	0.000	0.000
66	C	99	GLY	0	-0.027	-0.009	7.806	-0.030	-0.030	0.000	0.000	0.000	0.000
67	C	100	PHE	0	0.006	0.000	2.650	-1.655	-0.157	1.035	-0.661	-1.872	-0.008
68	C	101	GLU	-1	-0.931	-0.957	3.576	0.079	0.593	0.018	-0.126	-0.405	-0.001

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Interactive mode: IFIE and PIEDA for fragment #1(C:34:ILE)