FMO DATABASE

FMODB ID: GN3V1

Calculation Name: 3TBI-A-Xray372

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: 2023-06-20

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-414903.097151
FMO2-HF: Nuclear repulsion	386350.318025
FMO2-HF: Total energy	-28552.779126
FMO2-MP2: Total energy	-28635.319562

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:32:ALA)

Summations of interaction energy for fragment #1(A:32:ALA)

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.
-1.852	-0.107	-0.025	-0.809	-0.911	0.001

Interaction energy analysis for fragmet #1(A:32:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / 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	34	LEU	0	0.105	0.054	3.812	-0.722	1.023	-0.025	-0.809	-0.911	0.001
4	A	35	LEU	0	-0.094	-0.058	6.294	0.360	0.360	0.000	0.000	0.000	0.000
5	A	36	ASP	-1	-0.838	-0.915	9.123	0.357	0.357	0.000	0.000	0.000	0.000
6	A	37	ARG	1	0.934	0.973	10.944	-0.037	-0.037	0.000	0.000	0.000	0.000
7	A	38	GLN	0	-0.012	-0.010	13.552	-0.055	-0.055	0.000	0.000	0.000	0.000
8	A	39	GLU	-1	-0.854	-0.909	9.303	0.021	0.021	0.000	0.000	0.000	0.000
9	A	40	ASN	0	0.036	0.002	9.802	-0.079	-0.079	0.000	0.000	0.000	0.000
10	A	41	GLY	0	-0.054	-0.045	12.685	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	42	PHE	0	-0.015	-0.023	15.496	0.002	0.002	0.000	0.000	0.000	0.000
12	A	43	ILE	0	-0.091	-0.042	10.525	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	44	ILE	0	0.027	0.014	14.941	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	45	GLU	-1	-0.863	-0.953	17.412	-0.052	-0.052	0.000	0.000	0.000	0.000
15	A	46	LYS	1	0.925	0.985	14.047	0.275	0.275	0.000	0.000	0.000	0.000
16	A	47	MET	0	-0.038	-0.034	17.529	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	48	VAL	0	-0.033	-0.001	20.640	0.003	0.003	0.000	0.000	0.000	0.000
18	A	49	GLU	-1	-0.974	-0.972	23.248	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	50	GLU	-1	-1.009	-0.995	21.625	-0.131	-0.131	0.000	0.000	0.000	0.000
20	A	51	PHE	0	-0.075	-0.044	19.724	0.002	0.002	0.000	0.000	0.000	0.000
21	A	52	GLY	0	0.003	0.025	24.883	0.003	0.003	0.000	0.000	0.000	0.000
22	A	53	MET	0	-0.036	-0.002	22.556	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	54	SER	0	0.022	0.011	25.987	0.001	0.001	0.000	0.000	0.000	0.000
24	A	55	TYR	0	0.048	0.001	24.005	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	56	LEU	0	-0.052	-0.018	23.067	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	57	GLU	-1	-0.888	-0.952	23.058	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	58	ALA	0	0.029	0.000	20.901	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	59	THR	0	-0.073	-0.026	18.512	-0.041	-0.041	0.000	0.000	0.000	0.000
29	A	60	THR	0	-0.026	-0.028	18.456	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	61	ALA	0	0.017	0.011	18.987	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	62	PHE	0	-0.014	-0.009	11.287	-0.047	-0.047	0.000	0.000	0.000	0.000
32	A	63	LEU	0	-0.080	-0.047	13.865	-0.079	-0.079	0.000	0.000	0.000	0.000
