FMO DATABASE

FMODB ID: Q179Y

Calculation Name: 3WKR-C-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	70
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-386414.609115
FMO2-HF: Nuclear repulsion	358546.342224
FMO2-HF: Total energy	-27868.266891
FMO2-MP2: Total energy	-27950.110557

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:33:ACE )

Summations of interaction energy for fragment #1(C:33:ACE )

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.
0.477	1.135	-0.005	-0.263	-0.39	0

Interaction energy analysis for fragmet #1(C:33:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.011

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].
3	C	35	SER	0	-0.001	0.020	3.833	1.510	2.168	-0.005	-0.263	-0.390
4	C	36	TYR	0	0.051	0.004	6.432	-0.010	-0.010	0.000	0.000	0.000
5	C	37	LYS	1	0.896	0.940	9.525	0.169	0.169	0.000	0.000	0.000
6	C	38	ASP	-1	-0.876	-0.925	6.621	-0.912	-0.912	0.000	0.000	0.000
7	C	39	ALA	0	-0.040	-0.013	10.106	-0.001	-0.001	0.000	0.000	0.000
8	C	40	LYS	1	0.925	0.975	12.671	0.564	0.564	0.000	0.000	0.000
9	C	41	PRO	0	-0.009	-0.023	15.478	-0.007	-0.007	0.000	0.000	0.000
10	C	42	GLY	0	0.077	0.048	18.786	-0.005	-0.005	0.000	0.000	0.000
11	C	43	LYS	1	0.891	0.950	19.706	0.182	0.182	0.000	0.000	0.000
12	C	44	ILE	0	0.064	0.024	20.508	-0.019	-0.019	0.000	0.000	0.000
13	C	45	ASP	-1	-0.868	-0.940	21.107	-0.164	-0.164	0.000	0.000	0.000
14	C	46	VAL	0	0.026	0.000	22.907	-0.001	-0.001	0.000	0.000	0.000
15	C	47	ASN	0	-0.020	-0.016	25.767	0.009	0.009	0.000	0.000	0.000
16	C	48	GLU	-1	-0.842	-0.894	20.143	-0.183	-0.183	0.000	0.000	0.000
17	C	49	PHE	0	0.019	0.006	20.368	-0.005	-0.005	0.000	0.000	0.000
18	C	50	LYS	1	0.944	0.977	22.718	0.106	0.106	0.000	0.000	0.000
19	C	51	LYS	1	0.914	0.955	23.897	0.141	0.141	0.000	0.000	0.000
20	C	52	ALA	0	0.024	0.011	20.212	0.006	0.006	0.000	0.000	0.000
21	C	53	ILE	0	0.020	0.011	22.161	0.008	0.008	0.000	0.000	0.000
22	C	54	TYR	0	0.017	-0.010	24.602	0.009	0.009	0.000	0.000	0.000
23	C	55	LEU	0	0.010	0.021	22.525	0.005	0.005	0.000	0.000	0.000
24	C	56	LEU	0	0.003	-0.006	20.709	0.006	0.006	0.000	0.000	0.000
25	C	57	ILE	0	-0.027	-0.008	24.749	0.008	0.008	0.000	0.000	0.000
26	C	58	GLU	-1	-0.933	-0.967	28.247	-0.069	-0.069	0.000	0.000	0.000
27	C	59	ALA	0	-0.042	-0.030	25.443	0.006	0.006	0.000	0.000	0.000
28	C	60	ASP	-1	-0.896	-0.962	27.405	-0.044	-0.044	0.000	0.000	0.000
29	C	61	ASP	-1	-0.862	-0.930	29.109	-0.039	-0.039	0.000	0.000	0.000
30	C	62	PHE	0	-0.052	-0.031	28.738	0.005	0.005	0.000	0.000	0.000
31	C	63	LEU	0	-0.023	-0.010	26.882	0.005	0.005	0.000	0.000	0.000
