FMO DATABASE

FMODB ID: LNG19

Calculation Name: 1ZLK-A-Xray372

Preferred Name: Transcriptional regulatory protein devR (dosR)

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZLK

Chain ID: A

ChEMBL ID: CHEMBL6064

UniProt ID: P9WMF9

Base Structure: X-ray

Registration Date: 2023-09-23

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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-377672.529084
FMO2-HF: Nuclear repulsion	352116.73932
FMO2-HF: Total energy	-25555.789764
FMO2-MP2: Total energy	-25630.430297

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(A:145:ASP)

Summations of interaction energy for fragment #1(A:145:ASP)

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.
-99.284	-90.618	5.043	-6.252	-7.457	0.05

Interaction energy analysis for fragmet #1(A:145:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.865 / q_NPA : -0.949

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	A	147	LEU	0	0.003	-0.005	2.444	-24.476	-18.246	1.836	-3.841	-4.225	0.036
4	A	148	SER	0	-0.008	-0.008	4.729	-9.585	-9.434	-0.001	-0.023	-0.128	0.000
5	A	149	GLY	0	0.061	0.032	7.602	-2.718	-2.718	0.000	0.000	0.000	0.000
6	A	150	LEU	0	-0.057	-0.003	7.154	-3.784	-3.784	0.000	0.000	0.000	0.000
7	A	151	THR	0	0.018	-0.010	10.200	0.990	0.990	0.000	0.000	0.000	0.000
8	A	152	ASP	-1	-0.799	-0.896	11.462	25.801	25.801	0.000	0.000	0.000	0.000
9	A	153	GLN	0	0.027	0.015	12.334	0.586	0.586	0.000	0.000	0.000	0.000
10	A	154	GLU	-1	-0.730	-0.837	11.655	21.656	21.656	0.000	0.000	0.000	0.000
11	A	155	ARG	1	0.886	0.934	6.829	-31.634	-31.634	0.000	0.000	0.000	0.000
12	A	156	THR	0	0.021	0.009	9.250	1.560	1.560	0.000	0.000	0.000	0.000
13	A	157	LEU	0	-0.045	-0.018	12.057	-1.000	-1.000	0.000	0.000	0.000	0.000
14	A	158	LEU	0	0.006	0.001	6.690	-1.577	-1.577	0.000	0.000	0.000	0.000
15	A	159	GLY	0	0.022	0.022	10.453	0.071	0.071	0.000	0.000	0.000	0.000
16	A	160	LEU	0	-0.030	-0.029	10.975	-1.924	-1.924	0.000	0.000	0.000	0.000
17	A	161	LEU	0	-0.057	-0.035	13.282	-1.744	-1.744	0.000	0.000	0.000	0.000
18	A	162	SER	0	-0.009	-0.020	11.548	-0.303	-0.303	0.000	0.000	0.000	0.000
19	A	163	GLU	-1	-0.840	-0.878	13.552	22.329	22.329	0.000	0.000	0.000	0.000
20	A	164	GLY	0	-0.004	0.001	16.683	-1.261	-1.261	0.000	0.000	0.000	0.000
21	A	165	LEU	0	-0.035	0.006	18.113	-1.156	-1.156	0.000	0.000	0.000	0.000
22	A	166	THR	0	0.040	-0.011	20.016	0.308	0.308	0.000	0.000	0.000	0.000
23	A	167	ASN	0	0.021	-0.014	21.365	0.943	0.943	0.000	0.000	0.000	0.000
24	A	168	LYS	1	0.877	0.920	22.446	-11.162	-11.162	0.000	0.000	0.000	0.000
25	A	169	GLN	0	0.077	0.063	22.784	0.238	0.238	0.000	0.000	0.000	0.000
26	A	170	ILE	0	0.037	0.024	17.376	0.078	0.078	0.000	0.000	0.000	0.000
27	A	171	ALA	0	-0.019	-0.014	20.533	0.215	0.215	0.000	0.000	0.000	0.000
