FMO DATABASE

FMODB ID: JQY19

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

Total energy (hartree)

FMO2-HF: Electronic energy	-377180.218664
FMO2-HF: Nuclear repulsion	351625.485486
FMO2-HF: Total energy	-25554.733178
FMO2-MP2: Total energy	-25629.456339

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.
-85.01	-79.329	3.492	-4.014	-5.157	0.02

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 : -0.899 / q_NPA : -0.961

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	A	147	LEU	0	-0.023	-0.029	2.780	-18.497	-13.570	0.720	-2.627	-3.019	0.021
4	A	148	SER	0	-0.013	-0.010	5.520	-5.855	-5.732	-0.001	-0.005	-0.116	0.000
5	A	149	GLY	0	0.060	0.026	8.185	-1.731	-1.731	0.000	0.000	0.000	0.000
6	A	150	LEU	0	-0.060	-0.019	7.409	-2.756	-2.756	0.000	0.000	0.000	0.000
7	A	151	THR	0	-0.032	-0.030	10.906	0.560	0.560	0.000	0.000	0.000	0.000
8	A	152	ASP	-1	-0.876	-0.940	11.722	22.426	22.426	0.000	0.000	0.000	0.000
9	A	153	GLN	0	0.013	-0.004	12.272	1.221	1.221	0.000	0.000	0.000	0.000
10	A	154	GLU	-1	-0.734	-0.885	12.515	21.101	21.101	0.000	0.000	0.000	0.000
11	A	155	ARG	1	0.993	1.002	6.308	-33.270	-33.270	0.000	0.000	0.000	0.000
12	A	156	THR	0	-0.023	-0.008	9.764	2.043	2.043	0.000	0.000	0.000	0.000
13	A	157	LEU	0	-0.039	0.001	12.530	-1.629	-1.629	0.000	0.000	0.000	0.000
14	A	158	LEU	0	0.016	0.004	7.454	-1.397	-1.397	0.000	0.000	0.000	0.000
15	A	159	GLY	0	0.042	0.021	11.323	0.509	0.509	0.000	0.000	0.000	0.000
16	A	160	LEU	0	-0.011	0.008	12.176	-1.475	-1.475	0.000	0.000	0.000	0.000
17	A	161	LEU	0	-0.009	-0.023	13.739	-1.331	-1.331	0.000	0.000	0.000	0.000
18	A	162	SER	0	-0.065	-0.034	11.543	-0.074	-0.074	0.000	0.000	0.000	0.000
19	A	163	GLU	-1	-0.915	-0.937	13.676	20.350	20.350	0.000	0.000	0.000	0.000
20	A	164	GLY	0	-0.045	-0.018	16.839	-1.159	-1.159	0.000	0.000	0.000	0.000
21	A	165	LEU	0	-0.013	0.016	18.656	-1.133	-1.133	0.000	0.000	0.000	0.000
22	A	166	THR	0	0.014	-0.026	20.718	0.009	0.009	0.000	0.000	0.000	0.000
23	A	167	ASN	0	0.012	-0.011	21.776	0.761	0.761	0.000	0.000	0.000	0.000
24	A	168	LYS	1	1.002	1.005	23.022	-10.757	-10.757	0.000	0.000	0.000	0.000
25	A	169	GLN	0	0.055	0.048	23.370	0.158	0.158	0.000	0.000	0.000	0.000
26	A	170	ILE	0	-0.010	-0.016	17.915	0.079	0.079	0.000	0.000	0.000	0.000
27	A	171	ALA	0	-0.031	-0.020	21.369	0.260	0.260	0.000	0.000	0.000	0.000
28	A	172	ASP	-1	-0.847	-0.923	23.838	11.409	11.409	0.000	0.000	0.000	0.000
29	A	173	ARG	1	0.875	0.935	20.458	-14.398	-14.398	0.000	0.000	0.000	0.000
30	A	174	MET	0	-0.025	-0.015	17.890	0.876	0.876	0.000	0.000	0.000	0.000
