FMO DATABASE

FMODB ID: YVR72

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

Total energy (hartree)

FMO2-HF: Electronic energy	-243297.660047
FMO2-HF: Nuclear repulsion	222858.860653
FMO2-HF: Total energy	-20438.799394
FMO2-MP2: Total energy	-20497.94875

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.
-1.503	0.522	-0.015	-1.104	-0.905	0.005

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 : 0.032 / q_NPA : 0.016

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	-0.010	-0.022	3.802	-0.576	1.328	-0.013	-1.082	-0.809	0.005
4	A	152	ASP	-1	-0.854	-0.938	6.809	-0.614	-0.614	0.000	0.000	0.000	0.000
5	A	153	GLN	0	0.059	0.029	9.371	0.016	0.016	0.000	0.000	0.000	0.000
6	A	154	GLU	-1	-0.775	-0.853	7.449	-2.779	-2.779	0.000	0.000	0.000	0.000
7	A	155	ARG	1	0.951	0.975	4.173	0.532	0.606	-0.001	-0.013	-0.060	0.000
8	A	156	THR	0	0.037	0.028	9.006	0.260	0.260	0.000	0.000	0.000	0.000
9	A	157	LEU	0	-0.034	-0.015	12.532	0.113	0.113	0.000	0.000	0.000	0.000
10	A	158	LEU	0	0.010	-0.012	7.978	0.089	0.089	0.000	0.000	0.000	0.000
11	A	159	GLY	0	0.035	0.026	11.870	0.119	0.119	0.000	0.000	0.000	0.000
12	A	160	LEU	0	0.012	0.021	14.057	0.065	0.065	0.000	0.000	0.000	0.000
13	A	161	LEU	0	-0.027	-0.025	13.492	0.036	0.036	0.000	0.000	0.000	0.000
14	A	162	SER	0	-0.107	-0.054	14.250	0.060	0.060	0.000	0.000	0.000	0.000
15	A	163	GLU	-1	-0.833	-0.915	16.282	-0.148	-0.148	0.000	0.000	0.000	0.000
16	A	164	GLY	0	-0.016	-0.003	19.173	0.019	0.019	0.000	0.000	0.000	0.000
17	A	165	LEU	0	-0.070	-0.018	20.483	0.003	0.003	0.000	0.000	0.000	0.000
18	A	166	THR	0	0.029	0.002	21.106	-0.023	-0.023	0.000	0.000	0.000	0.000
19	A	167	ASN	0	0.009	-0.017	20.557	-0.037	-0.037	0.000	0.000	0.000	0.000
20	A	168	LYS	1	0.868	0.925	22.526	0.160	0.160	0.000	0.000	0.000	0.000
21	A	169	GLN	0	0.070	0.033	24.202	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	170	ILE	0	0.005	0.003	18.059	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	171	ALA	0	-0.042	-0.031	21.699	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	172	ASP	-1	-0.821	-0.892	23.592	-0.190	-0.190	0.000	0.000	0.000	0.000
25	A	173	ARG	1	0.820	0.915	20.215	0.217	0.217	0.000	0.000	0.000	0.000
26	A	174	MET	0	-0.060	-0.025	16.201	-0.026	-0.026	0.000	0.000	0.000	0.000
27	A	175	PHE	0	-0.004	0.016	22.160	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	176	LEU	0	-0.026	-0.002	19.671	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	177	ALA	0	0.028	0.007	24.242	0.023	0.023	0.000	0.000	0.000	0.000
30	A	178	GLU	-1	-0.798	-0.928	23.994	-0.229	-0.229	0.000	0.000	0.000	0.000
31	A	179	LYS	1	0.924	0.958	23.481	0.238	0.238	0.000	0.000	0.000	0.000
32	A	180	THR	0	0.031	0.011	20.461	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	181	VAL	0	0.052	0.044	18.998	-0.058	-0.058	0.000	0.000	0.000	0.000
34	A	182	LYS	1	0.988	0.999	18.648	0.194	0.194	0.000	0.000	0.000	0.000
35	A	183	ASN	0	-0.034	-0.015	18.972	0.009	0.009	0.000	0.000	0.000	0.000
36	A	184	TYR	0	0.016	0.005	14.798	-0.073	-0.073	0.000	0.000	0.000	0.000
37	A	185	VAL	0	0.035	0.023	14.197	-0.115	-0.115	0.000	0.000	0.000	0.000
38	A	186	SER	0	-0.047	-0.036	14.541	0.000	0.000	0.000	0.000	0.000	0.000
39	A	187	ARG	1	0.887	0.939	10.993	1.245	1.245	0.000	0.000	0.000	0.000
40	A	188	LEU	0	-0.022	-0.011	8.652	-0.125	-0.125	0.000	0.000	0.000	0.000
41	A	189	LEU	0	0.030	0.001	10.015	-0.044	-0.044	0.000	0.000	0.000	0.000
42	A	190	ALA	0	-0.001	0.002	11.993	0.071	0.071	0.000	0.000	0.000	0.000
43	A	191	LYS	1	0.808	0.879	6.614	2.945	2.945	0.000	0.000	0.000	0.000
44	A	192	LEU	0	-0.034	-0.023	6.259	0.036	0.036	0.000	0.000	0.000	0.000
45	A	193	GLY	0	-0.001	0.021	8.454	0.237	0.237	0.000	0.000	0.000	0.000
46	A	194	MET	0	-0.065	-0.022	9.665	0.105	0.105	0.000	0.000	0.000	0.000
47	A	195	GLU	-1	-0.908	-0.948	8.061	0.743	0.743	0.000	0.000	0.000	0.000
48	A	196	ARG	1	0.901	0.939	4.603	-4.112	-4.065	-0.001	-0.009	-0.036	0.000
49	A	197	ARG	1	1.017	1.006	9.033	-0.063	-0.063	0.000	0.000	0.000	0.000
50	A	198	THR	0	-0.012	-0.001	11.494	-0.076	-0.076	0.000	0.000	0.000	0.000
51	A	199	GLN	0	0.006	0.010	11.325	0.329	0.329	0.000	0.000	0.000	0.000

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