FMO DATABASE

FMODB ID: 82YQY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-414400.81118
FMO2-HF: Nuclear repulsion	385847.118431
FMO2-HF: Total energy	-28553.692749
FMO2-MP2: Total energy	-28636.13669

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.
-2.283	-0.524	-0.024	-0.813	-0.922	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 : 0.024 / q_NPA : -0.004

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	0.127	0.067	3.812	-0.797	0.962	-0.024	-0.813	-0.922	0.001
4	A	35	LEU	0	-0.089	-0.049	6.262	0.391	0.391	0.000	0.000	0.000	0.000
5	A	36	ASP	-1	-0.833	-0.909	9.091	0.243	0.243	0.000	0.000	0.000	0.000
6	A	37	ARG	1	0.918	0.966	10.904	-0.016	-0.016	0.000	0.000	0.000	0.000
7	A	38	GLN	0	-0.031	-0.026	13.516	-0.072	-0.072	0.000	0.000	0.000	0.000
8	A	39	GLU	-1	-0.858	-0.912	9.537	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	40	ASN	0	0.022	-0.012	9.653	-0.134	-0.134	0.000	0.000	0.000	0.000
10	A	41	GLY	0	-0.037	-0.049	12.658	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	42	PHE	0	-0.053	-0.035	15.489	0.003	0.003	0.000	0.000	0.000	0.000
12	A	43	ILE	0	-0.059	-0.030	10.678	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	44	ILE	0	0.001	0.006	14.922	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	45	GLU	-1	-0.805	-0.891	17.394	-0.065	-0.065	0.000	0.000	0.000	0.000
15	A	46	LYS	1	0.873	0.937	16.255	0.224	0.224	0.000	0.000	0.000	0.000
16	A	47	MET	0	-0.031	-0.033	17.362	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	48	VAL	0	-0.021	-0.008	20.609	0.004	0.004	0.000	0.000	0.000	0.000
18	A	49	GLU	-1	-0.971	-0.972	23.231	-0.056	-0.056	0.000	0.000	0.000	0.000
19	A	50	GLU	-1	-0.910	-0.939	20.711	-0.163	-0.163	0.000	0.000	0.000	0.000
20	A	51	PHE	0	-0.093	-0.055	20.126	0.002	0.002	0.000	0.000	0.000	0.000
21	A	52	GLY	0	0.004	0.027	24.881	0.003	0.003	0.000	0.000	0.000	0.000
22	A	53	MET	0	-0.048	-0.011	22.678	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	54	SER	0	-0.002	-0.034	25.874	0.000	0.000	0.000	0.000	0.000	0.000
24	A	55	TYR	0	0.045	0.001	23.828	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	56	LEU	0	-0.054	-0.015	23.052	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	57	GLU	-1	-0.832	-0.880	23.045	-0.153	-0.153	0.000	0.000	0.000	0.000
27	A	58	ALA	0	0.031	0.000	20.927	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	59	THR	0	-0.059	-0.025	18.498	-0.033	-0.033	0.000	0.000	0.000	0.000
29	A	60	THR	0	-0.058	-0.049	18.472	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	61	ALA	0	0.000	0.008	19.000	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	62	PHE	0	0.015	0.005	11.107	-0.052	-0.052	0.000	0.000	0.000	0.000
32	A	63	LEU	0	-0.058	-0.027	13.878	-0.085	-0.085	0.000	0.000	0.000	0.000
33	A	64	GLU	-1	-0.899	-0.937	13.855	-0.429	-0.429	0.000	0.000	0.000	0.000
34	A	65	GLU	-1	-0.961	-0.983	13.910	-0.441	-0.441	0.000	0.000	0.000	0.000
35	A	66	ASN	0	-0.109	-0.069	9.377	-0.283	-0.283	0.000	0.000	0.000	0.000
36	A	67	SER	0	-0.064	-0.025	9.944	-0.134	-0.134	0.000	0.000	0.000	0.000
37	A	68	ILE	0	-0.065	-0.027	9.562	0.010	0.010	0.000	0.000	0.000	0.000
38	A	69	PRO	0	0.025	0.010	13.155	0.055	0.055	0.000	0.000	0.000	0.000
39	A	70	GLU	-1	-0.759	-0.894	16.684	-0.240	-0.240	0.000	0.000	0.000	0.000
40	A	71	THR	0	-0.068	-0.028	19.203	0.008	0.008	0.000	0.000	0.000	0.000
41	A	72	GLN	0	-0.075	-0.044	14.746	0.026	0.026	0.000	0.000	0.000	0.000
42	A	73	PHE	0	0.056	0.022	15.660	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	74	ALA	0	0.034	0.024	17.098	0.010	0.010	0.000	0.000	0.000	0.000
44	A	75	LYS	1	0.884	0.924	13.052	0.145	0.145	0.000	0.000	0.000	0.000
45	A	76	PHE	0	-0.004	0.006	8.464	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	77	ILE	0	0.057	0.037	13.323	0.002	0.002	0.000	0.000	0.000	0.000
47	A	78	PRO	0	-0.018	0.032	15.621	0.032	0.032	0.000	0.000	0.000	0.000
48	A	79	SER	0	-0.001	-0.011	18.224	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	80	GLY	0	0.003	0.006	21.192	0.005	0.005	0.000	0.000	0.000	0.000
50	A	81	ILE	0	0.034	0.006	18.889	0.001	0.001	0.000	0.000	0.000	0.000
51	A	82	ILE	0	0.017	0.002	20.489	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	83	GLU	-1	-0.896	-0.927	23.441	-0.046	-0.046	0.000	0.000	0.000	0.000
53	A	84	LYS	1	0.828	0.898	23.900	0.062	0.062	0.000	0.000	0.000	0.000
54	A	85	ILE	0	-0.012	0.003	22.180	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	86	GLN	0	-0.098	-0.054	26.758	0.001	0.001	0.000	0.000	0.000	0.000
56	A	87	SER	0	-0.021	-0.011	29.413	0.005	0.005	0.000	0.000	0.000	0.000
57	A	88	GLU	-1	-0.742	-0.879	27.901	-0.103	-0.103	0.000	0.000	0.000	0.000
58	A	89	ALA	0	-0.028	-0.019	30.413	0.001	0.001	0.000	0.000	0.000	0.000
59	A	90	ILE	0	-0.042	-0.025	32.191	0.003	0.003	0.000	0.000	0.000	0.000
60	A	91	ASP	-1	-0.912	-0.942	34.647	-0.050	-0.050	0.000	0.000	0.000	0.000
61	A	92	GLU	-1	-0.930	-0.958	34.076	-0.070	-0.070	0.000	0.000	0.000	0.000
62	A	93	ASN	0	-0.157	-0.082	36.084	0.003	0.003	0.000	0.000	0.000	0.000
63	A	94	LEU	0	0.006	0.009	31.002	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	95	LEU	0	-0.027	-0.004	31.351	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	96	ARG	1	0.953	0.965	35.428	0.061	0.061	0.000	0.000	0.000	0.000
66	A	97	PRO	0	0.117	0.046	38.235	0.001	0.001	0.000	0.000	0.000	0.000
67	A	98	SER	0	-0.101	-0.065	39.603	0.002	0.002	0.000	0.000	0.000	0.000
68	A	99	VAL	0	-0.040	-0.031	33.504	0.003	0.003	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.041	0.039	35.962	0.000	0.000	0.000	0.000	0.000	0.000
70	A	101	ARG	1	0.905	0.963	37.259	0.037	0.037	0.000	0.000	0.000	0.000
71	A	102	CYS	0	0.019	0.027	34.660	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)