FMO DATABASE

FMODB ID: N1YLQ

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:

Apendix: None

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-414232.150038
FMO2-HF: Nuclear repulsion	385677.900362
FMO2-HF: Total energy	-28554.249675
FMO2-MP2: Total energy	-28636.595138

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.
-1.972	-0.161	-0.014	-0.814	-0.983	0

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 : 0.030 / q_NPA : 0.000

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].
3	A	34	LEU	0	0.105	0.059	3.604	-0.681	1.130	-0.014	-0.814	-0.983
4	A	35	LEU	0	-0.033	-0.023	5.965	0.173	0.173	0.000	0.000	0.000
5	A	36	ASP	-1	-0.850	-0.907	8.719	0.321	0.321	0.000	0.000	0.000
6	A	37	ARG	1	0.907	0.939	10.784	-0.013	-0.013	0.000	0.000	0.000
7	A	38	GLN	0	-0.068	-0.036	13.603	-0.075	-0.075	0.000	0.000	0.000
8	A	39	GLU	-1	-0.881	-0.936	9.738	0.183	0.183	0.000	0.000	0.000
9	A	40	ASN	0	-0.051	-0.048	9.615	-0.082	-0.082	0.000	0.000	0.000
10	A	41	GLY	0	0.000	0.001	12.513	-0.031	-0.031	0.000	0.000	0.000
11	A	42	PHE	0	-0.030	-0.017	15.361	-0.011	-0.011	0.000	0.000	0.000
12	A	43	ILE	0	-0.027	-0.008	10.413	-0.018	-0.018	0.000	0.000	0.000
13	A	44	ILE	0	-0.009	-0.011	14.584	-0.017	-0.017	0.000	0.000	0.000
14	A	45	GLU	-1	-0.802	-0.895	16.831	-0.026	-0.026	0.000	0.000	0.000
15	A	46	LYS	1	0.790	0.885	16.343	0.138	0.138	0.000	0.000	0.000
16	A	47	MET	0	-0.022	-0.009	16.439	-0.005	-0.005	0.000	0.000	0.000
17	A	48	VAL	0	0.017	0.010	19.978	-0.001	-0.001	0.000	0.000	0.000
18	A	49	GLU	-1	-0.977	-0.976	23.043	-0.026	-0.026	0.000	0.000	0.000
19	A	50	GLU	-1	-0.889	-0.917	20.042	-0.116	-0.116	0.000	0.000	0.000
20	A	51	PHE	0	-0.064	-0.046	19.598	-0.001	-0.001	0.000	0.000	0.000
21	A	52	GLY	0	-0.025	0.004	24.704	0.001	0.001	0.000	0.000	0.000
22	A	53	MET	0	-0.065	-0.011	22.189	-0.002	-0.002	0.000	0.000	0.000
23	A	54	SER	0	0.010	-0.032	25.703	0.002	0.002	0.000	0.000	0.000
24	A	55	TYR	0	0.015	-0.021	22.778	-0.011	-0.011	0.000	0.000	0.000
25	A	56	LEU	0	-0.034	0.001	22.349	-0.017	-0.017	0.000	0.000	0.000
26	A	57	GLU	-1	-0.853	-0.878	22.677	-0.131	-0.131	0.000	0.000	0.000
27	A	58	ALA	0	0.057	0.025	20.049	-0.023	-0.023	0.000	0.000	0.000
28	A	59	THR	0	-0.081	-0.065	17.947	-0.032	-0.032	0.000	0.000	0.000
29	A	60	THR	0	-0.053	-0.035	17.698	-0.035	-0.035	0.000	0.000	0.000
30	A	61	ALA	0	-0.014	0.002	18.369	-0.030	-0.030	0.000	0.000	0.000
31	A	62	PHE	0	0.063	0.022	10.767	-0.054	-0.054	0.000	0.000	0.000
32	A	63	LEU	0	-0.058	-0.022	13.321	-0.083	-0.083	0.000	0.000	0.000
33	A	64	GLU	-1	-0.910	-0.944	13.574	-0.426	-0.426	0.000	0.000	0.000
