FMO DATABASE

FMODB ID: 3JZ6L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-377328.355842
FMO2-HF: Nuclear repulsion	351772.894636
FMO2-HF: Total energy	-25555.461206
FMO2-MP2: Total energy	-25630.155905

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.
-85.867	-79.106	4.514	-4.914	-6.36	0.031

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 : -0.876 / q_NPA : -0.957

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	-0.010	-0.020	2.761	-19.237	-14.075	0.835	-2.699	-3.298	0.024
4	A	148	SER	0	-0.010	-0.005	5.243	-7.037	-6.901	-0.001	-0.007	-0.128	0.000
5	A	149	GLY	0	0.058	0.023	8.245	-1.684	-1.684	0.000	0.000	0.000	0.000
6	A	150	LEU	0	-0.062	-0.013	7.367	-3.095	-3.095	0.000	0.000	0.000	0.000
7	A	151	THR	0	0.002	-0.024	10.672	0.679	0.679	0.000	0.000	0.000	0.000
8	A	152	ASP	-1	-0.818	-0.913	11.589	24.032	24.032	0.000	0.000	0.000	0.000
9	A	153	GLN	0	-0.001	-0.009	12.138	1.224	1.224	0.000	0.000	0.000	0.000
10	A	154	GLU	-1	-0.716	-0.841	12.030	21.067	21.067	0.000	0.000	0.000	0.000
11	A	155	ARG	1	0.939	0.981	6.918	-30.767	-30.767	0.000	0.000	0.000	0.000
12	A	156	THR	0	-0.004	-0.006	9.350	1.979	1.979	0.000	0.000	0.000	0.000
13	A	157	LEU	0	-0.053	-0.015	12.103	-1.752	-1.752	0.000	0.000	0.000	0.000
14	A	158	LEU	0	0.002	-0.001	7.180	-1.553	-1.553	0.000	0.000	0.000	0.000
15	A	159	GLY	0	0.042	0.027	10.961	0.501	0.501	0.000	0.000	0.000	0.000
16	A	160	LEU	0	-0.011	-0.011	11.507	-1.667	-1.667	0.000	0.000	0.000	0.000
17	A	161	LEU	0	-0.019	-0.024	13.822	-1.423	-1.423	0.000	0.000	0.000	0.000
18	A	162	SER	0	-0.023	-0.024	11.520	-0.210	-0.210	0.000	0.000	0.000	0.000
19	A	163	GLU	-1	-0.877	-0.903	13.662	22.212	22.212	0.000	0.000	0.000	0.000
20	A	164	GLY	0	-0.006	0.003	16.796	-1.196	-1.196	0.000	0.000	0.000	0.000
21	A	165	LEU	0	-0.011	0.018	18.328	-1.157	-1.157	0.000	0.000	0.000	0.000
22	A	166	THR	0	0.030	-0.017	20.628	0.062	0.062	0.000	0.000	0.000	0.000
23	A	167	ASN	0	-0.005	-0.007	21.853	0.818	0.818	0.000	0.000	0.000	0.000
24	A	168	LYS	1	0.906	0.930	22.866	-10.996	-10.996	0.000	0.000	0.000	0.000
25	A	169	GLN	0	0.067	0.057	23.091	0.172	0.172	0.000	0.000	0.000	0.000
26	A	170	ILE	0	-0.008	-0.012	17.598	0.056	0.056	0.000	0.000	0.000	0.000
27	A	171	ALA	0	-0.017	-0.006	20.772	0.272	0.272	0.000	0.000	0.000	0.000
28	A	172	ASP	-1	-0.793	-0.875	23.266	11.520	11.520	0.000	0.000	0.000	0.000
29	A	173	ARG	1	0.858	0.926	20.092	-14.257	-14.257	0.000	0.000	0.000	0.000
30	A	174	MET	0	-0.026	-0.012	17.215	0.761	0.761	0.000	0.000	0.000	0.000
31	A	175	PHE	0	0.000	0.014	21.531	-0.153	-0.153	0.000	0.000	0.000	0.000
