FMO DATABASE

FMODB ID: ZY3ZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-382429.12102
FMO2-HF: Nuclear repulsion	354731.786699
FMO2-HF: Total energy	-27697.33432
FMO2-MP2: Total energy	-27778.640065

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.
-2.033	1.24	2.836	-1.73	-4.38	-0.002

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 : 0.013 / q_NPA : -0.003

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	0.046	0.001	3.805	-1.547	0.538	-0.029	-0.899	-1.158	0.004
4	C	37	LYS	1	0.899	0.940	5.334	-0.468	-0.379	-0.001	-0.002	-0.085	0.000
5	C	38	ASP	-1	-0.877	-0.926	4.607	2.931	3.042	-0.001	-0.008	-0.102	0.000
6	C	39	ALA	0	-0.040	-0.014	7.111	-0.105	-0.105	0.000	0.000	0.000	0.000
7	C	40	LYS	1	0.924	0.975	8.061	-0.393	-0.393	0.000	0.000	0.000	0.000
8	C	41	PRO	0	-0.008	-0.023	11.022	-0.067	-0.067	0.000	0.000	0.000	0.000
9	C	42	GLY	0	0.074	0.047	13.077	0.008	0.008	0.000	0.000	0.000	0.000
10	C	43	LYS	1	0.892	0.952	14.037	0.106	0.106	0.000	0.000	0.000	0.000
11	C	44	ILE	0	0.065	0.025	14.264	-0.024	-0.024	0.000	0.000	0.000	0.000
12	C	45	ASP	-1	-0.869	-0.941	14.791	-0.177	-0.177	0.000	0.000	0.000	0.000
13	C	46	VAL	0	0.028	0.001	16.573	-0.021	-0.021	0.000	0.000	0.000	0.000
14	C	47	ASN	0	-0.020	-0.016	19.232	-0.003	-0.003	0.000	0.000	0.000	0.000
15	C	48	GLU	-1	-0.846	-0.896	13.704	-0.297	-0.297	0.000	0.000	0.000	0.000
16	C	49	PHE	0	0.017	0.005	13.878	-0.029	-0.029	0.000	0.000	0.000	0.000
17	C	50	LYS	1	0.946	0.978	16.178	0.141	0.141	0.000	0.000	0.000	0.000
18	C	51	LYS	1	0.914	0.955	17.605	0.211	0.211	0.000	0.000	0.000	0.000
19	C	52	ALA	0	0.026	0.012	14.224	-0.002	-0.002	0.000	0.000	0.000	0.000
20	C	53	ILE	0	0.024	0.013	16.186	-0.004	-0.004	0.000	0.000	0.000	0.000
21	C	54	TYR	0	0.013	-0.012	18.595	0.011	0.011	0.000	0.000	0.000	0.000
22	C	55	LEU	0	0.009	0.020	16.821	0.006	0.006	0.000	0.000	0.000	0.000
23	C	56	LEU	0	0.004	-0.006	15.436	-0.002	-0.002	0.000	0.000	0.000	0.000
24	C	57	ILE	0	-0.028	-0.008	19.624	0.012	0.012	0.000	0.000	0.000	0.000
25	C	58	GLU	-1	-0.933	-0.967	23.043	-0.176	-0.176	0.000	0.000	0.000	0.000
26	C	59	ALA	0	-0.040	-0.028	20.738	0.007	0.007	0.000	0.000	0.000	0.000
27	C	60	ASP	-1	-0.898	-0.964	22.694	-0.168	-0.168	0.000	0.000	0.000	0.000
28	C	61	ASP	-1	-0.862	-0.930	24.577	-0.129	-0.129	0.000	0.000	0.000	0.000
29	C	62	PHE	0	-0.050	-0.031	24.336	0.008	0.008	0.000	0.000	0.000	0.000
30	C	63	LEU	0	-0.025	-0.011	22.874	0.004	0.004	0.000	0.000	0.000	0.000
31	C	64	TYR	0	-0.033	0.004	26.992	0.015	0.015	0.000	0.000	0.000	0.000
32	C	65	LYS	1	0.887	0.932	30.141	0.131	0.131	0.000	0.000	0.000	0.000
