FMO DATABASE

FMODB ID: VQYZ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-244389.943328
FMO2-HF: Nuclear repulsion	223951.018942
FMO2-HF: Total energy	-20438.924386
FMO2-MP2: Total energy	-20498.03089

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.
-0.487	1.195	-0.01	-0.875	-0.796	0.003

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 : 0.044 / q_NPA : 0.020

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	151	THR	0	-0.003	-0.031	3.858	-0.068	1.514	-0.008	-0.860	-0.714	0.003
4	A	152	ASP	-1	-0.862	-0.941	6.760	-0.566	-0.566	0.000	0.000	0.000	0.000
5	A	153	GLN	0	0.087	0.050	9.469	0.019	0.019	0.000	0.000	0.000	0.000
6	A	154	GLU	-1	-0.790	-0.848	7.157	-2.987	-2.987	0.000	0.000	0.000	0.000
7	A	155	ARG	1	0.944	0.970	4.364	0.644	0.703	-0.001	-0.007	-0.050	0.000
8	A	156	THR	0	0.049	0.030	8.801	0.264	0.264	0.000	0.000	0.000	0.000
9	A	157	LEU	0	-0.031	-0.015	12.335	0.106	0.106	0.000	0.000	0.000	0.000
10	A	158	LEU	0	0.011	-0.005	8.269	0.086	0.086	0.000	0.000	0.000	0.000
11	A	159	GLY	0	0.033	0.025	12.032	0.117	0.117	0.000	0.000	0.000	0.000
12	A	160	LEU	0	0.010	0.015	14.120	0.064	0.064	0.000	0.000	0.000	0.000
13	A	161	LEU	0	-0.021	-0.020	13.525	0.033	0.033	0.000	0.000	0.000	0.000
14	A	162	SER	0	-0.103	-0.055	14.762	0.057	0.057	0.000	0.000	0.000	0.000
15	A	163	GLU	-1	-0.775	-0.859	16.758	-0.164	-0.164	0.000	0.000	0.000	0.000
16	A	164	GLY	0	-0.015	0.005	19.347	0.018	0.018	0.000	0.000	0.000	0.000
17	A	165	LEU	0	-0.075	-0.021	20.535	0.004	0.004	0.000	0.000	0.000	0.000
18	A	166	THR	0	0.040	0.007	21.100	-0.024	-0.024	0.000	0.000	0.000	0.000
19	A	167	ASN	0	-0.013	-0.026	20.419	-0.042	-0.042	0.000	0.000	0.000	0.000
20	A	168	LYS	1	0.867	0.925	22.449	0.161	0.161	0.000	0.000	0.000	0.000
21	A	169	GLN	0	0.069	0.034	24.215	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	170	ILE	0	0.002	-0.001	17.960	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	171	ALA	0	-0.032	-0.023	21.580	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	172	ASP	-1	-0.829	-0.895	23.505	-0.194	-0.194	0.000	0.000	0.000	0.000
25	A	173	ARG	1	0.751	0.840	20.375	0.223	0.223	0.000	0.000	0.000	0.000
26	A	174	MET	0	-0.054	-0.021	15.922	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	175	PHE	0	-0.001	0.014	21.982	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	176	LEU	0	-0.030	0.000	19.443	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	177	ALA	0	0.040	0.017	24.098	0.026	0.026	0.000	0.000	0.000	0.000
30	A	178	GLU	-1	-0.799	-0.929	23.803	-0.235	-0.235	0.000	0.000	0.000	0.000
31	A	179	LYS	1	0.913	0.954	23.175	0.265	0.265	0.000	0.000	0.000	0.000
32	A	180	THR	0	0.024	0.007	20.448	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	181	VAL	0	0.046	0.044	18.824	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	182	LYS	1	0.997	1.003	18.325	0.193	0.193	0.000	0.000	0.000	0.000
35	A	183	ASN	0	-0.026	-0.008	18.655	0.019	0.019	0.000	0.000	0.000	0.000
36	A	184	TYR	0	0.022	0.008	14.439	-0.079	-0.079	0.000	0.000	0.000	0.000
37	A	185	VAL	0	0.035	0.014	13.935	-0.122	-0.122	0.000	0.000	0.000	0.000
38	A	186	SER	0	-0.052	-0.038	14.195	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	187	ARG	1	0.857	0.921	10.517	1.346	1.346	0.000	0.000	0.000	0.000
40	A	188	LEU	0	-0.019	-0.007	8.601	-0.160	-0.160	0.000	0.000	0.000	0.000
41	A	189	LEU	0	0.028	0.001	9.627	-0.048	-0.048	0.000	0.000	0.000	0.000
42	A	190	ALA	0	-0.007	0.000	11.673	0.074	0.074	0.000	0.000	0.000	0.000
43	A	191	LYS	1	0.812	0.882	5.940	3.451	3.451	0.000	0.000	0.000	0.000
44	A	192	LEU	0	-0.019	-0.017	6.477	0.115	0.115	0.000	0.000	0.000	0.000
45	A	193	GLY	0	-0.009	0.020	8.494	0.223	0.223	0.000	0.000	0.000	0.000
46	A	194	MET	0	-0.051	-0.023	9.244	0.079	0.079	0.000	0.000	0.000	0.000
47	A	195	GLU	-1	-0.907	-0.949	7.792	0.821	0.821	0.000	0.000	0.000	0.000
48	A	196	ARG	1	0.917	0.953	4.799	-4.171	-4.130	-0.001	-0.008	-0.032	0.000
49	A	197	ARG	1	0.986	1.001	8.954	-0.094	-0.094	0.000	0.000	0.000	0.000
50	A	198	THR	0	-0.010	-0.011	11.247	-0.143	-0.143	0.000	0.000	0.000	0.000
51	A	199	GLN	0	0.011	0.016	11.076	0.373	0.373	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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