33	A	64	GLU	-1	-0.879	-0.922	13.839	-0.433	-0.433	0.000	0.000	0.000	0.000
34	A	65	GLU	-1	-0.950	-0.980	14.019	-0.432	-0.432	0.000	0.000	0.000	0.000
35	A	66	ASN	0	-0.130	-0.071	9.337	-0.195	-0.195	0.000	0.000	0.000	0.000
36	A	67	SER	0	-0.048	-0.022	9.928	-0.138	-0.138	0.000	0.000	0.000	0.000
37	A	68	ILE	0	-0.070	-0.026	10.043	0.005	0.005	0.000	0.000	0.000	0.000
38	A	69	PRO	0	0.010	0.001	13.135	0.059	0.059	0.000	0.000	0.000	0.000
39	A	70	GLU	-1	-0.765	-0.896	16.663	-0.235	-0.235	0.000	0.000	0.000	0.000
40	A	71	THR	0	-0.081	-0.031	19.182	0.008	0.008	0.000	0.000	0.000	0.000
41	A	72	GLN	0	-0.042	-0.026	14.761	0.030	0.030	0.000	0.000	0.000	0.000
42	A	73	PHE	0	0.052	0.018	15.638	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	74	ALA	0	0.020	0.021	17.098	0.010	0.010	0.000	0.000	0.000	0.000
44	A	75	LYS	1	0.869	0.912	12.860	0.124	0.124	0.000	0.000	0.000	0.000
45	A	76	PHE	0	-0.010	0.010	8.550	0.004	0.004	0.000	0.000	0.000	0.000
46	A	77	ILE	0	0.074	0.041	13.323	0.005	0.005	0.000	0.000	0.000	0.000
47	A	78	PRO	0	-0.026	0.026	15.929	0.031	0.031	0.000	0.000	0.000	0.000
48	A	79	SER	0	0.010	-0.018	18.257	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	80	GLY	0	0.022	0.014	21.229	0.004	0.004	0.000	0.000	0.000	0.000
50	A	81	ILE	0	0.025	-0.001	18.974	0.001	0.001	0.000	0.000	0.000	0.000
51	A	82	ILE	0	0.035	0.010	20.972	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	83	GLU	-1	-0.943	-0.954	23.468	-0.039	-0.039	0.000	0.000	0.000	0.000
53	A	84	LYS	1	0.885	0.945	23.849	0.049	0.049	0.000	0.000	0.000	0.000
54	A	85	ILE	0	-0.007	0.008	22.384	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	86	GLN	0	-0.030	-0.013	26.781	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	87	SER	0	-0.020	-0.018	29.438	0.005	0.005	0.000	0.000	0.000	0.000
57	A	88	GLU	-1	-0.745	-0.881	28.301	-0.095	-0.095	0.000	0.000	0.000	0.000
58	A	89	ALA	0	-0.030	-0.030	30.500	0.001	0.001	0.000	0.000	0.000	0.000
59	A	90	ILE	0	-0.062	-0.033	32.211	0.003	0.003	0.000	0.000	0.000	0.000
60	A	91	ASP	-1	-0.910	-0.936	34.647	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	92	GLU	-1	-0.915	-0.955	33.944	-0.065	-0.065	0.000	0.000	0.000	0.000
62	A	93	ASN	0	-0.161	-0.083	36.101	0.002	0.002	0.000	0.000	0.000	0.000
63	A	94	LEU	0	-0.011	0.015	31.882	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	95	LEU	0	-0.017	-0.002	31.376	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	96	ARG	1	0.951	0.963	35.409	0.060	0.060	0.000	0.000	0.000	0.000
66	A	97	PRO	0	0.097	0.036	38.215	0.001	0.001	0.000	0.000	0.000	0.000
67	A	98	SER	0	-0.132	-0.074	39.914	0.002	0.002	0.000	0.000	0.000	0.000
68	A	99	VAL	0	0.022	-0.001	33.473	0.002	0.002	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.035	0.037	35.942	0.001	0.001	0.000	0.000	0.000	0.000
70	A	101	ARG	1	0.898	0.956	37.286	0.035	0.035	0.000	0.000	0.000	0.000
71	A	102	CYS	0	0.020	0.026	34.535	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:32:ALA)