FMO DATABASE

FMODB ID: Q1QLY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-383578.133217
FMO2-HF: Nuclear repulsion	355880.066444
FMO2-HF: Total energy	-27698.066773
FMO2-MP2: Total energy	-27779.442483

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.
-5.964	0.454	2.187	-3.159	-5.448	-0.012

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 : 0.028 / q_NPA : 0.023

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	0.056	-0.001	3.867	-1.071	1.423	-0.021	-1.262	-1.211	0.006
4	C	37	LYS	1	0.906	0.956	5.656	1.169	1.169	0.000	0.000	0.000	0.000
5	C	38	ASP	-1	-0.793	-0.852	3.122	-3.032	-1.804	0.155	-0.754	-0.630	-0.006
6	C	39	ALA	0	-0.032	-0.012	6.355	0.297	0.297	0.000	0.000	0.000	0.000
7	C	40	LYS	1	0.802	0.904	7.044	-0.425	-0.425	0.000	0.000	0.000	0.000
8	C	41	PRO	0	-0.005	-0.024	10.908	-0.008	-0.008	0.000	0.000	0.000	0.000
9	C	42	GLY	0	0.058	0.036	12.779	0.032	0.032	0.000	0.000	0.000	0.000
10	C	43	LYS	1	0.828	0.922	13.818	-0.061	-0.061	0.000	0.000	0.000	0.000
11	C	44	ILE	0	0.086	0.042	14.073	0.015	0.015	0.000	0.000	0.000	0.000
12	C	45	ASP	-1	-0.834	-0.925	14.910	0.047	0.047	0.000	0.000	0.000	0.000
13	C	46	VAL	0	0.050	0.020	16.747	-0.005	-0.005	0.000	0.000	0.000	0.000
14	C	47	ASN	0	-0.003	-0.007	19.449	-0.010	-0.010	0.000	0.000	0.000	0.000
15	C	48	GLU	-1	-0.793	-0.875	13.763	0.067	0.067	0.000	0.000	0.000	0.000
16	C	49	PHE	0	0.038	0.005	14.301	-0.002	-0.002	0.000	0.000	0.000	0.000
17	C	50	LYS	1	0.915	0.973	16.182	-0.013	-0.013	0.000	0.000	0.000	0.000
18	C	51	LYS	1	0.853	0.918	17.425	-0.054	-0.054	0.000	0.000	0.000	0.000
19	C	52	ALA	0	0.023	0.008	14.278	0.000	0.000	0.000	0.000	0.000	0.000
20	C	53	ILE	0	0.026	0.012	16.198	-0.007	-0.007	0.000	0.000	0.000	0.000
21	C	54	TYR	0	-0.010	-0.018	18.737	-0.001	-0.001	0.000	0.000	0.000	0.000
22	C	55	LEU	0	0.029	0.024	17.354	0.000	0.000	0.000	0.000	0.000	0.000
23	C	56	LEU	0	-0.012	-0.011	15.492	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	57	ILE	0	-0.018	-0.003	19.780	-0.004	-0.004	0.000	0.000	0.000	0.000
25	C	58	GLU	-1	-0.931	-0.976	23.099	0.002	0.002	0.000	0.000	0.000	0.000
26	C	59	ALA	0	-0.014	-0.014	20.951	0.001	0.001	0.000	0.000	0.000	0.000
27	C	60	ASP	-1	-0.851	-0.928	22.905	-0.053	-0.053	0.000	0.000	0.000	0.000
28	C	61	ASP	-1	-0.801	-0.886	24.754	-0.018	-0.018	0.000	0.000	0.000	0.000
29	C	62	PHE	0	-0.011	-0.019	25.489	0.001	0.001	0.000	0.000	0.000	0.000
30	C	63	LEU	0	-0.031	-0.008	23.594	0.000	0.000	0.000	0.000	0.000	0.000
31	C	64	TYR	0	-0.082	-0.038	27.768	0.000	0.000	0.000	0.000	0.000	0.000
32	C	65	LYS	1	0.791	0.877	30.729	0.015	0.015	0.000	0.000	0.000	0.000
