FMO DATABASE

FMODB ID: 7Y47K

Calculation Name: 1FP0-A-Other547

Preferred Name: Transcription intermediary factor 1-beta

Target Type: SINGLE PROTEIN

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FP0

Chain ID: A

ChEMBL ID: CHEMBL3769297

UniProt ID: Q13263

Base Structure: SolutionNMR

Registration Date: 2025-09-02

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-477941.165468
FMO2-HF: Nuclear repulsion	440544.245236
FMO2-HF: Total energy	-37396.920231
FMO2-MP2: Total energy	-37496.939199

3D Structure Molmil

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:1:MET)

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

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.
-153.219	-151.202	0.018	-1.173	-0.862	-0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.904 / q_NPA : 0.943

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	3	GLY	0	0.027	0.002	3.245	-11.709	-9.692	0.018	-1.173	-0.862	-0.002
4	A	4	SER	0	0.048	0.019	6.113	3.015	3.015	0.000	0.000	0.000	0.000
5	A	5	HIS	0	-0.018	-0.001	7.677	2.666	2.666	0.000	0.000	0.000	0.000
6	A	6	HIS	0	-0.023	-0.035	7.873	-2.515	-2.515	0.000	0.000	0.000	0.000
7	A	7	HIS	0	-0.007	0.012	10.155	0.648	0.648	0.000	0.000	0.000	0.000
8	A	8	HIS	0	0.022	0.028	10.512	1.179	1.179	0.000	0.000	0.000	0.000
9	A	9	HIS	0	0.039	0.007	10.263	1.624	1.624	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.018	0.007	14.163	0.695	0.695	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.035	0.030	14.705	0.724	0.724	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.107	-0.079	11.802	-1.308	-1.308	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.851	-0.922	11.384	-19.960	-19.960	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.098	-0.052	5.953	-2.186	-2.186	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.049	-0.022	9.846	1.015	1.015	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.916	-0.942	7.799	-29.028	-29.028	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.953	-0.976	8.919	-22.233	-22.233	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.001	-0.009	11.597	0.574	0.574	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.027	0.018	15.252	0.178	0.178	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.092	-0.061	16.773	0.229	0.229	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.029	0.002	17.996	0.311	0.311	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.792	-0.901	21.239	-11.028	-11.028	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.943	-0.961	17.155	-14.209	-14.209	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.127	-0.074	18.647	-0.328	-0.328	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.014	0.001	20.675	0.427	0.427	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.004	-0.004	23.882	0.233	0.233	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.025	-0.003	25.677	-0.127	-0.127	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.072	0.008	27.937	0.342	0.342	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.925	0.932	29.810	8.668	8.668	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.066	0.023	32.411	0.173	0.173	0.000	0.000	0.000	0.000
31	A	31	CYS	0	-0.018	0.007	29.258	0.084	0.084	0.000	0.000	0.000	0.000
32	A	32	GLN	0	0.015	-0.006	25.395	0.083	0.083	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.838	0.913	25.953	9.147	9.147	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.013	0.014	21.582	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.043	0.006	20.226	-0.419	-0.419	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.886	-0.932	19.990	-11.917	-11.917	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.113	-0.056	21.978	0.579	0.579	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.040	0.051	23.953	-0.222	-0.222	0.000	0.000	0.000	0.000
39	A	39	MET	0	0.009	0.024	26.092	0.372	0.372	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.010	0.001	28.267	0.248	0.248	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.012	-0.005	28.791	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.068	-0.061	31.284	0.183	0.183	0.000	0.000	0.000	0.000
43	A	43	CYS	0	-0.077	-0.026	34.478	0.321	0.321	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.858	-0.928	33.363	-7.851	-7.851	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.016	-0.018	33.560	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.012	0.002	29.298	-0.228	-0.228	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.013	-0.009	29.711	0.274	0.274	0.000	0.000	0.000	0.000
48	A	48	HIS	1	0.922	0.928	25.600	9.736	9.736	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.084	0.037	27.493	0.272	0.272	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.892	-0.937	27.925	-9.419	-9.419	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.118	-0.060	30.995	0.082	0.082	0.000	0.000	0.000	0.000
52	A	52	HIS	0	0.033	0.038	32.877	0.079	0.079	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.003	-0.007	35.593	0.220	0.220	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.048	-0.020	37.248	-0.154	-0.154	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.042	-0.038	37.862	0.166	0.166	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.019	0.016	32.336	0.072	0.072	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.009	-0.011	32.415	-0.033	-0.033	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.888	-0.925	32.358	-8.407	-8.407	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.027	0.007	27.400	-0.067	-0.067	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.060	-0.016	29.073	-0.034	-0.034	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.010	-0.013	25.190	-0.164	-0.164	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.953	-0.986	22.605	-10.850	-10.850	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.752	-0.871	23.521	-9.804	-9.804	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.050	-0.055	26.023	0.179	0.179	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.015	-0.006	29.633	-0.100	-0.100	0.000	0.000	0.000	0.000
66	A	66	CYS	0	-0.057	0.008	32.364	0.267	0.267	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.002	-0.018	34.444	0.080	0.080	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.001	0.001	37.513	0.065	0.065	0.000	0.000	0.000	0.000
69	A	69	CYS	0	-0.048	-0.043	36.596	0.098	0.098	0.000	0.000	0.000	0.000
70	A	70	HIS	0	-0.016	-0.006	40.173	0.066	0.066	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.012	0.018	39.448	0.136	0.136	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.016	-0.009	42.620	-0.038	-0.038	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.032	-0.013	43.673	0.060	0.060	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.887	-0.951	45.833	-5.823	-5.823	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.075	-0.040	47.771	0.078	0.078	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.928	0.968	40.116	7.086	7.086	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.882	-0.935	45.683	-6.350	-6.350	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.991	-1.005	42.536	-7.183	-7.183	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.918	-0.952	45.748	-6.450	-6.450	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.096	-0.035	47.429	0.136	0.136	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.930	-0.969	50.805	-5.809	-5.809	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.071	-0.038	52.675	0.155	0.155	0.000	0.000	0.000	0.000
83	A	83	GLN	0	-0.017	-0.006	54.798	0.029	0.029	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.004	0.009	55.763	0.092	0.092	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.041	-0.023	54.747	0.083	0.083	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.945	0.965	58.006	4.910	4.910	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.086	-0.052	55.701	0.104	0.104	0.000	0.000	0.000	0.000
88	A	88	ASN	-1	-0.874	-0.916	56.358	-5.394	-5.394	0.000	0.000	0.000	0.000

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