34	A	65	GLU	-1	-0.959	-0.988	13.234	-0.385	-0.385	0.000	0.000	0.000
35	A	66	ASN	0	-0.108	-0.063	8.749	-0.287	-0.287	0.000	0.000	0.000
36	A	67	SER	0	-0.059	-0.030	9.771	-0.149	-0.149	0.000	0.000	0.000
37	A	68	ILE	0	-0.069	-0.022	9.317	0.000	0.000	0.000	0.000	0.000
38	A	69	PRO	0	0.026	0.004	12.714	0.059	0.059	0.000	0.000	0.000
39	A	70	GLU	-1	-0.701	-0.843	16.343	-0.246	-0.246	0.000	0.000	0.000
40	A	71	THR	0	-0.093	-0.070	19.141	0.006	0.006	0.000	0.000	0.000
41	A	72	GLN	0	-0.106	-0.061	14.303	-0.004	-0.004	0.000	0.000	0.000
42	A	73	PHE	0	0.089	0.050	15.348	-0.011	-0.011	0.000	0.000	0.000
43	A	74	ALA	0	0.046	0.027	16.226	0.004	0.004	0.000	0.000	0.000
44	A	75	LYS	1	0.864	0.928	12.792	0.235	0.235	0.000	0.000	0.000
45	A	76	PHE	0	-0.023	0.001	8.212	-0.012	-0.012	0.000	0.000	0.000
46	A	77	ILE	0	0.065	0.044	12.807	0.030	0.030	0.000	0.000	0.000
47	A	78	PRO	0	-0.014	0.005	15.622	0.020	0.020	0.000	0.000	0.000
48	A	79	SER	0	0.041	-0.002	18.153	-0.008	-0.008	0.000	0.000	0.000
49	A	80	GLY	0	-0.008	-0.001	21.559	-0.002	-0.002	0.000	0.000	0.000
50	A	81	ILE	0	0.019	0.014	18.473	0.001	0.001	0.000	0.000	0.000
51	A	82	ILE	0	-0.008	-0.007	19.865	-0.006	-0.006	0.000	0.000	0.000
52	A	83	GLU	-1	-0.863	-0.930	23.081	-0.039	-0.039	0.000	0.000	0.000
53	A	84	LYS	1	0.785	0.884	23.501	0.028	0.028	0.000	0.000	0.000
54	A	85	ILE	0	0.012	0.014	21.620	0.000	0.000	0.000	0.000	0.000
55	A	86	GLN	0	-0.114	-0.066	26.159	-0.003	-0.003	0.000	0.000	0.000
56	A	87	SER	0	-0.040	-0.029	28.895	0.004	0.004	0.000	0.000	0.000
57	A	88	GLU	-1	-0.714	-0.852	27.078	-0.085	-0.085	0.000	0.000	0.000
58	A	89	ALA	0	-0.033	-0.024	29.484	0.000	0.000	0.000	0.000	0.000
59	A	90	ILE	0	-0.073	-0.038	31.397	0.002	0.002	0.000	0.000	0.000
60	A	91	ASP	-1	-0.870	-0.922	33.798	-0.040	-0.040	0.000	0.000	0.000
61	A	92	GLU	-1	-0.949	-0.973	33.535	-0.057	-0.057	0.000	0.000	0.000
62	A	93	ASN	0	-0.145	-0.079	35.434	0.001	0.001	0.000	0.000	0.000
63	A	94	LEU	0	0.021	0.028	30.329	-0.001	-0.001	0.000	0.000	0.000
64	A	95	LEU	0	0.000	0.004	30.997	-0.005	-0.005	0.000	0.000	0.000
65	A	96	ARG	1	0.956	0.969	35.012	0.061	0.061	0.000	0.000	0.000
66	A	97	PRO	0	0.102	0.034	37.795	0.000	0.000	0.000	0.000	0.000
67	A	98	SER	0	-0.064	-0.040	39.853	0.003	0.003	0.000	0.000	0.000
68	A	99	VAL	0	0.006	0.011	33.112	0.002	0.002	0.000	0.000	0.000
69	A	100	VAL	0	0.048	0.052	35.759	0.002	0.002	0.000	0.000	0.000
70	A	101	ARG	1	0.898	0.958	36.784	0.036	0.036	0.000	0.000	0.000
71	A	102	CYS	0	-0.068	-0.041	34.630	0.003	0.003	0.000	0.000	0.000

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