FMO DATABASE

FMODB ID: N1VZQ

Calculation Name: 3TBI-A-Xray318

Preferred Name: DNA-directed RNA polymerase beta chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3TBI

Chain ID: A

ChEMBL ID: CHEMBL1852

UniProt ID: P0A8V2

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-418812.893381
FMO2-HF: Nuclear repulsion	390089.20649
FMO2-HF: Total energy	-28723.686891
FMO2-MP2: Total energy	-28806.770064

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:31:ACE )

Summations of interaction energy for fragment #1(A:31:ACE )

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.
1.539	2.72	-0.005	-0.614	-0.562	-0.001

Interaction energy analysis for fragmet #1(A:31:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.002

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	33	LYS	1	0.907	0.958	3.843	0.839	2.020	-0.005	-0.614	-0.562	-0.001
4	A	34	LEU	0	0.110	0.056	5.359	0.366	0.366	0.000	0.000	0.000	0.000
5	A	35	LEU	0	-0.097	-0.058	7.575	0.120	0.120	0.000	0.000	0.000	0.000
6	A	36	ASP	-1	-0.838	-0.915	9.967	0.226	0.226	0.000	0.000	0.000	0.000
7	A	37	ARG	1	0.934	0.972	11.638	0.049	0.049	0.000	0.000	0.000	0.000
8	A	38	GLN	0	-0.011	-0.010	13.981	-0.030	-0.030	0.000	0.000	0.000	0.000
9	A	39	GLU	-1	-0.855	-0.909	9.167	0.400	0.400	0.000	0.000	0.000	0.000
10	A	40	ASN	0	0.038	0.003	10.676	0.014	0.014	0.000	0.000	0.000	0.000
11	A	41	GLY	0	-0.050	-0.046	13.060	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	42	PHE	0	-0.022	-0.024	15.274	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	43	ILE	0	-0.089	-0.041	10.204	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	44	ILE	0	0.023	0.013	14.743	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	45	GLU	-1	-0.860	-0.952	17.552	0.058	0.058	0.000	0.000	0.000	0.000
16	A	46	LYS	1	0.923	0.985	13.541	-0.114	-0.114	0.000	0.000	0.000	0.000
17	A	47	MET	0	-0.038	-0.035	17.694	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	48	VAL	0	-0.033	0.000	20.486	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	49	GLU	-1	-0.972	-0.971	22.985	0.056	0.056	0.000	0.000	0.000	0.000
20	A	50	GLU	-1	-1.010	-0.996	20.903	0.070	0.070	0.000	0.000	0.000	0.000
21	A	51	PHE	0	-0.076	-0.045	19.374	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	52	GLY	0	0.004	0.027	24.642	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	53	MET	0	-0.037	-0.003	22.807	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	54	SER	0	0.022	0.009	26.198	0.002	0.002	0.000	0.000	0.000	0.000
25	A	55	TYR	0	0.048	0.001	24.432	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	56	LEU	0	-0.051	-0.018	23.697	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	57	GLU	-1	-0.885	-0.951	23.854	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	58	ALA	0	0.028	0.000	21.247	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	59	THR	0	-0.069	-0.025	19.249	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	60	THR	0	-0.031	-0.030	19.492	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	61	ALA	0	0.016	0.010	19.874	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	62	PHE	0	-0.012	-0.008	11.857	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	63	LEU	0	-0.079	-0.046	14.890	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	64	GLU	-1	-0.881	-0.923	15.722	-0.172	-0.172	0.000	0.000	0.000	0.000
35	A	65	GLU	-1	-0.949	-0.979	14.671	-0.078	-0.078	0.000	0.000	0.000	0.000
36	A	66	ASN	0	-0.133	-0.072	10.657	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	67	SER	0	-0.045	-0.021	12.460	-0.081	-0.081	0.000	0.000	0.000	0.000
38	A	68	ILE	0	-0.072	-0.027	12.085	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	69	PRO	0	0.012	0.001	15.873	0.030	0.030	0.000	0.000	0.000	0.000
40	A	70	GLU	-1	-0.763	-0.896	19.329	-0.105	-0.105	0.000	0.000	0.000	0.000
41	A	71	THR	0	-0.083	-0.031	21.624	0.002	0.002	0.000	0.000	0.000	0.000
42	A	72	GLN	0	-0.041	-0.026	17.608	0.002	0.002	0.000	0.000	0.000	0.000
43	A	73	PHE	0	0.054	0.018	17.959	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	74	ALA	0	0.018	0.022	18.671	0.010	0.010	0.000	0.000	0.000	0.000
45	A	75	LYS	1	0.869	0.912	15.459	0.156	0.156	0.000	0.000	0.000	0.000
46	A	76	PHE	0	-0.009	0.010	10.930	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	77	ILE	0	0.071	0.039	14.691	0.026	0.026	0.000	0.000	0.000	0.000
48	A	78	PRO	0	-0.028	0.025	16.686	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	79	SER	0	0.013	-0.016	19.105	0.001	0.001	0.000	0.000	0.000	0.000
50	A	80	GLY	0	0.023	0.014	21.964	0.000	0.000	0.000	0.000	0.000	0.000
51	A	81	ILE	0	0.023	-0.002	19.671	0.000	0.000	0.000	0.000	0.000	0.000
52	A	82	ILE	0	0.035	0.010	22.217	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	83	GLU	-1	-0.941	-0.952	24.392	0.003	0.003	0.000	0.000	0.000	0.000
54	A	84	LYS	1	0.886	0.945	24.060	-0.042	-0.042	0.000	0.000	0.000	0.000
55	A	85	ILE	0	-0.008	0.006	23.299	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	86	GLN	0	-0.029	-0.013	27.601	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	87	SER	0	-0.018	-0.016	30.383	0.000	0.000	0.000	0.000	0.000	0.000
58	A	88	GLU	-1	-0.746	-0.882	28.780	0.000	0.000	0.000	0.000	0.000	0.000
59	A	89	ALA	0	-0.032	-0.031	31.517	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	90	ILE	0	-0.065	-0.034	33.149	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	91	ASP	-1	-0.906	-0.934	35.294	0.004	0.004	0.000	0.000	0.000	0.000
62	A	92	GLU	-1	-0.914	-0.954	34.702	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	93	ASN	0	-0.162	-0.084	36.891	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	94	LEU	0	-0.010	0.016	32.985	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	95	LEU	0	-0.020	-0.004	32.957	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	96	ARG	1	0.953	0.962	36.918	0.026	0.026	0.000	0.000	0.000	0.000
67	A	97	PRO	0	0.097	0.037	39.804	0.000	0.000	0.000	0.000	0.000	0.000
68	A	98	SER	0	-0.126	-0.070	41.707	0.001	0.001	0.000	0.000	0.000	0.000
69	A	99	VAL	0	0.012	-0.007	35.229	0.000	0.000	0.000	0.000	0.000	0.000
70	A	100	VAL	0	0.053	0.042	37.409	0.000	0.000	0.000	0.000	0.000	0.000
71	A	101	ARG	1	0.895	0.953	38.458	0.012	0.012	0.000	0.000	0.000	0.000
72	A	102	CYS	0	-0.028	-0.010	38.670	0.001	0.001	0.000	0.000	0.000	0.000
73	A	103	NME	0	0.033	0.036	34.902	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:31:ACE )