32	C	64	TYR	0	-0.033	0.003	30.936	0.006	0.006	0.000	0.000	0.000
33	C	65	LYS	1	0.887	0.932	34.356	0.038	0.038	0.000	0.000	0.000
34	C	66	LYS	1	0.845	0.922	32.164	0.016	0.016	0.000	0.000	0.000
35	C	67	ALA	0	0.020	0.055	34.091	0.003	0.003	0.000	0.000	0.000
36	C	68	PRO	0	-0.041	-0.047	34.981	0.001	0.001	0.000	0.000	0.000
37	C	69	LYS	1	0.962	0.961	33.440	-0.003	-0.003	0.000	0.000	0.000
38	C	70	HIS	0	-0.031	-0.002	29.274	-0.001	-0.001	0.000	0.000	0.000
39	C	71	GLU	-1	-0.967	-0.975	29.421	0.007	0.007	0.000	0.000	0.000
40	C	72	LEU	0	-0.021	-0.006	27.034	-0.001	-0.001	0.000	0.000	0.000
41	C	73	ASN	0	0.039	0.021	30.698	0.002	0.002	0.000	0.000	0.000
42	C	74	GLU	-1	-0.910	-0.978	29.318	-0.011	-0.011	0.000	0.000	0.000
43	C	75	GLU	-1	-0.918	-0.966	29.411	-0.023	-0.023	0.000	0.000	0.000
44	C	76	GLU	-1	-0.769	-0.885	30.423	-0.019	-0.019	0.000	0.000	0.000
45	C	77	ALA	0	0.034	0.025	25.816	-0.005	-0.005	0.000	0.000	0.000
46	C	78	LYS	1	0.898	0.967	25.589	0.013	0.013	0.000	0.000	0.000
47	C	79	GLU	-1	-0.972	-0.981	26.149	-0.045	-0.045	0.000	0.000	0.000
48	C	80	PHE	0	0.016	0.007	23.031	-0.008	-0.008	0.000	0.000	0.000
49	C	81	CYS	0	-0.025	-0.040	21.474	-0.008	-0.008	0.000	0.000	0.000
50	C	82	LYS	1	0.943	0.985	21.451	0.047	0.047	0.000	0.000	0.000
51	C	83	LEU	0	0.008	0.004	22.818	-0.015	-0.015	0.000	0.000	0.000
52	C	84	ILE	0	0.025	0.012	18.041	-0.018	-0.018	0.000	0.000	0.000
53	C	85	ILE	0	0.020	0.011	17.584	-0.025	-0.025	0.000	0.000	0.000
54	C	86	LYS	1	0.941	0.970	17.931	0.076	0.076	0.000	0.000	0.000
55	C	87	CYS	0	-0.041	-0.005	19.331	-0.025	-0.025	0.000	0.000	0.000
56	C	88	GLN	0	0.043	0.007	13.250	-0.018	-0.018	0.000	0.000	0.000
57	C	89	GLU	-1	-0.945	-0.953	14.845	-0.235	-0.235	0.000	0.000	0.000
58	C	90	HIS	1	0.762	0.843	16.638	0.160	0.160	0.000	0.000	0.000
59	C	91	LEU	0	0.033	0.009	14.930	-0.013	-0.013	0.000	0.000	0.000
60	C	92	ASN	0	0.033	0.010	11.317	-0.117	-0.117	0.000	0.000	0.000
61	C	93	LYS	1	0.906	0.961	13.560	0.205	0.205	0.000	0.000	0.000
62	C	94	ILE	0	-0.046	-0.008	16.441	0.016	0.016	0.000	0.000	0.000
63	C	95	LEU	0	0.012	-0.004	10.061	0.018	0.018	0.000	0.000	0.000
64	C	96	ALA	0	0.012	0.022	13.105	-0.048	-0.048	0.000	0.000	0.000
65	C	97	ASN	0	-0.057	-0.016	14.328	0.029	0.029	0.000	0.000	0.000
66	C	98	PHE	0	-0.078	-0.035	13.876	0.053	0.053	0.000	0.000	0.000
67	C	99	GLY	0	-0.051	-0.030	12.891	-0.039	-0.039	0.000	0.000	0.000
68	C	100	PHE	0	-0.011	-0.002	7.389	-0.117	-0.117	0.000	0.000	0.000
69	C	101	GLU	-1	-0.921	-0.973	8.596	-0.462	-0.462	0.000	0.000	0.000
70	C	102	NME	0	-0.021	0.009	8.104	-0.237	-0.237	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:33:ACE )