31	A	175	PHE	0	0.007	0.021	21.922	-0.169	-0.169	0.000	0.000	0.000	0.000
32	A	176	LEU	0	-0.034	-0.006	21.362	-0.311	-0.311	0.000	0.000	0.000	0.000
33	A	177	ALA	0	0.047	0.026	25.646	-0.335	-0.335	0.000	0.000	0.000	0.000
34	A	178	GLU	-1	-0.869	-0.966	25.914	11.880	11.880	0.000	0.000	0.000	0.000
35	A	179	LYS	1	0.911	0.951	25.713	-10.873	-10.873	0.000	0.000	0.000	0.000
36	A	180	THR	0	0.019	0.007	23.557	0.048	0.048	0.000	0.000	0.000	0.000
37	A	181	VAL	0	0.051	0.029	20.299	0.460	0.460	0.000	0.000	0.000	0.000
38	A	182	LYS	1	0.906	0.960	21.171	-11.057	-11.057	0.000	0.000	0.000	0.000
39	A	183	ASN	0	0.026	0.012	21.971	0.236	0.236	0.000	0.000	0.000	0.000
40	A	184	TYR	0	-0.005	0.003	18.372	0.086	0.086	0.000	0.000	0.000	0.000
41	A	185	VAL	0	0.042	0.013	16.966	0.793	0.793	0.000	0.000	0.000	0.000
42	A	186	SER	0	-0.028	-0.009	17.115	0.746	0.746	0.000	0.000	0.000	0.000
43	A	187	ARG	1	0.887	0.943	17.645	-16.650	-16.650	0.000	0.000	0.000	0.000
44	A	188	LEU	0	0.006	0.005	11.162	0.132	0.132	0.000	0.000	0.000	0.000
45	A	189	LEU	0	-0.014	-0.006	13.534	1.179	1.179	0.000	0.000	0.000	0.000
46	A	190	ALA	0	0.047	0.035	15.082	0.314	0.314	0.000	0.000	0.000	0.000
47	A	191	LYS	1	0.737	0.858	12.848	-20.944	-20.944	0.000	0.000	0.000	0.000
48	A	192	LEU	0	-0.006	-0.009	8.364	1.176	1.176	0.000	0.000	0.000	0.000
49	A	193	GLY	0	-0.021	0.011	12.080	0.546	0.546	0.000	0.000	0.000	0.000
50	A	194	MET	0	-0.055	-0.012	10.021	-0.300	-0.300	0.000	0.000	0.000	0.000
51	A	195	GLU	-1	-0.867	-0.939	15.746	15.156	15.156	0.000	0.000	0.000	0.000
52	A	196	ARG	1	0.931	0.950	17.560	-15.222	-15.222	0.000	0.000	0.000	0.000
53	A	197	ARG	1	0.932	0.959	16.283	-14.848	-14.848	0.000	0.000	0.000	0.000
54	A	198	THR	0	0.013	-0.001	15.496	0.885	0.885	0.000	0.000	0.000	0.000
55	A	199	GLN	0	0.043	0.030	13.986	0.608	0.608	0.000	0.000	0.000	0.000
56	A	200	ALA	0	0.072	0.039	11.349	1.377	1.377	0.000	0.000	0.000	0.000
57	A	201	ALA	0	-0.004	0.007	10.494	2.409	2.409	0.000	0.000	0.000	0.000
58	A	202	VAL	0	0.012	0.012	11.374	1.433	1.433	0.000	0.000	0.000	0.000
59	A	203	PHE	0	0.077	0.038	5.065	1.345	1.345	0.000	0.000	0.000	0.000
60	A	204	ALA	0	0.015	-0.008	6.886	3.905	3.905	0.000	0.000	0.000	0.000
61	A	205	THR	0	-0.090	-0.063	7.532	2.792	2.792	0.000	0.000	0.000	0.000
62	A	206	GLU	-1	-0.982	-0.995	7.022	26.581	26.581	0.000	0.000	0.000	0.000
63	A	207	LEU	0	-0.010	0.021	2.147	0.652	1.090	2.774	-1.379	-1.833	-0.001
64	A	208	LYS	1	0.874	0.941	4.942	-26.505	-26.312	-0.001	-0.003	-0.189	0.000
65	A	209	ARG	1	0.908	0.962	6.913	-28.835	-28.835	0.000	0.000	0.000	0.000

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