33	C	66	LYS	1	0.845	0.922	28.315	0.126	0.126	0.000	0.000	0.000	0.000
34	C	67	ALA	0	0.019	0.055	30.675	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	68	PRO	0	-0.039	-0.045	31.789	0.006	0.006	0.000	0.000	0.000	0.000
36	C	69	LYS	1	0.961	0.959	30.537	0.090	0.090	0.000	0.000	0.000	0.000
37	C	70	HIS	0	-0.034	-0.003	26.034	-0.007	-0.007	0.000	0.000	0.000	0.000
38	C	71	GLU	-1	-0.964	-0.974	26.342	-0.126	-0.126	0.000	0.000	0.000	0.000
39	C	72	LEU	0	-0.020	-0.004	23.534	0.006	0.006	0.000	0.000	0.000	0.000
40	C	73	ASN	0	0.039	0.021	27.469	-0.004	-0.004	0.000	0.000	0.000	0.000
41	C	74	GLU	-1	-0.911	-0.979	26.418	-0.155	-0.155	0.000	0.000	0.000	0.000
42	C	75	GLU	-1	-0.919	-0.967	26.028	-0.132	-0.132	0.000	0.000	0.000	0.000
43	C	76	GLU	-1	-0.768	-0.885	26.519	-0.138	-0.138	0.000	0.000	0.000	0.000
44	C	77	ALA	0	0.033	0.024	22.537	-0.013	-0.013	0.000	0.000	0.000	0.000
45	C	78	LYS	1	0.898	0.967	21.762	0.133	0.133	0.000	0.000	0.000	0.000
46	C	79	GLU	-1	-0.971	-0.981	21.965	-0.169	-0.169	0.000	0.000	0.000	0.000
47	C	80	PHE	0	0.012	0.006	19.284	-0.015	-0.015	0.000	0.000	0.000	0.000
48	C	81	CYS	0	-0.023	-0.039	17.617	-0.026	-0.026	0.000	0.000	0.000	0.000
49	C	82	LYS	1	0.943	0.984	17.053	0.161	0.161	0.000	0.000	0.000	0.000
50	C	83	LEU	0	0.008	0.004	17.959	-0.022	-0.022	0.000	0.000	0.000	0.000
51	C	84	ILE	0	0.026	0.012	13.630	-0.027	-0.027	0.000	0.000	0.000	0.000
52	C	85	ILE	0	0.021	0.011	12.928	-0.057	-0.057	0.000	0.000	0.000	0.000
53	C	86	LYS	1	0.941	0.970	12.878	0.224	0.224	0.000	0.000	0.000	0.000
54	C	87	CYS	0	-0.042	-0.005	14.183	-0.019	-0.019	0.000	0.000	0.000	0.000
55	C	88	GLN	0	0.043	0.007	8.786	-0.002	-0.002	0.000	0.000	0.000	0.000
56	C	89	GLU	-1	-0.943	-0.952	9.008	-0.483	-0.483	0.000	0.000	0.000	0.000
57	C	90	HIS	1	0.761	0.842	10.732	0.347	0.347	0.000	0.000	0.000	0.000
58	C	91	LEU	0	0.029	0.009	8.719	0.025	0.025	0.000	0.000	0.000	0.000
59	C	92	ASN	0	0.036	0.010	5.250	-0.210	-0.210	0.000	0.000	0.000	0.000
60	C	93	LYS	1	0.907	0.961	7.128	0.441	0.441	0.000	0.000	0.000	0.000
61	C	94	ILE	0	-0.048	-0.008	9.889	0.080	0.080	0.000	0.000	0.000	0.000
62	C	95	LEU	0	0.015	-0.003	3.458	-0.191	0.075	0.011	-0.043	-0.234	0.000
63	C	96	ALA	0	0.011	0.020	7.235	0.100	0.100	0.000	0.000	0.000	0.000
64	C	97	ASN	0	-0.055	-0.016	8.870	0.102	0.102	0.000	0.000	0.000	0.000
65	C	98	PHE	0	-0.077	-0.033	7.920	0.051	0.051	0.000	0.000	0.000	0.000
66	C	99	GLY	0	-0.051	-0.030	7.911	0.103	0.103	0.000	0.000	0.000	0.000
67	C	100	PHE	0	-0.003	0.004	2.248	-0.921	-0.532	2.853	-0.733	-2.510	-0.006
68	C	101	GLU	-1	-0.949	-0.968	3.957	-1.289	-0.956	0.003	-0.045	-0.291	0.000

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