FMO DATABASE

FMODB ID: 5J5QZ

Calculation Name: 3C57-A-Xray372

Preferred Name: Transcriptional regulatory protein devR (dosR)

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3C57

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	51
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-243066.775638
FMO2-HF: Nuclear repulsion	222628.208168
FMO2-HF: Total energy	-20438.567471
FMO2-MP2: Total energy	-20497.735119

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:149:GLY)

Summations of interaction energy for fragment #1(A:149:GLY)

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.
-2.277	-0.336	-0.013	-1.066	-0.861	0.004

Interaction energy analysis for fragmet #1(A:149:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.010

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	151	THR	0	-0.012	-0.014	3.802	-0.449	1.401	-0.013	-1.046	-0.791	0.004
4	A	152	ASP	-1	-0.850	-0.935	6.809	-0.631	-0.631	0.000	0.000	0.000	0.000
5	A	153	GLN	0	0.051	0.023	9.371	0.028	0.028	0.000	0.000	0.000	0.000
6	A	154	GLU	-1	-0.816	-0.910	6.895	-3.229	-3.229	0.000	0.000	0.000	0.000
7	A	155	ARG	1	0.935	0.967	3.840	0.578	0.669	0.000	-0.020	-0.070	0.000
8	A	156	THR	0	0.031	0.026	9.006	0.270	0.270	0.000	0.000	0.000	0.000
9	A	157	LEU	0	-0.045	-0.019	12.415	0.121	0.121	0.000	0.000	0.000	0.000
10	A	158	LEU	0	0.022	-0.015	7.968	0.092	0.092	0.000	0.000	0.000	0.000
11	A	159	GLY	0	0.023	0.026	11.870	0.123	0.123	0.000	0.000	0.000	0.000
12	A	160	LEU	0	0.021	0.024	14.057	0.065	0.065	0.000	0.000	0.000	0.000
13	A	161	LEU	0	-0.038	-0.026	13.468	0.036	0.036	0.000	0.000	0.000	0.000
14	A	162	SER	0	-0.118	-0.063	14.264	0.062	0.062	0.000	0.000	0.000	0.000
15	A	163	GLU	-1	-0.921	-0.962	16.282	-0.143	-0.143	0.000	0.000	0.000	0.000
16	A	164	GLY	0	-0.026	-0.004	19.172	0.019	0.019	0.000	0.000	0.000	0.000
17	A	165	LEU	0	-0.060	-0.016	20.477	0.004	0.004	0.000	0.000	0.000	0.000
18	A	166	THR	0	0.036	0.007	21.106	-0.024	-0.024	0.000	0.000	0.000	0.000
19	A	167	ASN	0	0.037	-0.010	20.665	-0.030	-0.030	0.000	0.000	0.000	0.000
20	A	168	LYS	1	0.865	0.919	22.526	0.165	0.165	0.000	0.000	0.000	0.000
21	A	169	GLN	0	0.066	0.035	24.158	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	170	ILE	0	0.010	0.003	18.077	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	171	ALA	0	-0.024	-0.024	21.699	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	172	ASP	-1	-0.820	-0.891	23.592	-0.196	-0.196	0.000	0.000	0.000	0.000
25	A	173	ARG	1	0.909	0.960	20.811	0.225	0.225	0.000	0.000	0.000	0.000
26	A	174	MET	0	-0.057	-0.021	16.481	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	175	PHE	0	0.001	0.021	22.160	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	176	LEU	0	-0.028	-0.004	19.650	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	177	ALA	0	0.031	0.010	24.242	0.024	0.024	0.000	0.000	0.000	0.000
30	A	178	GLU	-1	-0.827	-0.937	23.994	-0.231	-0.231	0.000	0.000	0.000	0.000
31	A	179	LYS	1	0.927	0.960	23.481	0.223	0.223	0.000	0.000	0.000	0.000
32	A	180	THR	0	0.019	0.009	20.562	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	181	VAL	0	0.057	0.040	18.945	-0.057	-0.057	0.000	0.000	0.000	0.000
34	A	182	LYS	1	0.976	0.995	18.648	0.199	0.199	0.000	0.000	0.000	0.000
35	A	183	ASN	0	-0.024	-0.017	18.972	0.002	0.002	0.000	0.000	0.000	0.000
36	A	184	TYR	0	-0.001	-0.004	14.767	-0.076	-0.076	0.000	0.000	0.000	0.000
37	A	185	VAL	0	0.035	0.023	14.197	-0.116	-0.116	0.000	0.000	0.000	0.000
38	A	186	SER	0	-0.040	-0.026	14.541	0.000	0.000	0.000	0.000	0.000	0.000
39	A	187	ARG	1	0.951	0.982	12.008	1.057	1.057	0.000	0.000	0.000	0.000
40	A	188	LEU	0	-0.009	-0.005	8.588	-0.117	-0.117	0.000	0.000	0.000	0.000
41	A	189	LEU	0	0.036	0.003	10.015	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	190	ALA	0	-0.002	0.002	11.993	0.073	0.073	0.000	0.000	0.000	0.000
43	A	191	LYS	1	0.804	0.897	7.126	2.526	2.526	0.000	0.000	0.000	0.000
44	A	192	LEU	0	-0.026	-0.018	6.279	0.047	0.047	0.000	0.000	0.000	0.000
45	A	193	GLY	0	-0.004	0.020	8.454	0.240	0.240	0.000	0.000	0.000	0.000
46	A	194	MET	0	-0.067	-0.021	9.582	0.097	0.097	0.000	0.000	0.000	0.000
47	A	195	GLU	-1	-0.907	-0.947	8.104	0.742	0.742	0.000	0.000	0.000	0.000
48	A	196	ARG	1	0.890	0.931	4.828	-4.084	-4.084	0.000	0.000	0.000	0.000
49	A	197	ARG	1	1.027	1.011	9.071	-0.081	-0.081	0.000	0.000	0.000	0.000
50	A	198	THR	0	-0.043	-0.012	11.522	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	199	GLN	0	0.035	0.020	11.357	0.327	0.327	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:149:GLY)