33	C	66	LYS	1	0.805	0.898	28.789	0.021	0.021	0.000	0.000	0.000	0.000
34	C	67	ALA	0	0.021	0.048	31.485	-0.003	-0.003	0.000	0.000	0.000	0.000
35	C	68	PRO	0	-0.044	-0.043	32.743	0.003	0.003	0.000	0.000	0.000	0.000
36	C	69	LYS	1	0.899	0.953	31.481	0.033	0.033	0.000	0.000	0.000	0.000
37	C	70	HIS	0	-0.013	-0.014	26.580	-0.004	-0.004	0.000	0.000	0.000	0.000
38	C	71	GLU	-1	-0.911	-0.958	27.339	-0.032	-0.032	0.000	0.000	0.000	0.000
39	C	72	LEU	0	-0.007	0.008	23.975	0.003	0.003	0.000	0.000	0.000	0.000
40	C	73	ASN	0	0.009	0.001	28.081	0.003	0.003	0.000	0.000	0.000	0.000
41	C	74	GLU	-1	-0.814	-0.917	26.994	0.018	0.018	0.000	0.000	0.000	0.000
42	C	75	GLU	-1	-0.839	-0.913	26.485	0.018	0.018	0.000	0.000	0.000	0.000
43	C	76	GLU	-1	-0.772	-0.873	26.925	-0.011	-0.011	0.000	0.000	0.000	0.000
44	C	77	ALA	0	0.001	0.007	23.400	-0.002	-0.002	0.000	0.000	0.000	0.000
45	C	78	LYS	1	0.790	0.886	22.355	-0.019	-0.019	0.000	0.000	0.000	0.000
46	C	79	GLU	-1	-0.979	-0.988	22.429	0.006	0.006	0.000	0.000	0.000	0.000
47	C	80	PHE	0	0.026	0.011	19.999	0.001	0.001	0.000	0.000	0.000	0.000
48	C	81	CYS	0	-0.029	-0.033	18.286	-0.004	-0.004	0.000	0.000	0.000	0.000
49	C	82	LYS	1	0.938	0.975	17.701	-0.022	-0.022	0.000	0.000	0.000	0.000
50	C	83	LEU	0	-0.008	0.009	18.673	0.008	0.008	0.000	0.000	0.000	0.000
51	C	84	ILE	0	0.023	0.013	14.608	0.001	0.001	0.000	0.000	0.000	0.000
52	C	85	ILE	0	0.018	0.008	13.217	0.001	0.001	0.000	0.000	0.000	0.000
53	C	86	LYS	1	0.897	0.928	13.208	-0.057	-0.057	0.000	0.000	0.000	0.000
54	C	87	CYS	0	-0.050	-0.005	14.523	0.002	0.002	0.000	0.000	0.000	0.000
55	C	88	GLN	0	0.036	0.008	9.457	0.029	0.029	0.000	0.000	0.000	0.000
56	C	89	GLU	-1	-0.857	-0.900	9.419	0.121	0.121	0.000	0.000	0.000	0.000
57	C	90	HIS	1	0.827	0.909	11.267	-0.036	-0.036	0.000	0.000	0.000	0.000
58	C	91	LEU	0	0.030	0.007	8.972	0.010	0.010	0.000	0.000	0.000	0.000
59	C	92	ASN	0	0.047	0.012	5.124	-0.086	-0.010	-0.001	-0.001	-0.073	0.000
60	C	93	LYS	1	0.826	0.910	7.126	-0.094	-0.094	0.000	0.000	0.000	0.000
61	C	94	ILE	0	-0.052	-0.017	10.066	0.006	0.006	0.000	0.000	0.000	0.000
62	C	95	LEU	0	0.022	0.005	3.802	-0.194	-0.016	0.001	-0.021	-0.159	0.000
63	C	96	ALA	0	0.038	0.028	7.483	0.043	0.043	0.000	0.000	0.000	0.000
64	C	97	ASN	0	-0.069	-0.032	8.522	0.037	0.037	0.000	0.000	0.000	0.000
65	C	98	PHE	0	-0.048	-0.017	7.956	-0.041	-0.041	0.000	0.000	0.000	0.000
66	C	99	GLY	0	0.009	0.013	8.174	-0.021	-0.021	0.000	0.000	0.000	0.000
67	C	100	PHE	0	-0.023	-0.005	2.512	-1.631	-0.250	1.740	-0.716	-2.405	-0.007
68	C	101	GLU	-1	-0.919	-0.955	2.837	-0.950	0.111	0.313	-0.405	-0.970	-0.005

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