32	A	176	LEU	0	-0.031	0.000	20.891	-0.311	-0.311	0.000	0.000	0.000	0.000
33	A	177	ALA	0	0.052	0.028	25.199	-0.336	-0.336	0.000	0.000	0.000	0.000
34	A	178	GLU	-1	-0.730	-0.875	25.438	12.390	12.390	0.000	0.000	0.000	0.000
35	A	179	LYS	1	0.914	0.954	25.493	-11.138	-11.138	0.000	0.000	0.000	0.000
36	A	180	THR	0	0.051	0.014	23.236	0.084	0.084	0.000	0.000	0.000	0.000
37	A	181	VAL	0	0.046	0.025	19.998	0.496	0.496	0.000	0.000	0.000	0.000
38	A	182	LYS	1	0.795	0.883	21.049	-11.030	-11.030	0.000	0.000	0.000	0.000
39	A	183	ASN	0	0.015	0.017	21.928	0.177	0.177	0.000	0.000	0.000	0.000
40	A	184	TYR	0	0.006	0.004	17.663	0.166	0.166	0.000	0.000	0.000	0.000
41	A	185	VAL	0	0.043	0.020	16.896	0.856	0.856	0.000	0.000	0.000	0.000
42	A	186	SER	0	-0.023	-0.002	17.062	0.470	0.470	0.000	0.000	0.000	0.000
43	A	187	ARG	1	0.823	0.890	17.175	-17.072	-17.072	0.000	0.000	0.000	0.000
44	A	188	LEU	0	-0.006	0.001	11.078	0.119	0.119	0.000	0.000	0.000	0.000
45	A	189	LEU	0	-0.013	-0.005	13.470	1.232	1.232	0.000	0.000	0.000	0.000
46	A	190	ALA	0	0.041	0.031	14.998	0.339	0.339	0.000	0.000	0.000	0.000
47	A	191	LYS	1	0.740	0.845	12.839	-21.468	-21.468	0.000	0.000	0.000	0.000
48	A	192	LEU	0	-0.008	-0.002	8.463	1.221	1.221	0.000	0.000	0.000	0.000
49	A	193	GLY	0	-0.010	0.014	11.993	0.526	0.526	0.000	0.000	0.000	0.000
50	A	194	MET	0	-0.072	-0.024	9.772	-0.722	-0.722	0.000	0.000	0.000	0.000
51	A	195	GLU	-1	-0.767	-0.892	15.648	15.270	15.270	0.000	0.000	0.000	0.000
52	A	196	ARG	1	0.846	0.908	17.455	-15.627	-15.627	0.000	0.000	0.000	0.000
53	A	197	ARG	1	0.888	0.923	16.207	-14.960	-14.960	0.000	0.000	0.000	0.000
54	A	198	THR	0	0.017	0.003	15.435	0.939	0.939	0.000	0.000	0.000	0.000
55	A	199	GLN	0	0.035	0.025	13.873	-0.123	-0.123	0.000	0.000	0.000	0.000
56	A	200	ALA	0	0.068	0.033	11.259	1.444	1.444	0.000	0.000	0.000	0.000
57	A	201	ALA	0	-0.005	0.011	10.433	2.485	2.485	0.000	0.000	0.000	0.000
58	A	202	VAL	0	0.017	0.019	11.330	1.425	1.425	0.000	0.000	0.000	0.000
59	A	203	PHE	0	0.069	0.030	5.174	1.012	1.012	0.000	0.000	0.000	0.000
60	A	204	ALA	0	0.013	-0.006	6.860	4.001	4.001	0.000	0.000	0.000	0.000
61	A	205	THR	0	-0.055	-0.055	7.521	2.523	2.523	0.000	0.000	0.000	0.000
62	A	206	GLU	-1	-0.988	-0.997	7.164	25.976	25.976	0.000	0.000	0.000	0.000
63	A	207	LEU	0	-0.025	0.016	2.214	-1.226	0.074	3.681	-2.205	-2.776	0.007
64	A	208	LYS	1	0.814	0.912	4.937	-25.914	-25.751	-0.001	-0.003	-0.158	0.000
65	A	209	ARG	1	0.891	0.955	6.917	-28.262	-28.262	0.000	0.000	0.000	0.000

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