28	A	172	ASP	-1	-0.814	-0.887	23.111	11.797	11.797	0.000	0.000	0.000	0.000
29	A	173	ARG	1	0.866	0.930	19.933	-14.400	-14.400	0.000	0.000	0.000	0.000
30	A	174	MET	0	-0.040	-0.014	16.763	0.874	0.874	0.000	0.000	0.000	0.000
31	A	175	PHE	0	0.009	0.020	21.194	-0.172	-0.172	0.000	0.000	0.000	0.000
32	A	176	LEU	0	-0.021	0.003	20.518	-0.244	-0.244	0.000	0.000	0.000	0.000
33	A	177	ALA	0	0.062	0.032	24.887	-0.369	-0.369	0.000	0.000	0.000	0.000
34	A	178	GLU	-1	-0.745	-0.875	24.960	12.807	12.807	0.000	0.000	0.000	0.000
35	A	179	LYS	1	0.926	0.959	24.867	-11.398	-11.398	0.000	0.000	0.000	0.000
36	A	180	THR	0	0.024	0.013	22.601	-0.091	-0.091	0.000	0.000	0.000	0.000
37	A	181	VAL	0	0.039	0.022	19.520	0.516	0.516	0.000	0.000	0.000	0.000
38	A	182	LYS	1	0.808	0.882	20.450	-11.288	-11.288	0.000	0.000	0.000	0.000
39	A	183	ASN	0	0.022	0.016	21.610	0.147	0.147	0.000	0.000	0.000	0.000
40	A	184	TYR	0	-0.012	-0.016	16.957	0.158	0.158	0.000	0.000	0.000	0.000
41	A	185	VAL	0	0.035	0.014	16.528	1.035	1.035	0.000	0.000	0.000	0.000
42	A	186	SER	0	-0.036	-0.001	16.980	0.554	0.554	0.000	0.000	0.000	0.000
43	A	187	ARG	1	0.853	0.899	16.636	-17.537	-17.537	0.000	0.000	0.000	0.000
44	A	188	LEU	0	-0.012	0.002	10.472	0.342	0.342	0.000	0.000	0.000	0.000
45	A	189	LEU	0	-0.021	-0.012	13.317	1.310	1.310	0.000	0.000	0.000	0.000
46	A	190	ALA	0	0.024	0.015	14.828	0.416	0.416	0.000	0.000	0.000	0.000
47	A	191	LYS	1	0.761	0.852	12.332	-22.793	-22.793	0.000	0.000	0.000	0.000
48	A	192	LEU	0	-0.011	0.001	8.368	1.357	1.357	0.000	0.000	0.000	0.000
49	A	193	GLY	0	0.003	0.022	11.599	0.205	0.205	0.000	0.000	0.000	0.000
50	A	194	MET	0	-0.080	-0.034	10.037	-0.701	-0.701	0.000	0.000	0.000	0.000
51	A	195	GLU	-1	-0.754	-0.883	15.686	15.579	15.579	0.000	0.000	0.000	0.000
52	A	196	ARG	1	0.822	0.901	17.803	-15.967	-15.967	0.000	0.000	0.000	0.000
53	A	197	ARG	1	0.870	0.913	16.576	-15.307	-15.307	0.000	0.000	0.000	0.000
54	A	198	THR	0	0.032	0.003	15.477	1.134	1.134	0.000	0.000	0.000	0.000
55	A	199	GLN	0	0.022	0.023	13.895	-0.306	-0.306	0.000	0.000	0.000	0.000
56	A	200	ALA	0	0.076	0.039	11.064	1.481	1.481	0.000	0.000	0.000	0.000
57	A	201	ALA	0	0.004	0.006	10.647	2.468	2.468	0.000	0.000	0.000	0.000
58	A	202	VAL	0	-0.006	0.010	11.968	1.050	1.050	0.000	0.000	0.000	0.000
59	A	203	PHE	0	0.088	0.034	4.798	0.843	0.923	-0.001	-0.004	-0.075	0.000
60	A	204	ALA	0	-0.003	-0.002	7.084	4.359	4.359	0.000	0.000	0.000	0.000
61	A	205	THR	0	-0.005	-0.029	8.027	2.012	2.012	0.000	0.000	0.000	0.000
62	A	206	GLU	-1	-1.003	-0.993	7.951	25.538	25.538	0.000	0.000	0.000	0.000
63	A	207	LEU	0	0.005	0.011	2.185	-4.035	-1.949	3.210	-2.383	-2.913	0.014
64	A	208	LYS	1	0.774	0.889	5.296	-24.808	-24.689	-0.001	-0.001	-0.116	0.000
65	A	209	ARG	1	0.864	0.938	7.431	-28.301	-28.301	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:145:ASP)